Starting phenix.real_space_refine on Fri May 9 18:21:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7won_32652/05_2025/7won_32652.cif Found real_map, /net/cci-nas-00/data/ceres_data/7won_32652/05_2025/7won_32652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7won_32652/05_2025/7won_32652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7won_32652/05_2025/7won_32652.map" model { file = "/net/cci-nas-00/data/ceres_data/7won_32652/05_2025/7won_32652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7won_32652/05_2025/7won_32652.cif" } resolution = 3.9 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 15 5.16 5 C 2098 2.51 5 N 556 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3318 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 811 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.77, per 1000 atoms: 2.04 Number of scatterers: 3318 At special positions: 0 Unit cell: (73.132, 84.024, 80.912, 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 15 16.00 O 649 8.00 N 556 7.00 C 2098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 395.8 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 8 sheets defined 1.4% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.532A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 356 through 358 removed outlier: 3.564A pdb=" N LYS F 356 " --> pdb=" O ALA F 397 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS F 432 " --> pdb=" O LEU F 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.501A pdb=" N SER L 69 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER L 74 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 47 through 51 removed outlier: 5.896A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.748A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET H 83 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.113A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 102 through 104 66 hydrogen bonds defined for protein. 168 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: 0.78 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 538 1.30 - 1.43: 1004 1.43 - 1.56: 1840 1.56 - 1.69: 0 1.69 - 1.82: 19 Bond restraints: 3401 Sorted by residual: bond pdb=" C ARG H 106 " pdb=" N SER H 107 " ideal model delta sigma weight residual 1.332 1.240 0.092 1.40e-02 5.10e+03 4.33e+01 bond pdb=" C ARG H 106 " pdb=" O ARG H 106 " ideal model delta sigma weight residual 1.237 1.171 0.066 1.16e-02 7.43e+03 3.19e+01 bond pdb=" CA ASP H 113 " pdb=" C ASP H 113 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.28e-02 6.10e+03 2.98e+01 bond pdb=" CA ARG H 106 " pdb=" C ARG H 106 " ideal model delta sigma weight residual 1.524 1.477 0.046 1.26e-02 6.30e+03 1.35e+01 bond pdb=" CA ARG H 106 " pdb=" CB ARG H 106 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.58e-02 4.01e+03 1.27e+01 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 4523 2.84 - 5.69: 80 5.69 - 8.53: 12 8.53 - 11.37: 2 11.37 - 14.22: 3 Bond angle restraints: 4620 Sorted by residual: angle pdb=" N TYR H 103 " pdb=" CA TYR H 103 " pdb=" C TYR H 103 " ideal model delta sigma weight residual 109.52 121.19 -11.67 1.55e+00 4.16e-01 5.67e+01 angle pdb=" O VAL H 100 " pdb=" C VAL H 100 " pdb=" N GLN H 101 " ideal model delta sigma weight residual 122.57 114.38 8.19 1.25e+00 6.40e-01 4.30e+01 angle pdb=" N LEU H 112 " pdb=" CA LEU H 112 " pdb=" C LEU H 112 " ideal model delta sigma weight residual 110.35 101.53 8.82 1.36e+00 5.41e-01 4.21e+01 angle pdb=" C ARG H 106 " pdb=" N SER H 107 " pdb=" CA SER H 107 " ideal model delta sigma weight residual 121.54 109.28 12.26 1.91e+00 2.74e-01 4.12e+01 angle pdb=" CA ARG H 106 " pdb=" C ARG H 106 " pdb=" O ARG H 106 " ideal model delta sigma weight residual 120.70 127.27 -6.57 1.03e+00 9.43e-01 4.06e+01 ... (remaining 4615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.55: 1823 20.55 - 41.09: 143 41.09 - 61.64: 19 61.64 - 82.18: 6 82.18 - 102.73: 10 Dihedral angle restraints: 2001 sinusoidal: 787 harmonic: 1214 Sorted by residual: dihedral pdb=" CA PHE F 429 " pdb=" C PHE F 429 " pdb=" N THR F 430 " pdb=" CA THR F 430 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ASN F 460 " pdb=" C ASN F 460 " pdb=" N LEU F 461 " pdb=" CA LEU F 461 " ideal model delta harmonic sigma weight residual -180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA CYS F 336 " pdb=" C CYS F 336 " pdb=" N PRO F 337 " pdb=" CA PRO F 337 " ideal model delta harmonic sigma weight residual -180.00 -160.93 -19.07 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 365 0.059 - 0.119: 101 0.119 - 0.178: 19 0.178 - 0.238: 6 0.238 - 0.297: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ASP H 113 " pdb=" N ASP H 113 " pdb=" C ASP H 113 " pdb=" CB ASP H 113 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA TYR H 103 " pdb=" N TYR H 103 " pdb=" C TYR H 103 " pdb=" CB TYR H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN F 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 489 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 100 " 0.042 2.00e-02 2.50e+03 7.95e-02 6.33e+01 pdb=" C VAL H 100 " -0.138 2.00e-02 2.50e+03 pdb=" O VAL H 100 " 0.051 2.00e-02 2.50e+03 pdb=" N GLN H 101 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 462 " 0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO F 463 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 463 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 463 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 56 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO L 57 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO L 57 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 57 " 0.033 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 50 2.61 - 3.18: 2613 3.18 - 3.75: 4748 3.75 - 4.33: 6402 4.33 - 4.90: 10870 Nonbonded interactions: 24683 Sorted by model distance: nonbonded pdb=" O ARG H 106 " pdb=" C SER H 107 " model vdw 2.035 3.270 nonbonded pdb=" O SER F 371 " pdb=" NH1 ARG H 106 " model vdw 2.238 3.120 nonbonded pdb=" O ASN F 439 " pdb=" OG SER F 443 " model vdw 2.276 3.040 nonbonded pdb=" O ARG H 106 " pdb=" CA SER H 107 " model vdw 2.278 2.776 nonbonded pdb=" OG SER F 349 " pdb=" O LEU F 452 " model vdw 2.302 3.040 ... (remaining 24678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.960 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.730 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 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 : 0.006 0.092 3406 Z= 0.359 Angle : 0.978 14.217 4632 Z= 0.563 Chirality : 0.060 0.297 492 Planarity : 0.008 0.080 600 Dihedral : 16.809 102.726 1232 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.28 % Allowed : 10.14 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.35), residues: 419 helix: -4.82 (0.44), residues: 14 sheet: -2.40 (0.44), residues: 127 loop : -3.30 (0.30), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 436 HIS 0.006 0.003 HIS H 35 PHE 0.011 0.002 PHE F 400 TYR 0.021 0.002 TYR H 104 ARG 0.007 0.001 ARG H 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 1) link_NAG-ASN : angle 0.76846 ( 3) link_BETA1-4 : bond 0.01260 ( 1) link_BETA1-4 : angle 2.10600 ( 3) hydrogen bonds : bond 0.30355 ( 66) hydrogen bonds : angle 11.76116 ( 168) SS BOND : bond 0.00241 ( 3) SS BOND : angle 0.61938 ( 6) covalent geometry : bond 0.00604 ( 3401) covalent geometry : angle 0.97704 ( 4620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: F 354 ASN cc_start: 0.8755 (p0) cc_final: 0.8457 (p0) REVERT: F 474 GLN cc_start: 0.6126 (tp40) cc_final: 0.5872 (tm-30) REVERT: L 16 GLN cc_start: 0.8730 (mm110) cc_final: 0.8170 (mp10) REVERT: H 16 ARG cc_start: 0.2340 (mmt180) cc_final: 0.1977 (mmt180) outliers start: 1 outliers final: 1 residues processed: 95 average time/residue: 0.1865 time to fit residues: 20.8825 Evaluate side-chains 78 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 106 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 370 ASN F 388 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 GLN F 487 ASN L 6 GLN L 16 GLN L 40 GLN H 13 GLN H 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.109778 restraints weight = 5056.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.111951 restraints weight = 3623.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113401 restraints weight = 2905.065| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3406 Z= 0.222 Angle : 0.699 8.421 4632 Z= 0.355 Chirality : 0.048 0.214 492 Planarity : 0.005 0.045 600 Dihedral : 12.083 78.853 522 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 4.79 % Allowed : 19.72 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.38), residues: 419 helix: -4.52 (0.76), residues: 14 sheet: -2.34 (0.44), residues: 132 loop : -2.88 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 436 HIS 0.003 0.001 HIS H 35 PHE 0.018 0.002 PHE F 338 TYR 0.017 0.002 TYR F 495 ARG 0.004 0.001 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 1) link_NAG-ASN : angle 0.67391 ( 3) link_BETA1-4 : bond 0.00719 ( 1) link_BETA1-4 : angle 2.41143 ( 3) hydrogen bonds : bond 0.05669 ( 66) hydrogen bonds : angle 8.08524 ( 168) SS BOND : bond 0.00257 ( 3) SS BOND : angle 0.56362 ( 6) covalent geometry : bond 0.00509 ( 3401) covalent geometry : angle 0.69629 ( 4620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.332 Fit side-chains REVERT: F 346 ARG cc_start: 0.7299 (tpp-160) cc_final: 0.7093 (tpp80) REVERT: F 354 ASN cc_start: 0.8886 (p0) cc_final: 0.8562 (p0) REVERT: F 427 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7963 (t0) REVERT: F 474 GLN cc_start: 0.6092 (tp40) cc_final: 0.5767 (tm-30) REVERT: L 6 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8769 (pt0) REVERT: L 16 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8098 (mp10) REVERT: H 16 ARG cc_start: 0.2304 (mmt180) cc_final: 0.1996 (mmt180) outliers start: 17 outliers final: 10 residues processed: 98 average time/residue: 0.1852 time to fit residues: 21.2070 Evaluate side-chains 92 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 427 ASP Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN L 6 GLN L 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.113686 restraints weight = 4914.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.116380 restraints weight = 3275.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118220 restraints weight = 2491.818| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3406 Z= 0.157 Angle : 0.660 9.639 4632 Z= 0.326 Chirality : 0.047 0.246 492 Planarity : 0.004 0.038 600 Dihedral : 10.176 64.646 518 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 3.94 % Allowed : 20.28 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.39), residues: 419 helix: -4.60 (0.66), residues: 14 sheet: -2.03 (0.45), residues: 133 loop : -2.60 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 436 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE F 338 TYR 0.014 0.001 TYR H 114 ARG 0.004 0.000 ARG H 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00066 ( 1) link_NAG-ASN : angle 0.56831 ( 3) link_BETA1-4 : bond 0.00864 ( 1) link_BETA1-4 : angle 2.75518 ( 3) hydrogen bonds : bond 0.04459 ( 66) hydrogen bonds : angle 7.21723 ( 168) SS BOND : bond 0.00210 ( 3) SS BOND : angle 0.59015 ( 6) covalent geometry : bond 0.00368 ( 3401) covalent geometry : angle 0.65652 ( 4620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: F 354 ASN cc_start: 0.8877 (p0) cc_final: 0.8518 (p0) REVERT: F 474 GLN cc_start: 0.5983 (tp40) cc_final: 0.5384 (tm-30) REVERT: L 16 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8100 (mp10) REVERT: H 16 ARG cc_start: 0.2373 (mmt180) cc_final: 0.0154 (mmt180) outliers start: 14 outliers final: 10 residues processed: 92 average time/residue: 0.1972 time to fit residues: 21.0700 Evaluate side-chains 88 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.0270 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 409 GLN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.134690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.112894 restraints weight = 5052.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115741 restraints weight = 3343.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.117649 restraints weight = 2513.611| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3406 Z= 0.160 Angle : 0.659 9.900 4632 Z= 0.321 Chirality : 0.047 0.233 492 Planarity : 0.004 0.033 600 Dihedral : 9.146 56.388 518 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 4.79 % Allowed : 20.00 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.40), residues: 419 helix: -4.54 (0.72), residues: 14 sheet: -1.95 (0.46), residues: 133 loop : -2.50 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 436 HIS 0.004 0.002 HIS H 35 PHE 0.012 0.001 PHE F 338 TYR 0.024 0.002 TYR H 114 ARG 0.003 0.000 ARG F 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00027 ( 1) link_NAG-ASN : angle 0.69643 ( 3) link_BETA1-4 : bond 0.00989 ( 1) link_BETA1-4 : angle 3.00666 ( 3) hydrogen bonds : bond 0.04063 ( 66) hydrogen bonds : angle 6.75479 ( 168) SS BOND : bond 0.00205 ( 3) SS BOND : angle 0.59363 ( 6) covalent geometry : bond 0.00374 ( 3401) covalent geometry : angle 0.65445 ( 4620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.327 Fit side-chains REVERT: F 354 ASN cc_start: 0.8887 (p0) cc_final: 0.8571 (p0) REVERT: F 474 GLN cc_start: 0.5983 (tp40) cc_final: 0.5384 (tm-30) REVERT: L 6 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8820 (pt0) REVERT: L 16 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8117 (mp10) REVERT: H 16 ARG cc_start: 0.2239 (mmt180) cc_final: 0.0060 (mmt180) outliers start: 17 outliers final: 11 residues processed: 89 average time/residue: 0.1706 time to fit residues: 17.9533 Evaluate side-chains 84 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.7980 chunk 30 optimal weight: 0.0060 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 4 optimal weight: 0.6980 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.134578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.112143 restraints weight = 4999.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.114874 restraints weight = 3385.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.116729 restraints weight = 2598.507| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3406 Z= 0.143 Angle : 0.650 9.537 4632 Z= 0.316 Chirality : 0.046 0.205 492 Planarity : 0.004 0.033 600 Dihedral : 8.377 57.157 518 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 4.79 % Allowed : 20.56 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.40), residues: 419 helix: -4.60 (0.70), residues: 14 sheet: -1.82 (0.47), residues: 127 loop : -2.39 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.011 0.001 PHE F 338 TYR 0.022 0.001 TYR H 114 ARG 0.005 0.001 ARG F 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 1) link_NAG-ASN : angle 0.97423 ( 3) link_BETA1-4 : bond 0.01138 ( 1) link_BETA1-4 : angle 3.10764 ( 3) hydrogen bonds : bond 0.03768 ( 66) hydrogen bonds : angle 6.48122 ( 168) SS BOND : bond 0.00182 ( 3) SS BOND : angle 0.64871 ( 6) covalent geometry : bond 0.00332 ( 3401) covalent geometry : angle 0.64560 ( 4620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.336 Fit side-chains REVERT: F 354 ASN cc_start: 0.8868 (p0) cc_final: 0.8515 (p0) REVERT: F 474 GLN cc_start: 0.5973 (tp40) cc_final: 0.5415 (tm-30) REVERT: L 16 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8139 (mp10) REVERT: H 16 ARG cc_start: 0.2628 (mmt180) cc_final: 0.0304 (mmt180) REVERT: H 53 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7097 (t80) outliers start: 17 outliers final: 13 residues processed: 90 average time/residue: 0.1758 time to fit residues: 18.8178 Evaluate side-chains 89 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.135264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.113240 restraints weight = 5112.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.115984 restraints weight = 3379.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117907 restraints weight = 2558.471| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3406 Z= 0.153 Angle : 0.656 9.254 4632 Z= 0.320 Chirality : 0.047 0.226 492 Planarity : 0.004 0.032 600 Dihedral : 7.905 59.916 518 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 4.23 % Allowed : 22.54 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.40), residues: 419 helix: -4.92 (0.43), residues: 20 sheet: -1.71 (0.47), residues: 127 loop : -2.25 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.013 0.002 PHE F 429 TYR 0.029 0.002 TYR H 114 ARG 0.005 0.001 ARG H 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00073 ( 1) link_NAG-ASN : angle 1.20511 ( 3) link_BETA1-4 : bond 0.01187 ( 1) link_BETA1-4 : angle 3.16327 ( 3) hydrogen bonds : bond 0.03787 ( 66) hydrogen bonds : angle 6.32393 ( 168) SS BOND : bond 0.00199 ( 3) SS BOND : angle 0.67567 ( 6) covalent geometry : bond 0.00355 ( 3401) covalent geometry : angle 0.65048 ( 4620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.336 Fit side-chains REVERT: F 354 ASN cc_start: 0.8853 (p0) cc_final: 0.8497 (p0) REVERT: F 474 GLN cc_start: 0.5948 (tp40) cc_final: 0.5369 (tm-30) REVERT: L 16 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8099 (mp10) REVERT: H 16 ARG cc_start: 0.2600 (mmt180) cc_final: 0.2167 (mmt180) REVERT: H 53 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7262 (t80) outliers start: 15 outliers final: 13 residues processed: 87 average time/residue: 0.1759 time to fit residues: 18.1205 Evaluate side-chains 88 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 53 PHE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.110703 restraints weight = 5021.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113362 restraints weight = 3362.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.115172 restraints weight = 2575.338| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3406 Z= 0.192 Angle : 0.682 9.618 4632 Z= 0.335 Chirality : 0.047 0.234 492 Planarity : 0.004 0.032 600 Dihedral : 7.786 59.968 518 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 4.51 % Allowed : 22.25 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.40), residues: 419 helix: -4.93 (0.38), residues: 20 sheet: -1.75 (0.48), residues: 127 loop : -2.24 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.020 0.002 PHE F 429 TYR 0.026 0.002 TYR H 114 ARG 0.003 0.000 ARG F 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00026 ( 1) link_NAG-ASN : angle 1.28404 ( 3) link_BETA1-4 : bond 0.01187 ( 1) link_BETA1-4 : angle 3.16918 ( 3) hydrogen bonds : bond 0.03924 ( 66) hydrogen bonds : angle 6.30312 ( 168) SS BOND : bond 0.00263 ( 3) SS BOND : angle 0.68954 ( 6) covalent geometry : bond 0.00446 ( 3401) covalent geometry : angle 0.67667 ( 4620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.347 Fit side-chains REVERT: F 354 ASN cc_start: 0.8878 (p0) cc_final: 0.8531 (p0) REVERT: F 427 ASP cc_start: 0.8296 (t0) cc_final: 0.8076 (t0) REVERT: F 474 GLN cc_start: 0.5981 (tp40) cc_final: 0.5346 (tm-30) REVERT: L 16 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8079 (mp10) REVERT: H 16 ARG cc_start: 0.2331 (mmt180) cc_final: 0.1921 (mmt180) outliers start: 16 outliers final: 14 residues processed: 88 average time/residue: 0.1923 time to fit residues: 19.9024 Evaluate side-chains 89 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108869 restraints weight = 4992.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111567 restraints weight = 3350.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113474 restraints weight = 2566.192| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3406 Z= 0.213 Angle : 0.706 10.374 4632 Z= 0.344 Chirality : 0.047 0.234 492 Planarity : 0.004 0.032 600 Dihedral : 7.821 59.853 518 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 4.79 % Allowed : 22.82 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.40), residues: 419 helix: -4.92 (0.39), residues: 20 sheet: -1.68 (0.48), residues: 125 loop : -2.23 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 436 HIS 0.005 0.002 HIS H 35 PHE 0.014 0.002 PHE F 338 TYR 0.020 0.002 TYR H 114 ARG 0.006 0.001 ARG F 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00064 ( 1) link_NAG-ASN : angle 1.26943 ( 3) link_BETA1-4 : bond 0.01177 ( 1) link_BETA1-4 : angle 3.18298 ( 3) hydrogen bonds : bond 0.03962 ( 66) hydrogen bonds : angle 6.36698 ( 168) SS BOND : bond 0.00159 ( 3) SS BOND : angle 1.60348 ( 6) covalent geometry : bond 0.00499 ( 3401) covalent geometry : angle 0.69916 ( 4620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.308 Fit side-chains REVERT: F 354 ASN cc_start: 0.8871 (p0) cc_final: 0.8536 (p0) REVERT: F 474 GLN cc_start: 0.6035 (tp40) cc_final: 0.5356 (tm-30) REVERT: L 16 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8117 (mp10) REVERT: H 16 ARG cc_start: 0.2468 (mmt180) cc_final: 0.2058 (mmt180) outliers start: 17 outliers final: 15 residues processed: 81 average time/residue: 0.1834 time to fit residues: 17.6578 Evaluate side-chains 87 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 495 TYR Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.353 > 50: distance: 6 - 126: 3.373 distance: 41 - 46: 33.444 distance: 46 - 47: 41.363 distance: 47 - 48: 53.453 distance: 47 - 50: 52.222 distance: 48 - 49: 57.530 distance: 48 - 53: 39.926 distance: 50 - 51: 46.301 distance: 50 - 52: 38.638 distance: 53 - 54: 10.469 distance: 54 - 55: 58.781 distance: 54 - 57: 15.966 distance: 55 - 56: 40.464 distance: 55 - 62: 56.503 distance: 57 - 58: 47.388 distance: 58 - 59: 27.071 distance: 59 - 60: 48.303 distance: 60 - 61: 34.014 distance: 62 - 63: 40.607 distance: 63 - 64: 39.277 distance: 63 - 66: 55.971 distance: 64 - 65: 42.705 distance: 64 - 70: 70.254 distance: 66 - 67: 54.607 distance: 67 - 68: 43.019 distance: 67 - 69: 31.662 distance: 70 - 71: 27.789 distance: 71 - 72: 27.045 distance: 71 - 74: 37.898 distance: 72 - 73: 21.506 distance: 72 - 78: 32.326 distance: 74 - 75: 42.452 distance: 75 - 76: 17.667 distance: 75 - 77: 58.623 distance: 78 - 79: 31.479 distance: 79 - 80: 36.639 distance: 79 - 82: 39.506 distance: 80 - 81: 64.215 distance: 80 - 86: 40.502 distance: 82 - 83: 13.888 distance: 83 - 84: 31.172 distance: 83 - 85: 19.516 distance: 86 - 87: 15.020 distance: 87 - 88: 9.758 distance: 87 - 90: 34.186 distance: 88 - 89: 35.331 distance: 88 - 94: 42.220 distance: 90 - 91: 21.671 distance: 91 - 92: 16.037 distance: 91 - 93: 21.765 distance: 94 - 95: 36.767 distance: 95 - 96: 8.443 distance: 95 - 98: 32.279 distance: 96 - 97: 39.210 distance: 96 - 100: 12.672 distance: 98 - 99: 26.931 distance: 100 - 101: 20.225 distance: 101 - 102: 32.199 distance: 101 - 104: 15.358 distance: 102 - 103: 44.189 distance: 102 - 111: 40.628 distance: 104 - 105: 39.708 distance: 105 - 106: 29.784 distance: 105 - 107: 24.234 distance: 106 - 108: 25.814 distance: 107 - 109: 20.677 distance: 108 - 110: 9.968 distance: 109 - 110: 8.341 distance: 111 - 112: 29.148 distance: 112 - 113: 17.376 distance: 112 - 115: 45.860 distance: 113 - 114: 35.425 distance: 113 - 118: 35.701 distance: 115 - 116: 15.711 distance: 115 - 117: 21.648 distance: 118 - 119: 40.216 distance: 119 - 120: 4.871 distance: 119 - 122: 45.920 distance: 120 - 121: 35.493 distance: 120 - 126: 26.958 distance: 122 - 123: 32.185 distance: 123 - 124: 16.332 distance: 123 - 125: 20.096 distance: 133 - 143: 3.003