Starting phenix.real_space_refine on Sun Mar 10 20:55:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv8_35746/03_2024/8iv8_35746.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv8_35746/03_2024/8iv8_35746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv8_35746/03_2024/8iv8_35746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv8_35746/03_2024/8iv8_35746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv8_35746/03_2024/8iv8_35746.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv8_35746/03_2024/8iv8_35746.pdb" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 24 5.16 5 C 3137 2.51 5 N 808 2.21 5 O 975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 357": "NH1" <-> "NH2" Residue "G PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 408": "NH1" <-> "NH2" Residue "C GLU 16": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4944 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1435 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 1 Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "C" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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 Time building chain proxies: 3.29, per 1000 atoms: 0.67 Number of scatterers: 4944 At special positions: 0 Unit cell: (107.364, 87.914, 69.242, 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 24 16.00 O 975 8.00 N 808 7.00 C 3137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 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 A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN G 343 " Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 860.0 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 18 sheets defined 4.6% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.039A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'G' and resid 338 through 343 Processing helix chain 'G' and resid 349 through 353 removed outlier: 3.771A pdb=" N TRP G 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 370 Processing helix chain 'G' and resid 405 through 411 removed outlier: 4.579A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE G 410 " --> pdb=" O VAL G 407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.608A pdb=" N MET L 11 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP L 34 " --> pdb=" O PHE L 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 21 removed outlier: 3.592A pdb=" N ILE L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.873A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 35 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N CYS H 96 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TRP H 111 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG H 98 " --> pdb=" O ASP H 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.873A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER H 35 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 357 through 358 removed outlier: 3.558A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 376 through 379 removed outlier: 3.608A pdb=" N ILE G 402 " --> pdb=" O TYR G 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'D' and resid 5 through 6 removed outlier: 7.493A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE D 75 " --> pdb=" O VAL D 19 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 5 through 6 removed outlier: 7.493A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR D 72 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 48 removed outlier: 7.163A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 89 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 48 removed outlier: 7.163A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 89 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 102 " --> pdb=" O TYR D 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.530A pdb=" N VAL C 18 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.530A pdb=" N VAL C 18 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 78 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB8, first strand: chain 'C' and resid 37 through 39 removed outlier: 3.596A pdb=" N THR C 93 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 49 through 51 133 hydrogen bonds defined for protein. 315 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1539 1.34 - 1.46: 1342 1.46 - 1.58: 2155 1.58 - 1.70: 0 1.70 - 1.82: 33 Bond restraints: 5069 Sorted by residual: bond pdb=" C THR D 93 " pdb=" N TRP D 94 " ideal model delta sigma weight residual 1.331 1.280 0.051 1.59e-02 3.96e+03 1.05e+01 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.44e+00 ... (remaining 5064 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.36: 122 106.36 - 113.34: 2689 113.34 - 120.32: 1800 120.32 - 127.31: 2219 127.31 - 134.29: 57 Bond angle restraints: 6887 Sorted by residual: angle pdb=" N VAL H 48 " pdb=" CA VAL H 48 " pdb=" C VAL H 48 " ideal model delta sigma weight residual 113.53 109.40 4.13 9.80e-01 1.04e+00 1.78e+01 angle pdb=" C SER L 49 " pdb=" N THR L 50 " pdb=" CA THR L 50 " ideal model delta sigma weight residual 121.54 129.19 -7.65 1.91e+00 2.74e-01 1.60e+01 angle pdb=" C SER L 92 " pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C LEU G 461 " pdb=" N LYS G 462 " pdb=" CA LYS G 462 " ideal model delta sigma weight residual 120.69 132.16 -11.47 2.95e+00 1.15e-01 1.51e+01 angle pdb=" C SER D 40 " pdb=" N HIS D 41 " pdb=" CA HIS D 41 " ideal model delta sigma weight residual 122.07 127.29 -5.22 1.43e+00 4.89e-01 1.33e+01 ... (remaining 6882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 2782 22.47 - 44.93: 189 44.93 - 67.40: 9 67.40 - 89.86: 10 89.86 - 112.33: 4 Dihedral angle restraints: 2994 sinusoidal: 1181 harmonic: 1813 Sorted by residual: dihedral pdb=" CA TRP C 104 " pdb=" C TRP C 104 " pdb=" N TYR C 105 " pdb=" CA TYR C 105 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " pdb=" CB CYS G 361 " ideal model delta sinusoidal sigma weight residual 93.00 57.47 35.53 1 1.00e+01 1.00e-02 1.79e+01 dihedral pdb=" CA SER L 92 " pdb=" C SER L 92 " pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta harmonic sigma weight residual -180.00 -160.51 -19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 2991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 564 0.055 - 0.109: 145 0.109 - 0.164: 39 0.164 - 0.219: 5 0.219 - 0.273: 1 Chirality restraints: 754 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.27e+00 chirality pdb=" CB THR C 91 " pdb=" CA THR C 91 " pdb=" OG1 THR C 91 " pdb=" CG2 THR C 91 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 751 not shown) Planarity restraints: 872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 462 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO G 463 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 463 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 463 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS G 336 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO G 337 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO G 337 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 337 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO H 14 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.027 5.00e-02 4.00e+02 ... (remaining 869 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1348 2.80 - 3.32: 3976 3.32 - 3.85: 8028 3.85 - 4.37: 8639 4.37 - 4.90: 15466 Nonbonded interactions: 37457 Sorted by model distance: nonbonded pdb=" OH TYR H 59 " pdb=" OH TYR H 103 " model vdw 2.272 2.440 nonbonded pdb=" OG SER G 349 " pdb=" O LEU G 452 " model vdw 2.274 2.440 nonbonded pdb=" O SER L 62 " pdb=" OG1 THR L 73 " model vdw 2.288 2.440 nonbonded pdb=" OG1 THR D 14 " pdb=" OD2 ASP D 17 " model vdw 2.290 2.440 nonbonded pdb=" O SER H 30 " pdb=" OG SER H 30 " model vdw 2.307 2.440 ... (remaining 37452 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=0.83 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: 8.040 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: 38.400 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.050 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 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 : 0.005 0.051 5069 Z= 0.301 Angle : 0.813 11.467 6887 Z= 0.451 Chirality : 0.054 0.273 754 Planarity : 0.006 0.055 871 Dihedral : 15.131 112.328 1823 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.74 % Allowed : 7.39 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -3.56 (0.29), residues: 618 helix: -4.87 (0.33), residues: 12 sheet: -1.93 (0.35), residues: 212 loop : -2.65 (0.25), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.002 0.001 HIS H 99 PHE 0.022 0.002 PHE L 46 TYR 0.020 0.002 TYR C 105 ARG 0.002 0.000 ARG G 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 204 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8303 (tm-30) REVERT: L 73 THR cc_start: 0.7646 (p) cc_final: 0.7432 (p) REVERT: L 81 ASP cc_start: 0.7831 (m-30) cc_final: 0.7278 (m-30) REVERT: H 19 LYS cc_start: 0.8604 (tttt) cc_final: 0.8383 (tttp) REVERT: H 27 PHE cc_start: 0.8554 (p90) cc_final: 0.8298 (p90) REVERT: H 29 PHE cc_start: 0.7968 (t80) cc_final: 0.7722 (t80) REVERT: H 34 MET cc_start: 0.8570 (mtp) cc_final: 0.6943 (mmt) REVERT: H 60 TYR cc_start: 0.8774 (m-80) cc_final: 0.8492 (m-10) REVERT: H 73 ASP cc_start: 0.6767 (t70) cc_final: 0.6461 (t70) REVERT: H 76 MET cc_start: 0.8241 (ttt) cc_final: 0.7909 (tpt) REVERT: H 87 ARG cc_start: 0.7942 (mtt90) cc_final: 0.7002 (mpt180) REVERT: H 97 VAL cc_start: 0.9091 (m) cc_final: 0.8389 (m) REVERT: G 389 ASP cc_start: 0.7983 (t0) cc_final: 0.7563 (p0) REVERT: G 458 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8356 (tptt) REVERT: G 467 ASP cc_start: 0.7512 (p0) cc_final: 0.7192 (p0) REVERT: D 17 ASP cc_start: 0.5154 (m-30) cc_final: 0.4618 (t70) REVERT: D 47 LEU cc_start: 0.7765 (mt) cc_final: 0.7539 (mp) REVERT: D 105 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7586 (tm-30) REVERT: C 5 VAL cc_start: 0.6889 (p) cc_final: 0.6598 (m) REVERT: C 12 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7705 (mmtt) REVERT: C 16 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6726 (mt-10) REVERT: C 60 TYR cc_start: 0.9017 (m-80) cc_final: 0.8569 (m-10) REVERT: C 65 ARG cc_start: 0.7769 (ttp-110) cc_final: 0.7500 (mmm160) REVERT: C 82 LYS cc_start: 0.7994 (tttt) cc_final: 0.7467 (ttmm) REVERT: C 86 LEU cc_start: 0.7536 (mt) cc_final: 0.7294 (mp) REVERT: C 87 LYS cc_start: 0.8311 (mttt) cc_final: 0.7922 (ttmm) REVERT: C 104 TRP cc_start: 0.7882 (m-90) cc_final: 0.7135 (m-90) outliers start: 4 outliers final: 2 residues processed: 207 average time/residue: 0.1949 time to fit residues: 49.4250 Evaluate side-chains 131 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain C residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN H 99 HIS G 409 GLN G 439 ASN G 498 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 92 ASN D 107 ASN C 35 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5069 Z= 0.309 Angle : 0.639 7.151 6887 Z= 0.337 Chirality : 0.046 0.177 754 Planarity : 0.005 0.037 871 Dihedral : 9.033 66.087 752 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.62 % Allowed : 17.93 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.95 (0.32), residues: 618 helix: -4.34 (0.59), residues: 12 sheet: -1.68 (0.34), residues: 243 loop : -2.10 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 90 HIS 0.004 0.002 HIS D 34 PHE 0.022 0.002 PHE D 71 TYR 0.028 0.002 TYR G 351 ARG 0.005 0.001 ARG G 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8348 (tm-30) REVERT: L 19 ILE cc_start: 0.8054 (tp) cc_final: 0.7767 (tp) REVERT: L 32 MET cc_start: 0.6929 (tpp) cc_final: 0.6669 (tpp) REVERT: L 81 ASP cc_start: 0.7921 (m-30) cc_final: 0.7621 (m-30) REVERT: H 34 MET cc_start: 0.7708 (mtp) cc_final: 0.7309 (mtm) REVERT: H 87 ARG cc_start: 0.8139 (mtt90) cc_final: 0.7184 (mpt180) REVERT: H 93 MET cc_start: 0.7762 (ttt) cc_final: 0.7553 (tpp) REVERT: G 389 ASP cc_start: 0.7950 (t0) cc_final: 0.7394 (p0) REVERT: G 403 ARG cc_start: 0.7760 (mtt-85) cc_final: 0.7011 (mtt180) REVERT: G 458 LYS cc_start: 0.8746 (ttmt) cc_final: 0.8285 (tptt) REVERT: D 17 ASP cc_start: 0.5478 (m-30) cc_final: 0.4823 (t70) REVERT: D 47 LEU cc_start: 0.8015 (mt) cc_final: 0.7739 (mp) REVERT: D 79 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7647 (mm-30) REVERT: D 105 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 5 VAL cc_start: 0.6611 (p) cc_final: 0.6382 (m) REVERT: C 16 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6634 (mt-10) REVERT: C 65 ARG cc_start: 0.7789 (ttp-110) cc_final: 0.7453 (mmm160) REVERT: C 82 LYS cc_start: 0.7917 (tttt) cc_final: 0.7528 (ttmm) REVERT: C 86 LEU cc_start: 0.7440 (mt) cc_final: 0.7190 (mp) REVERT: C 87 LYS cc_start: 0.8254 (mttt) cc_final: 0.7858 (ttmm) REVERT: C 94 TYR cc_start: 0.8312 (m-80) cc_final: 0.7876 (m-80) REVERT: C 104 TRP cc_start: 0.7706 (m-90) cc_final: 0.7079 (m-90) outliers start: 25 outliers final: 16 residues processed: 161 average time/residue: 0.1859 time to fit residues: 37.1547 Evaluate side-chains 146 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain G residue 366 SER Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5069 Z= 0.208 Angle : 0.575 7.953 6887 Z= 0.301 Chirality : 0.044 0.173 754 Planarity : 0.004 0.035 871 Dihedral : 7.007 63.868 752 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.25 % Allowed : 19.96 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.51 (0.33), residues: 618 helix: -4.17 (0.70), residues: 13 sheet: -1.46 (0.35), residues: 243 loop : -1.71 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 353 HIS 0.003 0.001 HIS L 33 PHE 0.018 0.002 PHE H 68 TYR 0.023 0.002 TYR L 70 ARG 0.002 0.000 ARG G 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8218 (tm-30) REVERT: L 19 ILE cc_start: 0.8252 (tp) cc_final: 0.7906 (tp) REVERT: L 66 SER cc_start: 0.8089 (p) cc_final: 0.7868 (m) REVERT: H 34 MET cc_start: 0.7762 (mtp) cc_final: 0.7415 (mtm) REVERT: H 76 MET cc_start: 0.8427 (tpt) cc_final: 0.8220 (mmm) REVERT: G 389 ASP cc_start: 0.7877 (t0) cc_final: 0.7228 (p0) REVERT: G 458 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8271 (tptt) REVERT: G 461 LEU cc_start: 0.8969 (tp) cc_final: 0.8699 (tp) REVERT: D 17 ASP cc_start: 0.5401 (m-30) cc_final: 0.4710 (t70) REVERT: D 47 LEU cc_start: 0.7946 (mt) cc_final: 0.7679 (mp) REVERT: D 79 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7696 (mm-30) REVERT: D 105 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7766 (tm-30) REVERT: C 6 GLN cc_start: 0.7497 (tt0) cc_final: 0.7254 (tt0) REVERT: C 16 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6804 (mt-10) REVERT: C 65 ARG cc_start: 0.7695 (ttp-110) cc_final: 0.7393 (mmm160) REVERT: C 82 LYS cc_start: 0.7913 (tttt) cc_final: 0.7431 (mtmt) REVERT: C 86 LEU cc_start: 0.7442 (mt) cc_final: 0.7224 (mp) REVERT: C 87 LYS cc_start: 0.8202 (mttt) cc_final: 0.7823 (ttmm) REVERT: C 94 TYR cc_start: 0.8281 (m-80) cc_final: 0.7991 (m-80) REVERT: C 107 ASP cc_start: 0.7992 (t0) cc_final: 0.7773 (t0) outliers start: 23 outliers final: 20 residues processed: 144 average time/residue: 0.1822 time to fit residues: 32.8345 Evaluate side-chains 138 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 467 ASP Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN C 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5069 Z= 0.314 Angle : 0.600 9.046 6887 Z= 0.316 Chirality : 0.044 0.149 754 Planarity : 0.004 0.035 871 Dihedral : 6.246 59.357 751 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 6.28 % Allowed : 21.07 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.41 (0.33), residues: 618 helix: -4.32 (0.69), residues: 19 sheet: -1.46 (0.35), residues: 243 loop : -1.52 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 104 HIS 0.003 0.001 HIS L 88 PHE 0.018 0.002 PHE H 68 TYR 0.019 0.002 TYR G 351 ARG 0.005 0.000 ARG G 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ILE cc_start: 0.7784 (mp) cc_final: 0.7549 (mm) REVERT: L 17 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8068 (tm-30) REVERT: L 19 ILE cc_start: 0.8266 (tp) cc_final: 0.7939 (tp) REVERT: L 66 SER cc_start: 0.8106 (p) cc_final: 0.7854 (m) REVERT: H 87 ARG cc_start: 0.8044 (mtt90) cc_final: 0.7040 (mpt180) REVERT: G 389 ASP cc_start: 0.7849 (t0) cc_final: 0.7255 (p0) REVERT: G 427 ASP cc_start: 0.8615 (m-30) cc_final: 0.7873 (t0) REVERT: G 458 LYS cc_start: 0.8755 (ttmt) cc_final: 0.8252 (tptt) REVERT: G 461 LEU cc_start: 0.8988 (tp) cc_final: 0.8774 (tp) REVERT: D 17 ASP cc_start: 0.5613 (m-30) cc_final: 0.4887 (t70) REVERT: D 47 LEU cc_start: 0.7930 (mt) cc_final: 0.7669 (mp) REVERT: D 79 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7633 (mm-30) REVERT: D 105 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7562 (tm-30) REVERT: C 16 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6785 (mt-10) REVERT: C 31 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8180 (t0) REVERT: C 65 ARG cc_start: 0.7701 (ttp-110) cc_final: 0.7440 (mmm160) REVERT: C 82 LYS cc_start: 0.7919 (tttt) cc_final: 0.7485 (mtmt) REVERT: C 86 LEU cc_start: 0.7404 (mt) cc_final: 0.7152 (mp) REVERT: C 87 LYS cc_start: 0.8212 (mttt) cc_final: 0.7997 (ttmm) REVERT: C 94 TYR cc_start: 0.8333 (m-80) cc_final: 0.7986 (m-80) REVERT: C 104 TRP cc_start: 0.7731 (m-90) cc_final: 0.7273 (m-90) REVERT: C 107 ASP cc_start: 0.7939 (t0) cc_final: 0.7728 (t0) outliers start: 34 outliers final: 30 residues processed: 141 average time/residue: 0.1945 time to fit residues: 34.1210 Evaluate side-chains 147 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 467 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.0000 chunk 34 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5069 Z= 0.192 Angle : 0.547 9.074 6887 Z= 0.286 Chirality : 0.043 0.149 754 Planarity : 0.004 0.043 871 Dihedral : 5.827 54.965 751 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 6.10 % Allowed : 21.44 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.22 (0.33), residues: 618 helix: -3.54 (0.98), residues: 13 sheet: -1.28 (0.34), residues: 249 loop : -1.51 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 90 HIS 0.002 0.001 HIS L 33 PHE 0.014 0.001 PHE H 68 TYR 0.018 0.001 TYR G 351 ARG 0.006 0.001 ARG G 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 125 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ILE cc_start: 0.7820 (mp) cc_final: 0.7552 (mm) REVERT: L 17 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8361 (tm-30) REVERT: L 19 ILE cc_start: 0.8289 (tp) cc_final: 0.7916 (tp) REVERT: L 48 TYR cc_start: 0.6249 (p90) cc_final: 0.5951 (p90) REVERT: L 66 SER cc_start: 0.8128 (p) cc_final: 0.7879 (m) REVERT: H 87 ARG cc_start: 0.8044 (mtt90) cc_final: 0.7085 (mpt180) REVERT: G 364 ASP cc_start: 0.8606 (p0) cc_final: 0.8350 (p0) REVERT: G 389 ASP cc_start: 0.7856 (t0) cc_final: 0.7273 (p0) REVERT: G 458 LYS cc_start: 0.8748 (ttmt) cc_final: 0.8237 (tptt) REVERT: G 461 LEU cc_start: 0.8955 (tp) cc_final: 0.8743 (tp) REVERT: D 17 ASP cc_start: 0.5528 (m-30) cc_final: 0.4817 (t70) REVERT: D 47 LEU cc_start: 0.7878 (mt) cc_final: 0.7637 (mp) REVERT: D 79 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7724 (mm-30) REVERT: D 105 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7546 (tm-30) REVERT: C 16 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6802 (mt-10) REVERT: C 31 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8196 (t0) REVERT: C 65 ARG cc_start: 0.7631 (ttp-110) cc_final: 0.7386 (mmm160) REVERT: C 82 LYS cc_start: 0.7933 (tttt) cc_final: 0.7477 (mtmt) REVERT: C 86 LEU cc_start: 0.7398 (mt) cc_final: 0.7171 (mp) REVERT: C 87 LYS cc_start: 0.8204 (mttt) cc_final: 0.7987 (ttmm) REVERT: C 94 TYR cc_start: 0.8308 (m-80) cc_final: 0.8030 (m-80) REVERT: C 104 TRP cc_start: 0.7824 (m-90) cc_final: 0.7471 (m-90) REVERT: C 107 ASP cc_start: 0.7960 (t0) cc_final: 0.7739 (t0) outliers start: 33 outliers final: 23 residues processed: 146 average time/residue: 0.1885 time to fit residues: 34.4122 Evaluate side-chains 141 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 108 MET Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 418 ILE Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 467 ASP Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 88 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN G 450 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 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: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 5069 Z= 0.473 Angle : 0.700 9.826 6887 Z= 0.367 Chirality : 0.046 0.161 754 Planarity : 0.005 0.044 871 Dihedral : 6.401 56.631 751 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 7.76 % Allowed : 21.07 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.48 (0.33), residues: 618 helix: -4.01 (0.87), residues: 19 sheet: -1.49 (0.33), residues: 248 loop : -1.59 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 102 HIS 0.004 0.002 HIS L 88 PHE 0.023 0.002 PHE L 46 TYR 0.029 0.002 TYR G 351 ARG 0.006 0.001 ARG G 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 117 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ILE cc_start: 0.7756 (mp) cc_final: 0.7522 (mm) REVERT: L 11 MET cc_start: 0.7173 (mtt) cc_final: 0.6969 (mtt) REVERT: L 17 GLU cc_start: 0.8601 (tm-30) cc_final: 0.7930 (tm-30) REVERT: L 19 ILE cc_start: 0.8300 (tp) cc_final: 0.7923 (tp) REVERT: L 48 TYR cc_start: 0.6501 (p90) cc_final: 0.6199 (p90) REVERT: L 78 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7032 (mt-10) REVERT: H 87 ARG cc_start: 0.7991 (mtt90) cc_final: 0.7051 (mpt180) REVERT: G 355 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7508 (ttm-80) REVERT: G 389 ASP cc_start: 0.7991 (t0) cc_final: 0.7305 (p0) REVERT: G 409 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: G 417 LYS cc_start: 0.8106 (tppt) cc_final: 0.7660 (tppt) REVERT: G 458 LYS cc_start: 0.8730 (ttmt) cc_final: 0.8185 (tptt) REVERT: D 17 ASP cc_start: 0.5876 (m-30) cc_final: 0.5253 (t70) REVERT: D 47 LEU cc_start: 0.7945 (mt) cc_final: 0.7652 (mp) REVERT: D 79 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7678 (mm-30) REVERT: D 105 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7446 (tm-30) REVERT: C 12 LYS cc_start: 0.7424 (mmtt) cc_final: 0.6916 (mmtt) REVERT: C 16 GLU cc_start: 0.7059 (mt-10) cc_final: 0.5957 (mt-10) REVERT: C 31 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8237 (t0) REVERT: C 82 LYS cc_start: 0.7935 (tttt) cc_final: 0.7566 (ttmm) REVERT: C 86 LEU cc_start: 0.7377 (mt) cc_final: 0.7080 (mp) REVERT: C 87 LYS cc_start: 0.8163 (mttt) cc_final: 0.7933 (ttmm) REVERT: C 94 TYR cc_start: 0.8355 (m-80) cc_final: 0.7587 (m-10) REVERT: C 104 TRP cc_start: 0.7855 (m-90) cc_final: 0.7188 (m-90) REVERT: C 107 ASP cc_start: 0.7973 (t0) cc_final: 0.7734 (t0) outliers start: 42 outliers final: 36 residues processed: 145 average time/residue: 0.2017 time to fit residues: 36.4166 Evaluate side-chains 152 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 114 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 467 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5069 Z= 0.211 Angle : 0.580 10.447 6887 Z= 0.302 Chirality : 0.044 0.164 754 Planarity : 0.004 0.032 871 Dihedral : 5.877 52.122 751 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.55 % Allowed : 23.11 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.22 (0.33), residues: 618 helix: -3.82 (0.88), residues: 19 sheet: -1.25 (0.34), residues: 242 loop : -1.48 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 353 HIS 0.002 0.001 HIS L 88 PHE 0.016 0.001 PHE H 68 TYR 0.027 0.001 TYR G 351 ARG 0.006 0.001 ARG G 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 10 ILE cc_start: 0.7781 (mp) cc_final: 0.7570 (mm) REVERT: L 17 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8267 (tm-30) REVERT: L 19 ILE cc_start: 0.8353 (tp) cc_final: 0.8007 (tp) REVERT: L 66 SER cc_start: 0.8152 (p) cc_final: 0.7847 (m) REVERT: L 78 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6948 (mt-10) REVERT: H 87 ARG cc_start: 0.7983 (mtt90) cc_final: 0.7068 (mpt180) REVERT: G 364 ASP cc_start: 0.8626 (p0) cc_final: 0.8323 (p0) REVERT: G 389 ASP cc_start: 0.7965 (t0) cc_final: 0.7268 (p0) REVERT: G 417 LYS cc_start: 0.7761 (tppt) cc_final: 0.7508 (tppt) REVERT: G 458 LYS cc_start: 0.8777 (ttmt) cc_final: 0.8211 (tptt) REVERT: D 17 ASP cc_start: 0.5630 (m-30) cc_final: 0.4938 (t70) REVERT: D 47 LEU cc_start: 0.7861 (mt) cc_final: 0.7615 (mp) REVERT: D 79 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7719 (mm-30) REVERT: D 104 LEU cc_start: 0.8139 (tp) cc_final: 0.7813 (tt) REVERT: D 105 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7424 (tm-30) REVERT: C 16 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6784 (mt-10) REVERT: C 31 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8229 (t0) REVERT: C 82 LYS cc_start: 0.7911 (tttt) cc_final: 0.7483 (mtmt) REVERT: C 86 LEU cc_start: 0.7352 (mt) cc_final: 0.7100 (mp) REVERT: C 87 LYS cc_start: 0.8121 (mttt) cc_final: 0.7902 (ttmm) REVERT: C 94 TYR cc_start: 0.8222 (m-80) cc_final: 0.7824 (m-10) REVERT: C 104 TRP cc_start: 0.7841 (m-90) cc_final: 0.7312 (m-90) REVERT: C 107 ASP cc_start: 0.8003 (t0) cc_final: 0.7787 (t0) outliers start: 30 outliers final: 23 residues processed: 137 average time/residue: 0.1846 time to fit residues: 31.8977 Evaluate side-chains 138 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 467 ASP Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 88 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.0070 chunk 45 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5069 Z= 0.205 Angle : 0.568 9.695 6887 Z= 0.296 Chirality : 0.044 0.155 754 Planarity : 0.003 0.035 871 Dihedral : 5.484 48.385 751 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.81 % Allowed : 24.95 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.11 (0.33), residues: 618 helix: -3.48 (0.84), residues: 19 sheet: -1.14 (0.34), residues: 244 loop : -1.44 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 90 HIS 0.002 0.001 HIS L 88 PHE 0.013 0.001 PHE H 68 TYR 0.027 0.001 TYR G 351 ARG 0.006 0.000 ARG G 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8246 (tm-30) REVERT: L 19 ILE cc_start: 0.8333 (tp) cc_final: 0.7907 (tp) REVERT: L 66 SER cc_start: 0.8198 (p) cc_final: 0.7891 (m) REVERT: H 87 ARG cc_start: 0.8000 (mtt90) cc_final: 0.7140 (mpt180) REVERT: G 364 ASP cc_start: 0.8637 (p0) cc_final: 0.8332 (p0) REVERT: G 389 ASP cc_start: 0.7969 (t0) cc_final: 0.7239 (p0) REVERT: G 403 ARG cc_start: 0.7690 (mtt-85) cc_final: 0.7062 (mtt90) REVERT: G 458 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8182 (tptt) REVERT: D 17 ASP cc_start: 0.5680 (m-30) cc_final: 0.5015 (t70) REVERT: D 47 LEU cc_start: 0.7829 (mt) cc_final: 0.7601 (mp) REVERT: D 79 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7719 (mm-30) REVERT: D 89 GLN cc_start: 0.7192 (pp30) cc_final: 0.6731 (pp30) REVERT: D 90 GLN cc_start: 0.7397 (pt0) cc_final: 0.7106 (pt0) REVERT: D 104 LEU cc_start: 0.8178 (tp) cc_final: 0.7861 (tt) REVERT: D 105 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7396 (tm-30) REVERT: C 16 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6806 (mt-10) REVERT: C 31 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8247 (t0) REVERT: C 82 LYS cc_start: 0.7932 (tttt) cc_final: 0.7483 (mtmt) REVERT: C 86 LEU cc_start: 0.7349 (mt) cc_final: 0.7127 (mp) REVERT: C 87 LYS cc_start: 0.8120 (mttt) cc_final: 0.7913 (ttmm) REVERT: C 94 TYR cc_start: 0.8192 (m-80) cc_final: 0.7795 (m-10) REVERT: C 104 TRP cc_start: 0.7816 (m-90) cc_final: 0.7283 (m-90) REVERT: C 107 ASP cc_start: 0.8042 (t0) cc_final: 0.7815 (t0) outliers start: 26 outliers final: 24 residues processed: 139 average time/residue: 0.1961 time to fit residues: 34.1864 Evaluate side-chains 142 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 467 ASP Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 88 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5069 Z= 0.298 Angle : 0.601 9.777 6887 Z= 0.316 Chirality : 0.045 0.159 754 Planarity : 0.004 0.039 871 Dihedral : 5.586 48.512 751 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 5.36 % Allowed : 25.14 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.05 (0.33), residues: 618 helix: -3.26 (0.94), residues: 19 sheet: -1.15 (0.34), residues: 245 loop : -1.38 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 90 HIS 0.003 0.001 HIS L 88 PHE 0.023 0.002 PHE L 46 TYR 0.033 0.001 TYR G 351 ARG 0.007 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 17 GLU cc_start: 0.8575 (tm-30) cc_final: 0.7879 (tm-30) REVERT: L 19 ILE cc_start: 0.8407 (tp) cc_final: 0.7900 (tp) REVERT: L 66 SER cc_start: 0.8222 (p) cc_final: 0.7911 (m) REVERT: H 87 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7074 (mpt-90) REVERT: G 364 ASP cc_start: 0.8636 (p0) cc_final: 0.8312 (p0) REVERT: G 389 ASP cc_start: 0.7943 (t0) cc_final: 0.7198 (p0) REVERT: G 403 ARG cc_start: 0.7754 (mtt-85) cc_final: 0.7098 (mtt90) REVERT: G 458 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8189 (tptt) REVERT: D 17 ASP cc_start: 0.5587 (m-30) cc_final: 0.4866 (t70) REVERT: D 47 LEU cc_start: 0.7880 (mt) cc_final: 0.7633 (mp) REVERT: D 79 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7696 (mm-30) REVERT: D 104 LEU cc_start: 0.8199 (tp) cc_final: 0.7887 (tt) REVERT: D 105 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 16 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6799 (mt-10) REVERT: C 31 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8245 (t0) REVERT: C 82 LYS cc_start: 0.7898 (tttt) cc_final: 0.7475 (mtmt) REVERT: C 86 LEU cc_start: 0.7339 (mt) cc_final: 0.7093 (mp) REVERT: C 87 LYS cc_start: 0.8130 (mttt) cc_final: 0.7912 (ttmm) REVERT: C 94 TYR cc_start: 0.8200 (m-80) cc_final: 0.7815 (m-10) REVERT: C 104 TRP cc_start: 0.7823 (m-90) cc_final: 0.7277 (m-90) REVERT: C 107 ASP cc_start: 0.8010 (t0) cc_final: 0.7780 (t0) outliers start: 29 outliers final: 25 residues processed: 138 average time/residue: 0.1917 time to fit residues: 33.0128 Evaluate side-chains 145 residues out of total 541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 467 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 500 THR Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 505 TYR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 88 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 69.8758 > 50: distance: 9 - 110: 32.489 distance: 26 - 94: 30.044 distance: 29 - 91: 26.873 distance: 46 - 53: 34.099 distance: 53 - 54: 49.407 distance: 54 - 55: 44.488 distance: 54 - 57: 42.124 distance: 55 - 56: 27.959 distance: 55 - 59: 27.910 distance: 57 - 58: 69.788 distance: 59 - 60: 4.090 distance: 60 - 61: 56.082 distance: 60 - 63: 53.067 distance: 61 - 62: 41.528 distance: 61 - 69: 43.476 distance: 63 - 64: 46.592 distance: 64 - 65: 33.462 distance: 64 - 66: 43.111 distance: 65 - 67: 37.702 distance: 66 - 68: 35.380 distance: 67 - 68: 24.996 distance: 70 - 71: 38.780 distance: 70 - 73: 36.972 distance: 71 - 72: 42.074 distance: 71 - 78: 37.139 distance: 73 - 74: 35.646 distance: 74 - 75: 16.335 distance: 75 - 76: 17.190 distance: 75 - 77: 30.323 distance: 78 - 79: 26.945 distance: 79 - 80: 31.606 distance: 79 - 82: 17.892 distance: 80 - 81: 29.881 distance: 80 - 84: 25.611 distance: 84 - 85: 49.955 distance: 84 - 90: 44.946 distance: 85 - 86: 4.250 distance: 85 - 88: 57.153 distance: 86 - 87: 37.279 distance: 86 - 91: 57.969 distance: 88 - 89: 59.813 distance: 89 - 90: 41.351 distance: 91 - 92: 10.000 distance: 92 - 93: 24.169 distance: 92 - 95: 46.862 distance: 93 - 94: 46.468 distance: 93 - 102: 31.571 distance: 95 - 96: 26.774 distance: 96 - 97: 46.595 distance: 97 - 98: 19.018 distance: 98 - 99: 38.489 distance: 99 - 100: 37.699 distance: 99 - 101: 34.811 distance: 102 - 103: 62.323 distance: 103 - 104: 39.906 distance: 103 - 106: 28.770 distance: 104 - 105: 45.937 distance: 104 - 110: 63.568 distance: 106 - 107: 34.237 distance: 107 - 108: 28.338 distance: 107 - 109: 37.145 distance: 110 - 111: 10.823 distance: 111 - 112: 56.761 distance: 111 - 114: 57.044 distance: 112 - 113: 62.807 distance: 112 - 118: 39.227 distance: 114 - 115: 57.029 distance: 115 - 116: 29.320 distance: 115 - 117: 40.176 distance: 118 - 119: 58.219 distance: 119 - 120: 25.371 distance: 119 - 122: 58.637 distance: 120 - 121: 57.595 distance: 120 - 126: 52.364 distance: 122 - 123: 55.796 distance: 122 - 124: 41.105 distance: 123 - 125: 55.313 distance: 126 - 127: 52.847 distance: 127 - 128: 41.809 distance: 127 - 130: 39.399 distance: 128 - 129: 50.054 distance: 128 - 135: 27.993 distance: 130 - 131: 18.360 distance: 131 - 132: 10.843 distance: 132 - 133: 29.041 distance: 133 - 134: 41.104