Starting phenix.real_space_refine on Wed Sep 25 12:32:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny3_8980/09_2024/6ny3_8980.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny3_8980/09_2024/6ny3_8980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny3_8980/09_2024/6ny3_8980.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny3_8980/09_2024/6ny3_8980.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny3_8980/09_2024/6ny3_8980.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny3_8980/09_2024/6ny3_8980.cif" } resolution = 3.7 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= 0.004 sd= 0.110 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 164 5.49 5 S 21 5.16 5 C 5880 2.51 5 N 1863 2.21 5 O 2286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10214 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 614 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 485 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "Y" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 829 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "Y" Number of atoms: 5055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5055 Classifications: {'peptide': 678} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 121} Link IDs: {'PTRANS': 22, 'TRANS': 655} Chain breaks: 5 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 468 Unresolved non-hydrogen dihedrals: 249 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 4, 'TYR:plan': 1, 'UNK:plan-1': 57, 'ASP:plan': 15, 'GLU:plan': 23, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 237 Chain: "Y" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 887 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'UNK:plan-1': 64, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2344 Classifications: {'RNA': 110} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 45} Link IDs: {'rna2p': 10, 'rna3p': 99} Chain breaks: 2 Time building chain proxies: 6.62, per 1000 atoms: 0.65 Number of scatterers: 10214 At special positions: 0 Unit cell: (97.2, 139.5, 123.3, 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 21 16.00 P 164 15.00 O 2286 8.00 N 1863 7.00 C 5880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS Y 826 " - pdb=" SG CYS Y 928 " distance=2.02 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 Links applied TRANS " UNK Y 104 " - " SER Y 103 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 994.5 milliseconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 7 sheets defined 44.5% alpha, 7.7% beta 63 base pairs and 99 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'Y' and resid 4 through 13 removed outlier: 3.566A pdb=" N ILE Y 8 " --> pdb=" O ARG Y 4 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG Y 9 " --> pdb=" O ILE Y 5 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS Y 10 " --> pdb=" O ASN Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 42 Processing helix chain 'Y' and resid 60 through 88 removed outlier: 3.641A pdb=" N ASN Y 64 " --> pdb=" O ASN Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 90 through 98 Processing helix chain 'Y' and resid 222 through 260 removed outlier: 4.440A pdb=" N ASP Y 245 " --> pdb=" O SER Y 241 " (cutoff:3.500A) Processing helix chain 'Y' and resid 262 through 271 removed outlier: 4.476A pdb=" N ALA Y 268 " --> pdb=" O LEU Y 264 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 308 Processing helix chain 'Y' and resid 343 through 357 removed outlier: 3.953A pdb=" N LYS Y 357 " --> pdb=" O LEU Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 361 through 366 removed outlier: 3.917A pdb=" N TRP Y 365 " --> pdb=" O GLY Y 361 " (cutoff:3.500A) Processing helix chain 'Y' and resid 371 through 380 Processing helix chain 'Y' and resid 404 through 417 Processing helix chain 'Y' and resid 423 through 429 removed outlier: 4.306A pdb=" N ASP Y 427 " --> pdb=" O GLY Y 423 " (cutoff:3.500A) Processing helix chain 'Y' and resid 433 through 448 removed outlier: 3.575A pdb=" N LEU Y 440 " --> pdb=" O LYS Y 436 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS Y 443 " --> pdb=" O GLY Y 439 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU Y 445 " --> pdb=" O THR Y 441 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG Y 446 " --> pdb=" O SER Y 442 " (cutoff:3.500A) Processing helix chain 'Y' and resid 458 through 473 Processing helix chain 'Y' and resid 475 through 480 Processing helix chain 'Y' and resid 481 through 501 removed outlier: 4.371A pdb=" N TYR Y 485 " --> pdb=" O GLU Y 481 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA Y 486 " --> pdb=" O LYS Y 482 " (cutoff:3.500A) Processing helix chain 'Y' and resid 502 through 504 No H-bonds generated for 'chain 'Y' and resid 502 through 504' Processing helix chain 'Y' and resid 602 through 610 Processing helix chain 'Y' and resid 711 through 728 removed outlier: 3.884A pdb=" N ARG Y 728 " --> pdb=" O VAL Y 724 " (cutoff:3.500A) Processing helix chain 'Y' and resid 738 through 762 removed outlier: 3.904A pdb=" N ASN Y 742 " --> pdb=" O SER Y 738 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS Y 762 " --> pdb=" O HIS Y 758 " (cutoff:3.500A) Processing helix chain 'Y' and resid 783 through 787 Processing helix chain 'Y' and resid 790 through 802 removed outlier: 4.049A pdb=" N TYR Y 802 " --> pdb=" O ALA Y 798 " (cutoff:3.500A) Processing helix chain 'Y' and resid 886 through 892 Processing helix chain 'Y' and resid 897 through 904 Processing helix chain 'Y' and resid 906 through 914 removed outlier: 3.747A pdb=" N UNK Y 910 " --> pdb=" O UNK Y 906 " (cutoff:3.500A) Processing helix chain 'Y' and resid 945 through 950 Processing helix chain 'Y' and resid 965 through 978 removed outlier: 3.534A pdb=" N ARG Y 976 " --> pdb=" O ALA Y 972 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'Y' and resid 27 through 29 removed outlier: 3.605A pdb=" N ASN Y 626 " --> pdb=" O THR Y 651 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLU Y 653 " --> pdb=" O LEU Y 624 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU Y 624 " --> pdb=" O GLU Y 653 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG Y 510 " --> pdb=" O GLU Y 631 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 27 through 29 removed outlier: 3.605A pdb=" N ASN Y 626 " --> pdb=" O THR Y 651 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLU Y 653 " --> pdb=" O LEU Y 624 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU Y 624 " --> pdb=" O GLU Y 653 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Y' and resid 33 through 34 removed outlier: 3.695A pdb=" N ARG Y 33 " --> pdb=" O ALA Y 600 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 518 through 519 removed outlier: 4.031A pdb=" N SER Y 518 " --> pdb=" O GLN Y 527 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Y' and resid 557 through 558 removed outlier: 4.036A pdb=" N ARG Y 557 " --> pdb=" O THR Y 586 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 669 through 670 removed outlier: 6.363A pdb=" N ILE Y 669 " --> pdb=" O VAL Y 767 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA Y 769 " --> pdb=" O ILE Y 669 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU Y 766 " --> pdb=" O SER Y 812 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR Y 814 " --> pdb=" O LEU Y 766 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE Y 768 " --> pdb=" O THR Y 814 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 250 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 153 hydrogen bonds 288 hydrogen bond angles 0 basepair planarities 63 basepair parallelities 99 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1454 1.32 - 1.44: 3695 1.44 - 1.57: 5236 1.57 - 1.69: 323 1.69 - 1.81: 34 Bond restraints: 10742 Sorted by residual: bond pdb=" CA HIS Y 199 " pdb=" CB HIS Y 199 " ideal model delta sigma weight residual 1.530 1.488 0.042 1.69e-02 3.50e+03 6.27e+00 bond pdb=" CA LEU Y 615 " pdb=" CB LEU Y 615 " ideal model delta sigma weight residual 1.531 1.449 0.082 3.28e-02 9.30e+02 6.18e+00 bond pdb=" CG LEU Y 585 " pdb=" CD1 LEU Y 585 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.95e+00 bond pdb=" C SER Y 197 " pdb=" N ILE Y 198 " ideal model delta sigma weight residual 1.332 1.300 0.032 1.36e-02 5.41e+03 5.40e+00 bond pdb=" C ASN Y 501 " pdb=" N PRO Y 502 " ideal model delta sigma weight residual 1.334 1.353 -0.020 8.40e-03 1.42e+04 5.39e+00 ... (remaining 10737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 14984 3.27 - 6.55: 273 6.55 - 9.82: 30 9.82 - 13.09: 4 13.09 - 16.37: 1 Bond angle restraints: 15292 Sorted by residual: angle pdb=" N GLY Y 572 " pdb=" CA GLY Y 572 " pdb=" C GLY Y 572 " ideal model delta sigma weight residual 113.18 129.55 -16.37 2.37e+00 1.78e-01 4.77e+01 angle pdb=" CA TRP Y 534 " pdb=" CB TRP Y 534 " pdb=" CG TRP Y 534 " ideal model delta sigma weight residual 113.60 125.99 -12.39 1.90e+00 2.77e-01 4.25e+01 angle pdb=" N SER Y 197 " pdb=" CA SER Y 197 " pdb=" C SER Y 197 " ideal model delta sigma weight residual 114.64 104.98 9.66 1.52e+00 4.33e-01 4.04e+01 angle pdb=" C ILE Y 198 " pdb=" N HIS Y 199 " pdb=" CA HIS Y 199 " ideal model delta sigma weight residual 121.54 131.42 -9.88 1.91e+00 2.74e-01 2.68e+01 angle pdb=" N THR Y 954 " pdb=" CA THR Y 954 " pdb=" C THR Y 954 " ideal model delta sigma weight residual 114.62 109.13 5.49 1.14e+00 7.69e-01 2.32e+01 ... (remaining 15287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 5796 34.22 - 68.44: 555 68.44 - 102.65: 46 102.65 - 136.87: 1 136.87 - 171.09: 4 Dihedral angle restraints: 6402 sinusoidal: 3745 harmonic: 2657 Sorted by residual: dihedral pdb=" CA ILE Y 198 " pdb=" C ILE Y 198 " pdb=" N HIS Y 199 " pdb=" CA HIS Y 199 " ideal model delta harmonic sigma weight residual -180.00 -138.16 -41.84 0 5.00e+00 4.00e-02 7.00e+01 dihedral pdb=" O4' U B 17 " pdb=" C1' U B 17 " pdb=" N1 U B 17 " pdb=" C2 U B 17 " ideal model delta sinusoidal sigma weight residual 232.00 64.29 167.71 1 1.70e+01 3.46e-03 6.57e+01 dihedral pdb=" CA GLY Y 367 " pdb=" C GLY Y 367 " pdb=" N VAL Y 368 " pdb=" CA VAL Y 368 " ideal model delta harmonic sigma weight residual -180.00 -145.98 -34.02 0 5.00e+00 4.00e-02 4.63e+01 ... (remaining 6399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1507 0.068 - 0.137: 250 0.137 - 0.205: 48 0.205 - 0.273: 6 0.273 - 0.341: 5 Chirality restraints: 1816 Sorted by residual: chirality pdb=" CB ILE Y 677 " pdb=" CA ILE Y 677 " pdb=" CG1 ILE Y 677 " pdb=" CG2 ILE Y 677 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C3' G B 44 " pdb=" C4' G B 44 " pdb=" O3' G B 44 " pdb=" C2' G B 44 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' G B 30 " pdb=" C4' G B 30 " pdb=" O3' G B 30 " pdb=" C2' G B 30 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1813 not shown) Planarity restraints: 1364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP Y 534 " -0.025 2.00e-02 2.50e+03 1.97e-02 9.70e+00 pdb=" CG TRP Y 534 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP Y 534 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP Y 534 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP Y 534 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP Y 534 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP Y 534 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP Y 534 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP Y 534 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP Y 534 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 56 " -0.039 2.00e-02 2.50e+03 1.85e-02 9.41e+00 pdb=" N9 A B 56 " 0.045 2.00e-02 2.50e+03 pdb=" C8 A B 56 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 56 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 56 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A B 56 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A B 56 " -0.011 2.00e-02 2.50e+03 pdb=" N1 A B 56 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A B 56 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A B 56 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A B 56 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN Y 501 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO Y 502 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO Y 502 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO Y 502 " 0.040 5.00e-02 4.00e+02 ... (remaining 1361 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2340 2.78 - 3.31: 8487 3.31 - 3.84: 18053 3.84 - 4.37: 19591 4.37 - 4.90: 30769 Nonbonded interactions: 79240 Sorted by model distance: nonbonded pdb=" OH TYR Y 196 " pdb=" O SER Y 221 " model vdw 2.251 3.040 nonbonded pdb=" O4 U B 65 " pdb=" O6 G B 87 " model vdw 2.295 2.432 nonbonded pdb=" OG1 THR Y 603 " pdb=" OP2 A B 18 " model vdw 2.302 3.040 nonbonded pdb=" O SER Y 204 " pdb=" OG SER Y 204 " model vdw 2.321 3.040 nonbonded pdb=" O SER Y 661 " pdb=" OG SER Y 661 " model vdw 2.334 3.040 ... (remaining 79235 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.650 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.009 0.082 10742 Z= 0.564 Angle : 1.131 16.367 15292 Z= 0.624 Chirality : 0.056 0.341 1816 Planarity : 0.007 0.071 1363 Dihedral : 22.552 171.087 4672 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.64 % Allowed : 16.88 % Favored : 82.48 % Rotamer: Outliers : 0.33 % Allowed : 11.51 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -5.86 (0.20), residues: 782 helix: -3.34 (0.18), residues: 349 sheet: -4.27 (0.40), residues: 92 loop : -4.33 (0.24), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP Y 534 HIS 0.019 0.004 HIS Y 250 PHE 0.039 0.004 PHE Y 609 TYR 0.022 0.003 TYR Y 732 ARG 0.003 0.000 ARG Y 787 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.856 Fit side-chains REVERT: Y 498 LEU cc_start: 0.8628 (mt) cc_final: 0.8302 (mt) REVERT: Y 950 ASN cc_start: 0.8438 (p0) cc_final: 0.8233 (p0) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.3012 time to fit residues: 34.8873 Evaluate side-chains 64 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 84 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 60 ASN Y 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10742 Z= 0.167 Angle : 0.684 9.383 15292 Z= 0.360 Chirality : 0.038 0.212 1816 Planarity : 0.005 0.048 1363 Dihedral : 23.307 179.500 3232 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.96 % Favored : 84.78 % Rotamer: Outliers : 2.96 % Allowed : 15.62 % Favored : 81.41 % 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: -3.91 (0.26), residues: 782 helix: -1.17 (0.27), residues: 334 sheet: -3.84 (0.45), residues: 92 loop : -3.71 (0.27), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP Y 534 HIS 0.006 0.001 HIS Y 250 PHE 0.022 0.002 PHE Y 503 TYR 0.009 0.001 TYR Y 528 ARG 0.006 0.000 ARG Y 475 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.901 Fit side-chains REVERT: Y 35 MET cc_start: 0.8205 (mmm) cc_final: 0.7997 (mtp) REVERT: Y 639 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6166 (pt) REVERT: Y 920 GLN cc_start: 0.6773 (tp-100) cc_final: 0.6572 (tp-100) outliers start: 18 outliers final: 5 residues processed: 91 average time/residue: 0.2448 time to fit residues: 30.9318 Evaluate side-chains 70 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 782 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10742 Z= 0.173 Angle : 0.645 8.151 15292 Z= 0.337 Chirality : 0.036 0.212 1816 Planarity : 0.004 0.047 1363 Dihedral : 23.154 179.511 3232 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Rotamer: Outliers : 3.45 % Allowed : 19.08 % Favored : 77.47 % 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: -3.10 (0.28), residues: 782 helix: -0.28 (0.29), residues: 336 sheet: -3.29 (0.56), residues: 74 loop : -3.62 (0.27), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 250 PHE 0.020 0.002 PHE Y 775 TYR 0.011 0.001 TYR Y 528 ARG 0.003 0.000 ARG Y 475 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.891 Fit side-chains REVERT: Y 316 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7865 (tpt-90) REVERT: Y 639 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6257 (pt) REVERT: Y 735 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8268 (ttpp) REVERT: Y 920 GLN cc_start: 0.6679 (tp-100) cc_final: 0.6391 (tp40) outliers start: 21 outliers final: 12 residues processed: 86 average time/residue: 0.2202 time to fit residues: 27.7085 Evaluate side-chains 78 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 316 ARG Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 524 HIS Chi-restraints excluded: chain Y residue 594 LEU Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 765 VAL Chi-restraints excluded: chain Y residue 782 THR Chi-restraints excluded: chain Y residue 932 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 30.0000 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10742 Z= 0.168 Angle : 0.627 8.315 15292 Z= 0.328 Chirality : 0.036 0.211 1816 Planarity : 0.004 0.046 1363 Dihedral : 23.077 179.047 3232 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.32 % Favored : 85.68 % Rotamer: Outliers : 3.29 % Allowed : 20.89 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.29), residues: 782 helix: 0.18 (0.29), residues: 337 sheet: -3.35 (0.56), residues: 81 loop : -3.42 (0.27), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Y 534 HIS 0.014 0.002 HIS Y 933 PHE 0.028 0.002 PHE Y 775 TYR 0.012 0.001 TYR Y 575 ARG 0.003 0.000 ARG Y 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 70 time to evaluate : 0.870 Fit side-chains REVERT: Y 233 MET cc_start: 0.8714 (mmp) cc_final: 0.8344 (mmp) REVERT: Y 639 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6308 (pt) REVERT: Y 735 LYS cc_start: 0.8489 (ttpt) cc_final: 0.8238 (ttpp) outliers start: 20 outliers final: 13 residues processed: 85 average time/residue: 0.2118 time to fit residues: 26.5984 Evaluate side-chains 76 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 524 HIS Chi-restraints excluded: chain Y residue 594 LEU Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 782 THR Chi-restraints excluded: chain Y residue 932 VAL Chi-restraints excluded: chain Y residue 949 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10742 Z= 0.162 Angle : 0.614 8.177 15292 Z= 0.321 Chirality : 0.035 0.211 1816 Planarity : 0.004 0.046 1363 Dihedral : 23.012 178.676 3232 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Rotamer: Outliers : 3.29 % Allowed : 21.22 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.30), residues: 782 helix: 0.39 (0.29), residues: 345 sheet: -3.35 (0.57), residues: 75 loop : -3.27 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Y 534 HIS 0.008 0.001 HIS Y 933 PHE 0.032 0.002 PHE Y 775 TYR 0.009 0.001 TYR Y 196 ARG 0.003 0.000 ARG Y 706 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 0.855 Fit side-chains REVERT: Y 53 MET cc_start: 0.7573 (mmp) cc_final: 0.7367 (mmt) REVERT: Y 639 ILE cc_start: 0.6741 (OUTLIER) cc_final: 0.6295 (pt) REVERT: Y 735 LYS cc_start: 0.8437 (ttpt) cc_final: 0.8205 (ttpp) REVERT: Y 920 GLN cc_start: 0.6208 (tp-100) cc_final: 0.5639 (tp-100) outliers start: 20 outliers final: 14 residues processed: 79 average time/residue: 0.1896 time to fit residues: 22.7389 Evaluate side-chains 75 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 52 VAL Chi-restraints excluded: chain Y residue 57 ILE Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 273 LEU Chi-restraints excluded: chain Y residue 503 PHE Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 524 HIS Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 765 VAL Chi-restraints excluded: chain Y residue 782 THR Chi-restraints excluded: chain Y residue 949 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 0.0170 chunk 17 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 89 optimal weight: 30.0000 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 29 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10742 Z= 0.158 Angle : 0.605 8.072 15292 Z= 0.316 Chirality : 0.035 0.211 1816 Planarity : 0.004 0.044 1363 Dihedral : 22.982 178.343 3232 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.32 % Favored : 85.55 % Rotamer: Outliers : 3.45 % Allowed : 21.71 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.30), residues: 782 helix: 0.57 (0.29), residues: 346 sheet: -3.31 (0.57), residues: 75 loop : -3.20 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Y 534 HIS 0.007 0.001 HIS Y 933 PHE 0.034 0.001 PHE Y 775 TYR 0.012 0.001 TYR Y 528 ARG 0.003 0.000 ARG Y 706 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 0.820 Fit side-chains REVERT: Y 639 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6305 (pt) REVERT: Y 735 LYS cc_start: 0.8443 (ttpt) cc_final: 0.8223 (ttpp) REVERT: Y 920 GLN cc_start: 0.6212 (tp-100) cc_final: 0.5660 (tp40) outliers start: 21 outliers final: 18 residues processed: 85 average time/residue: 0.1979 time to fit residues: 25.1355 Evaluate side-chains 79 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 52 VAL Chi-restraints excluded: chain Y residue 57 ILE Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 273 LEU Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 418 TYR Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 517 PHE Chi-restraints excluded: chain Y residue 524 HIS Chi-restraints excluded: chain Y residue 594 LEU Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 782 THR Chi-restraints excluded: chain Y residue 932 VAL Chi-restraints excluded: chain Y residue 949 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 89 optimal weight: 30.0000 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 55 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10742 Z= 0.150 Angle : 0.596 7.921 15292 Z= 0.312 Chirality : 0.035 0.211 1816 Planarity : 0.004 0.043 1363 Dihedral : 22.970 178.133 3232 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.45 % Favored : 85.55 % Rotamer: Outliers : 3.62 % Allowed : 21.55 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.30), residues: 782 helix: 0.77 (0.30), residues: 344 sheet: -3.24 (0.57), residues: 75 loop : -3.12 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Y 534 HIS 0.006 0.001 HIS Y 933 PHE 0.024 0.001 PHE Y 775 TYR 0.013 0.001 TYR Y 528 ARG 0.003 0.000 ARG Y 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 0.855 Fit side-chains REVERT: Y 381 ASN cc_start: 0.8536 (t0) cc_final: 0.8267 (t0) REVERT: Y 639 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6331 (pt) REVERT: Y 794 ASP cc_start: 0.8499 (t0) cc_final: 0.8239 (t0) REVERT: Y 920 GLN cc_start: 0.6240 (tp-100) cc_final: 0.5680 (tp40) outliers start: 22 outliers final: 19 residues processed: 86 average time/residue: 0.2075 time to fit residues: 26.0596 Evaluate side-chains 83 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 52 VAL Chi-restraints excluded: chain Y residue 57 ILE Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 273 LEU Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 418 TYR Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 517 PHE Chi-restraints excluded: chain Y residue 524 HIS Chi-restraints excluded: chain Y residue 594 LEU Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 782 THR Chi-restraints excluded: chain Y residue 932 VAL Chi-restraints excluded: chain Y residue 949 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10742 Z= 0.192 Angle : 0.624 8.583 15292 Z= 0.325 Chirality : 0.036 0.213 1816 Planarity : 0.004 0.045 1363 Dihedral : 22.944 177.500 3232 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.45 % Favored : 85.42 % Rotamer: Outliers : 3.29 % Allowed : 21.71 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.30), residues: 782 helix: 0.78 (0.30), residues: 345 sheet: -3.11 (0.58), residues: 76 loop : -3.20 (0.28), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Y 534 HIS 0.005 0.001 HIS Y 933 PHE 0.021 0.002 PHE Y 775 TYR 0.015 0.001 TYR Y 528 ARG 0.003 0.000 ARG Y 706 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 0.818 Fit side-chains REVERT: Y 381 ASN cc_start: 0.8602 (t0) cc_final: 0.8343 (t0) REVERT: Y 639 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6301 (pt) REVERT: Y 794 ASP cc_start: 0.8461 (t0) cc_final: 0.8238 (t0) REVERT: Y 920 GLN cc_start: 0.6229 (tp-100) cc_final: 0.5684 (tp40) outliers start: 20 outliers final: 17 residues processed: 74 average time/residue: 0.1945 time to fit residues: 21.9862 Evaluate side-chains 77 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 52 VAL Chi-restraints excluded: chain Y residue 57 ILE Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 273 LEU Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 418 TYR Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 517 PHE Chi-restraints excluded: chain Y residue 524 HIS Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 782 THR Chi-restraints excluded: chain Y residue 949 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.0570 chunk 83 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 30.0000 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10742 Z= 0.153 Angle : 0.598 8.299 15292 Z= 0.313 Chirality : 0.035 0.211 1816 Planarity : 0.004 0.044 1363 Dihedral : 22.895 177.174 3232 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % Rotamer: Outliers : 2.96 % Allowed : 22.70 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.31), residues: 782 helix: 0.95 (0.30), residues: 344 sheet: -3.10 (0.60), residues: 75 loop : -3.07 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 933 PHE 0.035 0.002 PHE Y 775 TYR 0.013 0.001 TYR Y 528 ARG 0.003 0.000 ARG Y 706 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 0.927 Fit side-chains REVERT: Y 381 ASN cc_start: 0.8580 (t0) cc_final: 0.8319 (t0) REVERT: Y 409 ASP cc_start: 0.7945 (m-30) cc_final: 0.7626 (m-30) REVERT: Y 639 ILE cc_start: 0.6743 (OUTLIER) cc_final: 0.6318 (pt) REVERT: Y 794 ASP cc_start: 0.8515 (t0) cc_final: 0.8263 (t0) REVERT: Y 920 GLN cc_start: 0.5997 (tp-100) cc_final: 0.5380 (tp40) outliers start: 18 outliers final: 16 residues processed: 81 average time/residue: 0.1972 time to fit residues: 24.2435 Evaluate side-chains 80 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 52 VAL Chi-restraints excluded: chain Y residue 57 ILE Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 273 LEU Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 418 TYR Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 524 HIS Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 782 THR Chi-restraints excluded: chain Y residue 932 VAL Chi-restraints excluded: chain Y residue 949 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.1252 > 50: distance: 23 - 50: 34.311 distance: 27 - 32: 35.756 distance: 28 - 58: 31.839 distance: 33 - 34: 10.941 distance: 33 - 36: 40.009 distance: 34 - 35: 37.876 distance: 34 - 41: 26.756 distance: 35 - 63: 44.158 distance: 36 - 37: 39.433 distance: 42 - 43: 13.693 distance: 42 - 45: 19.021 distance: 43 - 44: 7.298 distance: 43 - 50: 14.995 distance: 45 - 46: 18.028 distance: 46 - 47: 40.490 distance: 47 - 48: 40.903 distance: 48 - 49: 27.683 distance: 50 - 51: 34.521 distance: 51 - 52: 5.229 distance: 51 - 54: 7.361 distance: 52 - 53: 41.119 distance: 53 - 75: 56.410 distance: 54 - 56: 56.908 distance: 55 - 57: 57.019 distance: 58 - 59: 34.727 distance: 59 - 60: 51.043 distance: 59 - 62: 40.068 distance: 60 - 61: 4.595 distance: 60 - 63: 3.392 distance: 61 - 82: 63.987 distance: 64 - 65: 68.684 distance: 65 - 67: 56.214 distance: 67 - 68: 38.950 distance: 68 - 71: 40.485 distance: 70 - 98: 3.222 distance: 71 - 72: 14.847 distance: 72 - 73: 59.606 distance: 72 - 74: 14.190 distance: 75 - 76: 6.241 distance: 76 - 77: 47.042 distance: 76 - 79: 42.294 distance: 77 - 78: 4.135 distance: 77 - 82: 33.689 distance: 79 - 80: 48.659 distance: 79 - 81: 27.709 distance: 82 - 83: 41.576 distance: 84 - 85: 9.017 distance: 84 - 88: 40.424 distance: 89 - 90: 39.034 distance: 89 - 92: 21.167 distance: 91 - 125: 35.314 distance: 92 - 93: 20.283 distance: 93 - 94: 23.619 distance: 93 - 95: 26.192 distance: 94 - 96: 41.129 distance: 95 - 97: 8.887 distance: 99 - 100: 38.721 distance: 99 - 102: 56.137 distance: 100 - 106: 34.824 distance: 101 - 132: 34.497 distance: 102 - 103: 39.932 distance: 102 - 104: 40.778 distance: 103 - 105: 11.975