Starting phenix.real_space_refine on Tue May 7 14:18:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/05_2024/8jlc_36392_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/05_2024/8jlc_36392.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/05_2024/8jlc_36392_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/05_2024/8jlc_36392_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/05_2024/8jlc_36392_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/05_2024/8jlc_36392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/05_2024/8jlc_36392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/05_2024/8jlc_36392_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlc_36392/05_2024/8jlc_36392_updated.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 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 47 5.16 5 C 5291 2.51 5 N 1362 2.21 5 O 1489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 532": "OE1" <-> "OE2" Residue "A ASP 620": "OD1" <-> "OD2" Residue "B TYR 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1064": "NH1" <-> "NH2" Residue "B GLU 1203": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 8189 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4674 Classifications: {'peptide': 592} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 576} Chain breaks: 1 Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3437 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'NAG': 2, 'UKX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.74, per 1000 atoms: 0.58 Number of scatterers: 8189 At special positions: 0 Unit cell: (87.98, 85.49, 147.74, 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 47 16.00 O 1489 8.00 N 1362 7.00 C 5291 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 BETA1-4 " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 498 " " NAG A 802 " - " ASN A 548 " " NAG F 1 " - " ASN A 573 " Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.6 seconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1866 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 13 sheets defined 40.7% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 138 through 159 Processing helix chain 'A' and resid 163 through 196 removed outlier: 4.099A pdb=" N ASP A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHE A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLY A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Proline residue: A 191 - end of helix removed outlier: 4.316A pdb=" N LYS A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 229 removed outlier: 4.615A pdb=" N VAL A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 220 " --> pdb=" O MET A 216 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 249 Processing helix chain 'A' and resid 256 through 283 removed outlier: 4.319A pdb=" N GLY A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N SER A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ILE A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Proline residue: A 274 - end of helix removed outlier: 4.124A pdb=" N GLU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 290 through 314 removed outlier: 4.281A pdb=" N LEU A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N CYS A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N MET A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N PHE A 299 " --> pdb=" O TRP A 295 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TRP A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 353 Proline residue: A 343 - end of helix removed outlier: 4.502A pdb=" N THR A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 368 through 385 Processing helix chain 'A' and resid 419 through 438 Processing helix chain 'A' and resid 445 through 482 Proline residue: A 469 - end of helix Processing helix chain 'A' and resid 563 through 565 No H-bonds generated for 'chain 'A' and resid 563 through 565' Processing helix chain 'A' and resid 592 through 622 removed outlier: 3.547A pdb=" N MET A 596 " --> pdb=" O GLY A 593 " (cutoff:3.500A) Proline residue: A 610 - end of helix removed outlier: 3.965A pdb=" N MET A 619 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 622 " --> pdb=" O MET A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 643 removed outlier: 3.678A pdb=" N MET A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 642 " --> pdb=" O SER A 638 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER A 643 " --> pdb=" O CYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 675 removed outlier: 3.720A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA A 664 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 707 removed outlier: 3.567A pdb=" N PHE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 732 removed outlier: 3.893A pdb=" N LYS A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 932 No H-bonds generated for 'chain 'B' and resid 930 through 932' Processing helix chain 'B' and resid 955 through 957 No H-bonds generated for 'chain 'B' and resid 955 through 957' Processing helix chain 'B' and resid 1081 through 1091 Processing helix chain 'B' and resid 1266 through 1272 Processing sheet with id= A, first strand: chain 'A' and resid 485 through 488 removed outlier: 6.283A pdb=" N PHE A 545 " --> pdb=" O PHE A 526 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 490 through 492 removed outlier: 6.162A pdb=" N LEU A 530 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR A 550 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG A 570 " --> pdb=" O PHE A 551 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 495 through 497 removed outlier: 3.718A pdb=" N LYS A 515 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR A 535 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 555 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR A 575 " --> pdb=" O PHE A 556 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 500 through 502 removed outlier: 6.600A pdb=" N ARG A 520 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.590A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B1074 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 880 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE B1072 " --> pdb=" O SER B 880 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 897 through 900 Processing sheet with id= G, first strand: chain 'B' and resid 914 through 916 Processing sheet with id= H, first strand: chain 'B' and resid 994 through 1000 removed outlier: 5.988A pdb=" N LEU B 978 " --> pdb=" O THR B 963 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N THR B 963 " --> pdb=" O LEU B 978 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id= J, first strand: chain 'B' and resid 1122 through 1124 Processing sheet with id= K, first strand: chain 'B' and resid 1142 through 1144 Processing sheet with id= L, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 4.119A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 1220 through 1224 removed outlier: 3.666A pdb=" N VAL B1220 " --> pdb=" O GLN B1240 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1041 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: 3.10 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1771 1.33 - 1.47: 3037 1.47 - 1.61: 3497 1.61 - 1.75: 3 1.75 - 1.89: 75 Bond restraints: 8383 Sorted by residual: bond pdb=" C GLY A 591 " pdb=" N GLU A 592 " ideal model delta sigma weight residual 1.335 1.458 -0.123 1.35e-02 5.49e+03 8.37e+01 bond pdb=" C5 UKX A 803 " pdb=" C6 UKX A 803 " ideal model delta sigma weight residual 1.527 1.709 -0.182 2.00e-02 2.50e+03 8.32e+01 bond pdb=" C1 UKX A 803 " pdb=" C2 UKX A 803 " ideal model delta sigma weight residual 1.465 1.580 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C GLY A 604 " pdb=" O GLY A 604 " ideal model delta sigma weight residual 1.233 1.290 -0.057 1.17e-02 7.31e+03 2.40e+01 bond pdb=" N GLU A 592 " pdb=" CA GLU A 592 " ideal model delta sigma weight residual 1.458 1.517 -0.059 1.30e-02 5.92e+03 2.07e+01 ... (remaining 8378 not shown) Histogram of bond angle deviations from ideal: 92.98 - 101.68: 27 101.68 - 110.37: 1815 110.37 - 119.07: 4940 119.07 - 127.77: 4486 127.77 - 136.47: 67 Bond angle restraints: 11335 Sorted by residual: angle pdb=" C GLY A 591 " pdb=" N GLU A 592 " pdb=" CA GLU A 592 " ideal model delta sigma weight residual 120.60 136.47 -15.87 1.60e+00 3.91e-01 9.84e+01 angle pdb=" OD1 ASN A 498 " pdb=" CG ASN A 498 " pdb=" ND2 ASN A 498 " ideal model delta sigma weight residual 122.60 116.64 5.96 1.00e+00 1.00e+00 3.55e+01 angle pdb=" N VAL A 671 " pdb=" CA VAL A 671 " pdb=" C VAL A 671 " ideal model delta sigma weight residual 110.62 115.27 -4.65 1.02e+00 9.61e-01 2.08e+01 angle pdb=" CA ASP B1256 " pdb=" CB ASP B1256 " pdb=" CG ASP B1256 " ideal model delta sigma weight residual 112.60 117.08 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" N ILE B1148 " pdb=" CA ILE B1148 " pdb=" C ILE B1148 " ideal model delta sigma weight residual 111.62 108.13 3.49 7.90e-01 1.60e+00 1.95e+01 ... (remaining 11330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.69: 4437 15.69 - 31.38: 417 31.38 - 47.07: 73 47.07 - 62.76: 15 62.76 - 78.45: 12 Dihedral angle restraints: 4954 sinusoidal: 2031 harmonic: 2923 Sorted by residual: dihedral pdb=" CA ILE B1053 " pdb=" C ILE B1053 " pdb=" N MET B1054 " pdb=" CA MET B1054 " ideal model delta harmonic sigma weight residual -180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLU B1210 " pdb=" C GLU B1210 " pdb=" N ILE B1211 " pdb=" CA ILE B1211 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHE A 497 " pdb=" C PHE A 497 " pdb=" N ASN A 498 " pdb=" CA ASN A 498 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.252: 1237 0.252 - 0.504: 6 0.504 - 0.755: 0 0.755 - 1.007: 0 1.007 - 1.259: 1 Chirality restraints: 1244 Sorted by residual: chirality pdb=" C1 FUC F 3 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 3 " pdb=" O5 FUC F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.32e+01 chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 498 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.14 -1.26 2.00e-01 2.50e+01 3.96e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.67e+01 ... (remaining 1241 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 467 " 0.067 2.00e-02 2.50e+03 5.61e-02 7.88e+01 pdb=" CG TRP A 467 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 467 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP A 467 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP A 467 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TRP A 467 " 0.076 2.00e-02 2.50e+03 pdb=" CE3 TRP A 467 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 467 " 0.085 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 467 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 467 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 548 " 0.066 2.00e-02 2.50e+03 7.39e-02 6.82e+01 pdb=" CG ASN A 548 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 548 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 548 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG A 802 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " -0.073 2.00e-02 2.50e+03 6.05e-02 4.57e+01 pdb=" C7 NAG A 802 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " 0.098 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " 0.011 2.00e-02 2.50e+03 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 614 2.74 - 3.28: 8244 3.28 - 3.82: 13687 3.82 - 4.36: 16864 4.36 - 4.90: 28705 Nonbonded interactions: 68114 Sorted by model distance: nonbonded pdb=" O TRP B1266 " pdb=" NE2 GLN B1270 " model vdw 2.195 2.520 nonbonded pdb=" OG1 THR B1195 " pdb=" O ILE B1205 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR A 279 " pdb=" O PRO A 355 " model vdw 2.228 2.440 nonbonded pdb=" NE2 GLN A 323 " pdb=" O GLY A 325 " model vdw 2.272 2.520 nonbonded pdb=" OD1 ASP A 470 " pdb=" NH2 ARG A 473 " model vdw 2.288 2.520 ... (remaining 68109 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.830 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: 0.000 Extract box with map and model: 6.050 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 26.250 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 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 : 0.011 0.182 8383 Z= 0.687 Angle : 1.183 15.868 11335 Z= 0.775 Chirality : 0.085 1.259 1244 Planarity : 0.011 0.149 1428 Dihedral : 12.983 78.450 3088 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.12 (0.26), residues: 1006 helix: 1.06 (0.25), residues: 405 sheet: -0.08 (0.33), residues: 241 loop : -1.33 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.012 TRP A 467 HIS 0.013 0.004 HIS A 161 PHE 0.068 0.011 PHE A 299 TYR 0.053 0.009 TYR A 169 ARG 0.024 0.003 ARG B1140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.6366 (tpp80) cc_final: 0.5741 (mtp85) REVERT: A 197 MET cc_start: 0.6566 (mtm) cc_final: 0.5263 (tpt) REVERT: A 227 ASP cc_start: 0.8194 (m-30) cc_final: 0.7946 (m-30) REVERT: A 366 LYS cc_start: 0.6546 (mtmt) cc_final: 0.6283 (mttm) REVERT: A 372 MET cc_start: 0.7261 (mtm) cc_final: 0.7027 (mmm) REVERT: A 444 ARG cc_start: 0.6477 (ttp-110) cc_final: 0.6245 (ttt180) REVERT: A 491 ARG cc_start: 0.7519 (tmt170) cc_final: 0.7252 (tmt170) REVERT: A 520 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7509 (tmm-80) REVERT: A 542 SER cc_start: 0.8059 (t) cc_final: 0.7844 (t) REVERT: A 563 GLU cc_start: 0.8138 (pt0) cc_final: 0.7196 (tp30) REVERT: A 567 VAL cc_start: 0.7421 (t) cc_final: 0.7180 (t) REVERT: A 568 ASN cc_start: 0.8211 (t0) cc_final: 0.7877 (p0) REVERT: A 581 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 910 ASP cc_start: 0.5165 (t0) cc_final: 0.4352 (t0) REVERT: B 925 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7527 (mm-30) REVERT: B 1097 LEU cc_start: 0.6800 (mm) cc_final: 0.6475 (tt) REVERT: B 1127 ASN cc_start: 0.8545 (m-40) cc_final: 0.8332 (p0) REVERT: B 1203 GLU cc_start: 0.5470 (mt-10) cc_final: 0.4936 (mm-30) REVERT: B 1219 GLN cc_start: 0.7566 (pt0) cc_final: 0.6767 (pt0) REVERT: B 1246 ASP cc_start: 0.7038 (p0) cc_final: 0.6682 (p0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 1.3555 time to fit residues: 252.7737 Evaluate side-chains 131 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 91 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS A 513 ASN B1073 ASN B1115 ASN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8383 Z= 0.179 Angle : 0.560 7.712 11335 Z= 0.296 Chirality : 0.045 0.436 1244 Planarity : 0.003 0.032 1428 Dihedral : 6.209 55.629 1211 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.82 % Allowed : 10.47 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.44 (0.27), residues: 1006 helix: 1.74 (0.25), residues: 406 sheet: 0.12 (0.34), residues: 231 loop : -1.23 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 300 HIS 0.004 0.001 HIS A 387 PHE 0.017 0.001 PHE A 512 TYR 0.013 0.001 TYR A 306 ARG 0.005 0.000 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5984 (tpp80) cc_final: 0.5708 (mtp85) REVERT: A 146 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7744 (tm-30) REVERT: A 197 MET cc_start: 0.6316 (mtm) cc_final: 0.5803 (ttm) REVERT: A 227 ASP cc_start: 0.7976 (m-30) cc_final: 0.7346 (m-30) REVERT: A 366 LYS cc_start: 0.6546 (mtmt) cc_final: 0.6281 (mttm) REVERT: A 372 MET cc_start: 0.7358 (mtm) cc_final: 0.7087 (mmm) REVERT: A 379 ASP cc_start: 0.5975 (m-30) cc_final: 0.5764 (m-30) REVERT: A 444 ARG cc_start: 0.6348 (ttp-110) cc_final: 0.6055 (ttt180) REVERT: A 491 ARG cc_start: 0.7425 (tmt170) cc_final: 0.7103 (tpt-90) REVERT: A 520 ARG cc_start: 0.8002 (mtt90) cc_final: 0.7545 (tpt170) REVERT: A 522 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7152 (tppt) REVERT: A 563 GLU cc_start: 0.8183 (pt0) cc_final: 0.7290 (tp30) REVERT: A 567 VAL cc_start: 0.7562 (t) cc_final: 0.7344 (m) REVERT: B 910 ASP cc_start: 0.5168 (t0) cc_final: 0.4675 (t0) REVERT: B 1061 ARG cc_start: 0.6360 (mtm-85) cc_final: 0.6053 (ptp-170) REVERT: B 1219 GLN cc_start: 0.7292 (pt0) cc_final: 0.6935 (pt0) outliers start: 16 outliers final: 8 residues processed: 146 average time/residue: 1.2696 time to fit residues: 196.8744 Evaluate side-chains 137 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 522 LYS Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1146 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 30.0000 chunk 62 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS A 387 HIS A 434 ASN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8383 Z= 0.218 Angle : 0.548 6.836 11335 Z= 0.288 Chirality : 0.046 0.443 1244 Planarity : 0.003 0.025 1428 Dihedral : 5.913 55.011 1211 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.62 % Allowed : 12.74 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.45 (0.26), residues: 1006 helix: 1.64 (0.25), residues: 410 sheet: 0.15 (0.33), residues: 241 loop : -1.18 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 300 HIS 0.005 0.001 HIS A 387 PHE 0.014 0.001 PHE B1055 TYR 0.016 0.001 TYR A 306 ARG 0.005 0.000 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5954 (tpp80) cc_final: 0.5718 (mtp85) REVERT: A 146 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7709 (tm-30) REVERT: A 197 MET cc_start: 0.6249 (mtm) cc_final: 0.5798 (ttm) REVERT: A 227 ASP cc_start: 0.8102 (m-30) cc_final: 0.7317 (m-30) REVERT: A 301 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7536 (ttp) REVERT: A 366 LYS cc_start: 0.6610 (mtmt) cc_final: 0.6339 (mttm) REVERT: A 372 MET cc_start: 0.7311 (mtm) cc_final: 0.7032 (mmp) REVERT: A 444 ARG cc_start: 0.6560 (ttp-110) cc_final: 0.6211 (ttt180) REVERT: A 491 ARG cc_start: 0.7452 (tmt170) cc_final: 0.7180 (tpt-90) REVERT: A 520 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7461 (tpt170) REVERT: A 563 GLU cc_start: 0.8182 (pt0) cc_final: 0.7335 (tp30) REVERT: A 567 VAL cc_start: 0.7696 (t) cc_final: 0.7481 (m) REVERT: A 742 GLN cc_start: 0.7116 (tm-30) cc_final: 0.6848 (tm-30) REVERT: B 910 ASP cc_start: 0.5305 (t0) cc_final: 0.5029 (t0) REVERT: B 947 ILE cc_start: 0.7741 (tt) cc_final: 0.7536 (tp) REVERT: B 1061 ARG cc_start: 0.6338 (mtm-85) cc_final: 0.6032 (ptp-170) REVERT: B 1097 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5705 (tt) REVERT: B 1226 LYS cc_start: 0.6974 (pttm) cc_final: 0.6685 (ptmm) outliers start: 23 outliers final: 12 residues processed: 143 average time/residue: 1.2912 time to fit residues: 195.5978 Evaluate side-chains 134 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1097 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1146 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 9.9990 chunk 47 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8383 Z= 0.193 Angle : 0.536 8.591 11335 Z= 0.280 Chirality : 0.045 0.403 1244 Planarity : 0.003 0.043 1428 Dihedral : 5.804 56.411 1211 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.84 % Allowed : 14.90 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.48 (0.26), residues: 1006 helix: 1.66 (0.25), residues: 410 sheet: 0.19 (0.34), residues: 233 loop : -1.13 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 985 HIS 0.004 0.001 HIS A 494 PHE 0.016 0.001 PHE A 512 TYR 0.014 0.001 TYR A 306 ARG 0.010 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5971 (tpp80) cc_final: 0.5742 (mtp85) REVERT: A 146 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7701 (tm-30) REVERT: A 197 MET cc_start: 0.6266 (mtm) cc_final: 0.5870 (ttm) REVERT: A 227 ASP cc_start: 0.8074 (m-30) cc_final: 0.7398 (m-30) REVERT: A 301 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7614 (ttp) REVERT: A 366 LYS cc_start: 0.6577 (mtmt) cc_final: 0.6326 (mttm) REVERT: A 372 MET cc_start: 0.7319 (mtm) cc_final: 0.7056 (mmp) REVERT: A 444 ARG cc_start: 0.6555 (ttp-110) cc_final: 0.6148 (ttt180) REVERT: A 491 ARG cc_start: 0.7446 (tmt170) cc_final: 0.6963 (tpt-90) REVERT: A 520 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7467 (tpt170) REVERT: A 563 GLU cc_start: 0.8194 (pt0) cc_final: 0.7353 (tp30) REVERT: A 567 VAL cc_start: 0.7685 (t) cc_final: 0.7468 (m) REVERT: A 742 GLN cc_start: 0.7019 (tm-30) cc_final: 0.6801 (tm-30) REVERT: B 910 ASP cc_start: 0.5208 (t0) cc_final: 0.4987 (t0) REVERT: B 1061 ARG cc_start: 0.6387 (mtm-85) cc_final: 0.6070 (ptp-170) REVERT: B 1068 MET cc_start: 0.5643 (OUTLIER) cc_final: 0.4697 (mmt) REVERT: B 1106 GLN cc_start: 0.6603 (OUTLIER) cc_final: 0.6061 (mp10) REVERT: B 1226 LYS cc_start: 0.6957 (pttm) cc_final: 0.6688 (ptmm) outliers start: 25 outliers final: 10 residues processed: 145 average time/residue: 1.3104 time to fit residues: 201.5009 Evaluate side-chains 135 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1068 MET Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 988 GLN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8383 Z= 0.274 Angle : 0.571 9.821 11335 Z= 0.299 Chirality : 0.046 0.359 1244 Planarity : 0.004 0.038 1428 Dihedral : 5.797 57.882 1211 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.73 % Allowed : 15.81 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.36 (0.26), residues: 1006 helix: 1.52 (0.25), residues: 407 sheet: 0.15 (0.33), residues: 237 loop : -1.15 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 985 HIS 0.005 0.001 HIS A 494 PHE 0.012 0.001 PHE A 640 TYR 0.021 0.002 TYR B1133 ARG 0.008 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5944 (tpp80) cc_final: 0.5650 (mtp85) REVERT: A 146 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7671 (tm-30) REVERT: A 197 MET cc_start: 0.6223 (mtm) cc_final: 0.5748 (ttm) REVERT: A 301 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7675 (ttp) REVERT: A 372 MET cc_start: 0.7280 (mtm) cc_final: 0.7041 (mmp) REVERT: A 444 ARG cc_start: 0.6720 (ttp-110) cc_final: 0.6371 (ttt180) REVERT: A 491 ARG cc_start: 0.7416 (tmt170) cc_final: 0.6911 (tpt-90) REVERT: A 520 ARG cc_start: 0.8025 (mtt90) cc_final: 0.7523 (tpt170) REVERT: A 563 GLU cc_start: 0.8217 (pt0) cc_final: 0.7456 (tp30) REVERT: A 567 VAL cc_start: 0.7677 (t) cc_final: 0.7427 (m) REVERT: A 742 GLN cc_start: 0.7013 (tm-30) cc_final: 0.6605 (tm-30) REVERT: B 1061 ARG cc_start: 0.6322 (mtm-85) cc_final: 0.5984 (ptp-170) REVERT: B 1106 GLN cc_start: 0.6611 (OUTLIER) cc_final: 0.6121 (mp10) REVERT: B 1133 TYR cc_start: 0.5137 (p90) cc_final: 0.4633 (p90) REVERT: B 1193 LEU cc_start: 0.5811 (OUTLIER) cc_final: 0.5556 (mm) REVERT: B 1226 LYS cc_start: 0.6922 (pttm) cc_final: 0.6672 (ptmm) outliers start: 24 outliers final: 16 residues processed: 139 average time/residue: 1.1996 time to fit residues: 177.4947 Evaluate side-chains 139 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 988 GLN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8383 Z= 0.210 Angle : 0.543 10.368 11335 Z= 0.282 Chirality : 0.044 0.328 1244 Planarity : 0.003 0.033 1428 Dihedral : 5.588 58.485 1211 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.39 % Allowed : 16.50 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.36 (0.26), residues: 1006 helix: 1.52 (0.25), residues: 409 sheet: 0.13 (0.33), residues: 237 loop : -1.16 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1014 HIS 0.005 0.001 HIS A 494 PHE 0.016 0.001 PHE A 512 TYR 0.014 0.001 TYR A 306 ARG 0.010 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5939 (tpp80) cc_final: 0.5644 (mtp85) REVERT: A 146 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7693 (tm-30) REVERT: A 197 MET cc_start: 0.6229 (mtm) cc_final: 0.5763 (ttm) REVERT: A 301 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7632 (ttp) REVERT: A 372 MET cc_start: 0.7306 (mtm) cc_final: 0.7074 (mmp) REVERT: A 444 ARG cc_start: 0.6600 (ttp-110) cc_final: 0.6231 (ttt180) REVERT: A 491 ARG cc_start: 0.7423 (tmt170) cc_final: 0.6748 (tpt-90) REVERT: A 493 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6784 (pt0) REVERT: A 520 ARG cc_start: 0.8019 (mtt90) cc_final: 0.7516 (tpt170) REVERT: A 563 GLU cc_start: 0.8208 (pt0) cc_final: 0.7406 (tp30) REVERT: A 567 VAL cc_start: 0.7684 (t) cc_final: 0.7436 (m) REVERT: A 742 GLN cc_start: 0.6941 (tm-30) cc_final: 0.6636 (tm-30) REVERT: B 1061 ARG cc_start: 0.6349 (mtm-85) cc_final: 0.6022 (ptp-170) REVERT: B 1106 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.6132 (mp10) REVERT: B 1133 TYR cc_start: 0.5088 (p90) cc_final: 0.4622 (p90) REVERT: B 1226 LYS cc_start: 0.6984 (pttm) cc_final: 0.6731 (ptmm) outliers start: 21 outliers final: 11 residues processed: 132 average time/residue: 1.2873 time to fit residues: 180.6668 Evaluate side-chains 133 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1146 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 97 optimal weight: 0.0980 chunk 60 optimal weight: 0.2980 chunk 59 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS B 988 GLN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8383 Z= 0.178 Angle : 0.530 11.363 11335 Z= 0.276 Chirality : 0.043 0.304 1244 Planarity : 0.003 0.034 1428 Dihedral : 5.368 59.872 1211 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.28 % Allowed : 15.93 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.26), residues: 1006 helix: 1.65 (0.26), residues: 409 sheet: 0.21 (0.33), residues: 234 loop : -1.15 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 985 HIS 0.005 0.001 HIS A 494 PHE 0.009 0.001 PHE A 499 TYR 0.012 0.001 TYR A 306 ARG 0.010 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5898 (tpp80) cc_final: 0.5594 (mtp85) REVERT: A 146 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7706 (tm-30) REVERT: A 197 MET cc_start: 0.6220 (mtm) cc_final: 0.5749 (ttm) REVERT: A 301 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7609 (ttp) REVERT: A 372 MET cc_start: 0.7307 (mtm) cc_final: 0.7060 (mmp) REVERT: A 444 ARG cc_start: 0.6650 (ttp-110) cc_final: 0.6272 (ttt180) REVERT: A 491 ARG cc_start: 0.7429 (tmt170) cc_final: 0.6907 (tmt170) REVERT: A 493 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6801 (pt0) REVERT: A 520 ARG cc_start: 0.8018 (mtt90) cc_final: 0.7513 (tpt170) REVERT: A 563 GLU cc_start: 0.8209 (pt0) cc_final: 0.7414 (tp30) REVERT: A 567 VAL cc_start: 0.7681 (t) cc_final: 0.7449 (m) REVERT: A 742 GLN cc_start: 0.6914 (tm-30) cc_final: 0.6615 (tm-30) REVERT: B 1061 ARG cc_start: 0.6336 (mtm-85) cc_final: 0.6004 (ptp-170) REVERT: B 1106 GLN cc_start: 0.6231 (OUTLIER) cc_final: 0.5855 (mp10) REVERT: B 1133 TYR cc_start: 0.5030 (p90) cc_final: 0.4577 (p90) REVERT: B 1219 GLN cc_start: 0.6641 (pt0) cc_final: 0.5771 (pp30) REVERT: B 1226 LYS cc_start: 0.6969 (pttm) cc_final: 0.6708 (ptmm) outliers start: 20 outliers final: 11 residues processed: 135 average time/residue: 1.3057 time to fit residues: 187.1152 Evaluate side-chains 135 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 646 ASN Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1081 GLU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1108 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 988 GLN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8383 Z= 0.242 Angle : 0.561 13.125 11335 Z= 0.291 Chirality : 0.044 0.314 1244 Planarity : 0.003 0.029 1428 Dihedral : 5.232 59.650 1211 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.39 % Allowed : 16.84 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.34 (0.26), residues: 1006 helix: 1.51 (0.25), residues: 408 sheet: 0.13 (0.33), residues: 238 loop : -1.18 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1014 HIS 0.005 0.001 HIS A 494 PHE 0.015 0.001 PHE A 512 TYR 0.017 0.001 TYR A 306 ARG 0.009 0.001 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5885 (tpp80) cc_final: 0.5560 (mtp85) REVERT: A 146 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7673 (tm-30) REVERT: A 197 MET cc_start: 0.6222 (mtm) cc_final: 0.5756 (ttm) REVERT: A 301 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7661 (ttp) REVERT: A 372 MET cc_start: 0.7290 (mtm) cc_final: 0.7040 (mmp) REVERT: A 382 MET cc_start: 0.5950 (mmt) cc_final: 0.5685 (mpt) REVERT: A 444 ARG cc_start: 0.6598 (ttp-110) cc_final: 0.6216 (ttt180) REVERT: A 491 ARG cc_start: 0.7429 (tmt170) cc_final: 0.6882 (tmt170) REVERT: A 493 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6804 (pt0) REVERT: A 520 ARG cc_start: 0.8028 (mtt90) cc_final: 0.7533 (tpt170) REVERT: A 563 GLU cc_start: 0.8214 (pt0) cc_final: 0.7442 (tp30) REVERT: A 567 VAL cc_start: 0.7719 (t) cc_final: 0.7465 (m) REVERT: A 742 GLN cc_start: 0.6997 (tm-30) cc_final: 0.6731 (tm-30) REVERT: B 1106 GLN cc_start: 0.6297 (OUTLIER) cc_final: 0.5892 (mp10) REVERT: B 1133 TYR cc_start: 0.5084 (p90) cc_final: 0.4771 (p90) REVERT: B 1226 LYS cc_start: 0.6972 (pttm) cc_final: 0.6714 (ptmm) outliers start: 21 outliers final: 11 residues processed: 134 average time/residue: 1.2421 time to fit residues: 176.9248 Evaluate side-chains 136 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1209 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.0040 chunk 93 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 58 optimal weight: 0.0980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 988 GLN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8383 Z= 0.182 Angle : 0.547 13.452 11335 Z= 0.283 Chirality : 0.043 0.292 1244 Planarity : 0.003 0.028 1428 Dihedral : 5.070 59.053 1211 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.62 % Allowed : 16.72 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.42 (0.26), residues: 1006 helix: 1.64 (0.26), residues: 409 sheet: 0.09 (0.33), residues: 238 loop : -1.17 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1014 HIS 0.005 0.001 HIS A 494 PHE 0.009 0.001 PHE A 497 TYR 0.012 0.001 TYR A 306 ARG 0.009 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5891 (tpp80) cc_final: 0.5525 (mtp85) REVERT: A 146 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7693 (tm-30) REVERT: A 197 MET cc_start: 0.6213 (mtm) cc_final: 0.5763 (ttm) REVERT: A 298 MET cc_start: 0.8088 (mmt) cc_final: 0.7688 (mmt) REVERT: A 301 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7642 (ttp) REVERT: A 372 MET cc_start: 0.7321 (mtm) cc_final: 0.7067 (mmp) REVERT: A 382 MET cc_start: 0.5859 (mmt) cc_final: 0.5607 (mpt) REVERT: A 444 ARG cc_start: 0.6599 (ttp-110) cc_final: 0.6217 (ttt180) REVERT: A 491 ARG cc_start: 0.7420 (tmt170) cc_final: 0.6884 (tmt170) REVERT: A 493 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6809 (pt0) REVERT: A 520 ARG cc_start: 0.8033 (mtt90) cc_final: 0.7537 (tpt170) REVERT: A 563 GLU cc_start: 0.8205 (pt0) cc_final: 0.7457 (tp30) REVERT: A 567 VAL cc_start: 0.7701 (t) cc_final: 0.7454 (m) REVERT: A 742 GLN cc_start: 0.6964 (tm-30) cc_final: 0.6615 (tm-30) REVERT: B 1061 ARG cc_start: 0.6374 (mtm-85) cc_final: 0.6038 (ptp-170) REVERT: B 1226 LYS cc_start: 0.7058 (pttm) cc_final: 0.6825 (ptmm) REVERT: B 1252 PHE cc_start: 0.7663 (p90) cc_final: 0.7457 (p90) outliers start: 23 outliers final: 14 residues processed: 136 average time/residue: 1.2161 time to fit residues: 175.8402 Evaluate side-chains 139 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 944 SER Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 0.1980 chunk 92 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 988 GLN B1106 GLN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8383 Z= 0.186 Angle : 0.557 13.672 11335 Z= 0.289 Chirality : 0.043 0.284 1244 Planarity : 0.003 0.031 1428 Dihedral : 4.962 59.219 1211 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.39 % Allowed : 17.52 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.39 (0.26), residues: 1006 helix: 1.61 (0.26), residues: 409 sheet: 0.10 (0.33), residues: 233 loop : -1.19 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1014 HIS 0.005 0.001 HIS A 494 PHE 0.014 0.001 PHE A 512 TYR 0.019 0.001 TYR B1133 ARG 0.008 0.000 ARG A 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5988 (tpp80) cc_final: 0.5586 (mtp85) REVERT: A 146 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7695 (tm-30) REVERT: A 197 MET cc_start: 0.6206 (mtm) cc_final: 0.5889 (ttm) REVERT: A 301 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7634 (ttp) REVERT: A 372 MET cc_start: 0.7316 (mtm) cc_final: 0.7059 (mmp) REVERT: A 382 MET cc_start: 0.5881 (mmt) cc_final: 0.5613 (mpt) REVERT: A 444 ARG cc_start: 0.6570 (ttp-110) cc_final: 0.6180 (ttt180) REVERT: A 491 ARG cc_start: 0.7421 (tmt170) cc_final: 0.6876 (tmt170) REVERT: A 493 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6801 (pt0) REVERT: A 520 ARG cc_start: 0.8016 (mtt90) cc_final: 0.7523 (tpt170) REVERT: A 563 GLU cc_start: 0.8213 (pt0) cc_final: 0.7479 (tp30) REVERT: A 567 VAL cc_start: 0.7705 (t) cc_final: 0.7469 (m) REVERT: A 742 GLN cc_start: 0.6984 (tm-30) cc_final: 0.6729 (tm-30) REVERT: B 1061 ARG cc_start: 0.6440 (mtm-85) cc_final: 0.6081 (ptp-170) REVERT: B 1106 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.6244 (mt0) REVERT: B 1133 TYR cc_start: 0.5043 (p90) cc_final: 0.4571 (p90) REVERT: B 1226 LYS cc_start: 0.7046 (pttm) cc_final: 0.6799 (ptmm) REVERT: B 1252 PHE cc_start: 0.7624 (p90) cc_final: 0.7423 (p90) outliers start: 21 outliers final: 12 residues processed: 133 average time/residue: 1.2103 time to fit residues: 171.1929 Evaluate side-chains 139 residues out of total 879 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain B residue 914 ILE Chi-restraints excluded: chain B residue 1019 ILE Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1289 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/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-5322/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-5322/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-5322/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-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/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-5322/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-5322/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: 64.4925 > 50: distance: 75 - 96: 12.924 distance: 81 - 107: 30.908 distance: 84 - 89: 3.784 distance: 85 - 113: 17.726 distance: 89 - 90: 4.043 distance: 90 - 91: 3.864 distance: 90 - 93: 5.795 distance: 91 - 92: 17.034 distance: 91 - 96: 4.098 distance: 92 - 125: 32.272 distance: 93 - 94: 11.344 distance: 93 - 95: 8.629 distance: 96 - 97: 12.171 distance: 97 - 98: 5.639 distance: 97 - 100: 9.416 distance: 98 - 99: 17.312 distance: 98 - 107: 17.819 distance: 99 - 136: 33.717 distance: 100 - 101: 5.950 distance: 101 - 102: 11.450 distance: 101 - 103: 10.743 distance: 102 - 104: 11.613 distance: 103 - 105: 4.314 distance: 104 - 106: 9.225 distance: 105 - 106: 10.407 distance: 107 - 108: 42.247 distance: 108 - 109: 25.389 distance: 108 - 111: 17.157 distance: 109 - 110: 22.387 distance: 109 - 113: 7.204 distance: 111 - 112: 7.574 distance: 113 - 114: 27.423 distance: 114 - 115: 35.713 distance: 114 - 117: 29.482 distance: 115 - 116: 27.205 distance: 115 - 125: 14.511 distance: 117 - 118: 26.678 distance: 118 - 119: 3.632 distance: 118 - 120: 33.541 distance: 119 - 121: 13.421 distance: 120 - 122: 8.865 distance: 121 - 123: 32.396 distance: 122 - 123: 10.575 distance: 123 - 124: 10.528 distance: 125 - 126: 7.135 distance: 126 - 127: 18.692 distance: 126 - 129: 10.727 distance: 127 - 128: 29.849 distance: 127 - 136: 8.654 distance: 129 - 130: 6.661 distance: 130 - 131: 14.378 distance: 130 - 132: 14.746 distance: 131 - 133: 11.536 distance: 132 - 134: 8.350 distance: 133 - 135: 10.935 distance: 134 - 135: 14.191 distance: 136 - 137: 20.608 distance: 137 - 138: 10.105 distance: 137 - 140: 36.651 distance: 138 - 139: 21.057 distance: 138 - 142: 29.473 distance: 140 - 141: 23.691 distance: 142 - 143: 13.919 distance: 143 - 144: 34.158 distance: 143 - 146: 8.034 distance: 144 - 145: 3.861 distance: 144 - 151: 16.401 distance: 146 - 147: 15.403 distance: 148 - 149: 14.146 distance: 148 - 150: 18.632 distance: 151 - 152: 13.599 distance: 152 - 153: 11.252 distance: 152 - 155: 36.824 distance: 153 - 154: 3.613 distance: 153 - 162: 10.529 distance: 155 - 156: 19.575 distance: 156 - 157: 9.242 distance: 156 - 158: 19.347 distance: 157 - 159: 18.738 distance: 158 - 160: 16.169 distance: 159 - 161: 11.424 distance: 160 - 161: 18.513 distance: 162 - 163: 22.972 distance: 163 - 164: 8.538 distance: 163 - 166: 17.478 distance: 164 - 165: 23.197 distance: 164 - 170: 9.984 distance: 166 - 167: 31.060 distance: 167 - 168: 7.863 distance: 167 - 169: 19.009 distance: 170 - 171: 7.590 distance: 171 - 172: 15.221 distance: 171 - 174: 14.575 distance: 172 - 173: 9.567 distance: 172 - 175: 10.755