Starting phenix.real_space_refine on Fri Aug 2 15:34:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/08_2024/8drq_27681.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/08_2024/8drq_27681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/08_2024/8drq_27681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/08_2024/8drq_27681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/08_2024/8drq_27681.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8drq_27681/08_2024/8drq_27681.cif" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 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 8 5.16 5 C 2135 2.51 5 N 583 2.21 5 O 595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 473": "OE1" <-> "OE2" Residue "E TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 519": "OE1" <-> "OE2" Residue "E GLU 520": "OE1" <-> "OE2" Residue "E ASP 538": "OD1" <-> "OD2" Residue "E ASP 620": "OD1" <-> "OD2" Residue "E GLU 760": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3321 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Time building chain proxies: 3.09, per 1000 atoms: 0.93 Number of scatterers: 3321 At special positions: 0 Unit cell: (75.456, 81.744, 78.6, 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 8 16.00 O 595 8.00 N 583 7.00 C 2135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 588.5 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 31.4% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'E' and resid 402 through 411 Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 439 through 444 removed outlier: 3.790A pdb=" N PHE E 443 " --> pdb=" O PRO E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 removed outlier: 3.589A pdb=" N ILE E 465 " --> pdb=" O PRO E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 510 through 514 removed outlier: 4.056A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 541 removed outlier: 3.702A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 removed outlier: 3.788A pdb=" N THR E 563 " --> pdb=" O PRO E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 638 removed outlier: 3.750A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 removed outlier: 3.525A pdb=" N LEU E 661 " --> pdb=" O ILE E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 684 removed outlier: 3.647A pdb=" N CYS E 684 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 707 removed outlier: 3.953A pdb=" N ILE E 704 " --> pdb=" O PRO E 701 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 707 " --> pdb=" O ILE E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 730 removed outlier: 3.629A pdb=" N PHE E 728 " --> pdb=" O PRO E 724 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS E 730 " --> pdb=" O GLU E 726 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 753 Processing helix chain 'E' and resid 771 through 776 removed outlier: 3.560A pdb=" N CYS E 776 " --> pdb=" O GLU E 772 " (cutoff:3.500A) Processing helix chain 'E' and resid 788 through 793 Processing helix chain 'E' and resid 795 through 808 Processing sheet with id=AA1, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.410A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 474 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LYS E 501 " --> pdb=" O LEU E 474 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU E 476 " --> pdb=" O LYS E 501 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU E 498 " --> pdb=" O HIS E 522 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR E 524 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE E 500 " --> pdb=" O THR E 524 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 596 " --> pdb=" O GLU E 618 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP E 620 " --> pdb=" O LEU E 596 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 598 " --> pdb=" O ASP E 620 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 459 through 460 removed outlier: 6.483A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 666 through 668 removed outlier: 6.334A pdb=" N TYR E 689 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU E 690 " --> pdb=" O ALA E 714 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 159 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: 0.87 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1098 1.34 - 1.46: 490 1.46 - 1.58: 1779 1.58 - 1.69: 1 1.69 - 1.81: 10 Bond restraints: 3378 Sorted by residual: bond pdb=" N PRO E 678 " pdb=" CD PRO E 678 " ideal model delta sigma weight residual 1.473 1.417 0.056 1.40e-02 5.10e+03 1.59e+01 bond pdb=" CB PRO E 678 " pdb=" CG PRO E 678 " ideal model delta sigma weight residual 1.492 1.614 -0.122 5.00e-02 4.00e+02 5.92e+00 bond pdb=" CB ASN E 712 " pdb=" CG ASN E 712 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.36e+00 bond pdb=" CG PRO E 678 " pdb=" CD PRO E 678 " ideal model delta sigma weight residual 1.503 1.460 0.043 3.40e-02 8.65e+02 1.57e+00 bond pdb=" N TYR E 534 " pdb=" CA TYR E 534 " ideal model delta sigma weight residual 1.459 1.471 -0.012 1.15e-02 7.56e+03 1.15e+00 ... (remaining 3373 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.36: 114 107.36 - 114.03: 1986 114.03 - 120.70: 1286 120.70 - 127.37: 1160 127.37 - 134.03: 34 Bond angle restraints: 4580 Sorted by residual: angle pdb=" CA MET E 590 " pdb=" CB MET E 590 " pdb=" CG MET E 590 " ideal model delta sigma weight residual 114.10 121.55 -7.45 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CB MET E 590 " pdb=" CG MET E 590 " pdb=" SD MET E 590 " ideal model delta sigma weight residual 112.70 122.86 -10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C ASN E 712 " pdb=" CA ASN E 712 " pdb=" CB ASN E 712 " ideal model delta sigma weight residual 109.38 115.03 -5.65 1.80e+00 3.09e-01 9.85e+00 angle pdb=" N PRO E 678 " pdb=" CD PRO E 678 " pdb=" CG PRO E 678 " ideal model delta sigma weight residual 103.20 107.80 -4.60 1.50e+00 4.44e-01 9.42e+00 angle pdb=" C LEU E 603 " pdb=" N GLU E 604 " pdb=" CA GLU E 604 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.02e+00 ... (remaining 4575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 1759 15.43 - 30.85: 250 30.85 - 46.28: 67 46.28 - 61.70: 17 61.70 - 77.13: 1 Dihedral angle restraints: 2094 sinusoidal: 892 harmonic: 1202 Sorted by residual: dihedral pdb=" CA LEU E 468 " pdb=" C LEU E 468 " pdb=" N THR E 469 " pdb=" CA THR E 469 " ideal model delta harmonic sigma weight residual 180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ILE E 535 " pdb=" C ILE E 535 " pdb=" N VAL E 536 " pdb=" CA VAL E 536 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR E 662 " pdb=" C THR E 662 " pdb=" N ASN E 663 " pdb=" CA ASN E 663 " ideal model delta harmonic sigma weight residual -180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 2091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 316 0.036 - 0.071: 163 0.071 - 0.107: 53 0.107 - 0.143: 15 0.143 - 0.178: 2 Chirality restraints: 549 Sorted by residual: chirality pdb=" CB VAL E 786 " pdb=" CA VAL E 786 " pdb=" CG1 VAL E 786 " pdb=" CG2 VAL E 786 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA VAL E 786 " pdb=" N VAL E 786 " pdb=" C VAL E 786 " pdb=" CB VAL E 786 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA ILE E 654 " pdb=" N ILE E 654 " pdb=" C ILE E 654 " pdb=" CB ILE E 654 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 546 not shown) Planarity restraints: 578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 677 " -0.047 5.00e-02 4.00e+02 7.27e-02 8.45e+00 pdb=" N PRO E 678 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 678 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 678 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 490 " -0.007 2.00e-02 2.50e+03 1.84e-02 5.90e+00 pdb=" CG PHE E 490 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE E 490 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE E 490 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE E 490 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 490 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 490 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 746 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO E 747 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 747 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 747 " 0.026 5.00e-02 4.00e+02 ... (remaining 575 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 850 2.81 - 3.33: 3133 3.33 - 3.85: 5736 3.85 - 4.38: 7140 4.38 - 4.90: 11097 Nonbonded interactions: 27956 Sorted by model distance: nonbonded pdb=" O VAL E 591 " pdb=" ND2 ASN E 615 " model vdw 2.283 3.120 nonbonded pdb=" O LEU E 476 " pdb=" N LYS E 501 " model vdw 2.300 3.120 nonbonded pdb=" OH TYR E 689 " pdb=" OE1 GLN E 711 " model vdw 2.315 3.040 nonbonded pdb=" O GLN E 560 " pdb=" OG1 THR E 563 " model vdw 2.328 3.040 nonbonded pdb=" O LEU E 790 " pdb=" OG1 THR E 793 " model vdw 2.329 3.040 ... (remaining 27951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.130 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.930 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 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 : 0.004 0.122 3378 Z= 0.295 Angle : 0.891 10.159 4580 Z= 0.486 Chirality : 0.048 0.178 549 Planarity : 0.006 0.073 578 Dihedral : 15.597 77.126 1306 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 19.31 % Favored : 80.69 % 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: -3.30 (0.39), residues: 405 helix: -3.27 (0.37), residues: 114 sheet: -2.33 (0.78), residues: 54 loop : -1.55 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 475 HIS 0.011 0.002 HIS E 694 PHE 0.039 0.003 PHE E 490 TYR 0.012 0.002 TYR E 477 ARG 0.003 0.000 ARG E 545 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 419 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8130 (tpt-90) REVERT: E 458 ASP cc_start: 0.7150 (m-30) cc_final: 0.6770 (t0) REVERT: E 465 ILE cc_start: 0.9158 (tt) cc_final: 0.8907 (tt) REVERT: E 474 LEU cc_start: 0.8956 (tt) cc_final: 0.8426 (tt) REVERT: E 496 ARG cc_start: 0.8407 (mtt90) cc_final: 0.8046 (mpt180) REVERT: E 507 GLU cc_start: 0.6049 (mt-10) cc_final: 0.5197 (mt-10) REVERT: E 520 GLU cc_start: 0.8635 (tt0) cc_final: 0.8389 (tt0) REVERT: E 555 LEU cc_start: 0.7678 (tp) cc_final: 0.7448 (tp) REVERT: E 581 LEU cc_start: 0.7922 (mp) cc_final: 0.7232 (tt) REVERT: E 592 ASN cc_start: 0.8192 (m-40) cc_final: 0.7941 (m110) REVERT: E 650 HIS cc_start: 0.6995 (m-70) cc_final: 0.6632 (m-70) REVERT: E 723 LEU cc_start: 0.5309 (mt) cc_final: 0.4532 (tt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2371 time to fit residues: 38.0667 Evaluate side-chains 97 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 711 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3378 Z= 0.215 Angle : 0.749 10.661 4580 Z= 0.359 Chirality : 0.048 0.191 549 Planarity : 0.006 0.060 578 Dihedral : 5.664 18.617 439 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.26 % Allowed : 5.56 % Favored : 94.18 % 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: -3.82 (0.37), residues: 405 helix: -2.99 (0.36), residues: 141 sheet: -2.56 (0.69), residues: 58 loop : -2.10 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.006 TRP E 647 HIS 0.017 0.003 HIS E 499 PHE 0.017 0.002 PHE E 490 TYR 0.034 0.004 TYR E 668 ARG 0.008 0.001 ARG E 541 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 429 GLU cc_start: 0.6205 (pt0) cc_final: 0.5802 (pt0) REVERT: E 443 PHE cc_start: 0.8119 (m-80) cc_final: 0.7817 (m-80) REVERT: E 454 GLU cc_start: 0.8301 (tp30) cc_final: 0.7745 (tp30) REVERT: E 496 ARG cc_start: 0.8263 (mtt90) cc_final: 0.7923 (mpt-90) REVERT: E 507 GLU cc_start: 0.6064 (mt-10) cc_final: 0.5741 (mt-10) REVERT: E 521 LEU cc_start: 0.8475 (tt) cc_final: 0.7998 (mt) REVERT: E 592 ASN cc_start: 0.8160 (m-40) cc_final: 0.7851 (m110) REVERT: E 601 CYS cc_start: 0.8097 (t) cc_final: 0.7861 (t) REVERT: E 603 LEU cc_start: 0.8188 (mt) cc_final: 0.7799 (mt) REVERT: E 640 ARG cc_start: 0.5265 (mpp-170) cc_final: 0.3869 (mmp-170) REVERT: E 737 HIS cc_start: 0.7337 (m90) cc_final: 0.7118 (m90) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.2172 time to fit residues: 28.2182 Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 694 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3378 Z= 0.193 Angle : 0.680 7.173 4580 Z= 0.328 Chirality : 0.045 0.163 549 Planarity : 0.005 0.051 578 Dihedral : 5.262 15.979 439 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % 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: -3.33 (0.39), residues: 405 helix: -2.83 (0.39), residues: 129 sheet: -1.70 (0.81), residues: 48 loop : -1.94 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP E 647 HIS 0.009 0.002 HIS E 522 PHE 0.012 0.002 PHE E 490 TYR 0.016 0.002 TYR E 477 ARG 0.005 0.001 ARG E 666 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 443 PHE cc_start: 0.8161 (m-80) cc_final: 0.7861 (m-80) REVERT: E 454 GLU cc_start: 0.8277 (tp30) cc_final: 0.7969 (tp30) REVERT: E 507 GLU cc_start: 0.6175 (mt-10) cc_final: 0.5947 (mt-10) REVERT: E 592 ASN cc_start: 0.8275 (m-40) cc_final: 0.7960 (m110) REVERT: E 640 ARG cc_start: 0.5187 (mpp-170) cc_final: 0.3837 (mmp-170) REVERT: E 685 ARG cc_start: 0.7230 (mmp-170) cc_final: 0.6336 (tpt-90) REVERT: E 732 LYS cc_start: 0.7091 (tptp) cc_final: 0.6185 (mptt) REVERT: E 737 HIS cc_start: 0.7228 (m90) cc_final: 0.6980 (m90) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2000 time to fit residues: 24.1237 Evaluate side-chains 77 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 0.0000 chunk 38 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.0670 chunk 32 optimal weight: 0.0030 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 overall best weight: 0.3132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 694 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3378 Z= 0.149 Angle : 0.633 6.948 4580 Z= 0.303 Chirality : 0.044 0.194 549 Planarity : 0.005 0.046 578 Dihedral : 4.904 15.411 439 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: -3.22 (0.40), residues: 405 helix: -2.72 (0.40), residues: 131 sheet: -1.86 (0.74), residues: 55 loop : -1.77 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP E 647 HIS 0.007 0.001 HIS E 522 PHE 0.011 0.001 PHE E 490 TYR 0.013 0.002 TYR E 653 ARG 0.004 0.000 ARG E 762 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 423 ASN cc_start: 0.7629 (p0) cc_final: 0.7239 (p0) REVERT: E 443 PHE cc_start: 0.8020 (m-80) cc_final: 0.7718 (m-80) REVERT: E 475 TRP cc_start: 0.8191 (m-10) cc_final: 0.7829 (m-10) REVERT: E 496 ARG cc_start: 0.8186 (mpt-90) cc_final: 0.7790 (mpp80) REVERT: E 507 GLU cc_start: 0.6177 (mt-10) cc_final: 0.5895 (mt-10) REVERT: E 521 LEU cc_start: 0.8493 (tt) cc_final: 0.8081 (mt) REVERT: E 592 ASN cc_start: 0.8143 (m-40) cc_final: 0.7831 (m110) REVERT: E 640 ARG cc_start: 0.4971 (mpp-170) cc_final: 0.3645 (mmp-170) REVERT: E 685 ARG cc_start: 0.6910 (mmp-170) cc_final: 0.6358 (tpt170) REVERT: E 732 LYS cc_start: 0.6996 (tptp) cc_final: 0.6273 (mptt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1834 time to fit residues: 21.4459 Evaluate side-chains 75 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 0.6707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3378 Z= 0.205 Angle : 0.699 8.960 4580 Z= 0.332 Chirality : 0.046 0.163 549 Planarity : 0.005 0.049 578 Dihedral : 5.078 16.732 439 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: -3.34 (0.39), residues: 405 helix: -2.71 (0.41), residues: 128 sheet: -2.19 (0.67), residues: 55 loop : -1.87 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP E 647 HIS 0.005 0.001 HIS E 522 PHE 0.012 0.002 PHE E 490 TYR 0.009 0.001 TYR E 689 ARG 0.007 0.001 ARG E 545 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 430 LEU cc_start: 0.8652 (pp) cc_final: 0.8364 (pp) REVERT: E 476 LEU cc_start: 0.8877 (mt) cc_final: 0.8593 (mt) REVERT: E 521 LEU cc_start: 0.8534 (tt) cc_final: 0.8112 (mt) REVERT: E 592 ASN cc_start: 0.8154 (m-40) cc_final: 0.7861 (m110) REVERT: E 640 ARG cc_start: 0.5132 (mpp-170) cc_final: 0.3713 (mmp-170) REVERT: E 668 TYR cc_start: 0.5609 (m-10) cc_final: 0.5330 (m-10) REVERT: E 685 ARG cc_start: 0.6753 (mmp-170) cc_final: 0.6223 (tpt170) REVERT: E 732 LYS cc_start: 0.7202 (tptp) cc_final: 0.6507 (mptt) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1829 time to fit residues: 19.7958 Evaluate side-chains 68 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 0.0980 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 554 ASN E 694 HIS E 741 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.7089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3378 Z= 0.166 Angle : 0.673 8.641 4580 Z= 0.315 Chirality : 0.046 0.172 549 Planarity : 0.004 0.048 578 Dihedral : 4.819 15.818 439 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.26 % Allowed : 1.59 % Favored : 98.15 % 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: -3.28 (0.39), residues: 405 helix: -2.63 (0.42), residues: 128 sheet: -2.00 (0.70), residues: 48 loop : -1.93 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP E 647 HIS 0.005 0.001 HIS E 522 PHE 0.011 0.002 PHE E 490 TYR 0.009 0.001 TYR E 689 ARG 0.005 0.000 ARG E 545 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 452 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7725 (mtmm) REVERT: E 458 ASP cc_start: 0.7081 (m-30) cc_final: 0.6806 (t0) REVERT: E 521 LEU cc_start: 0.8479 (tt) cc_final: 0.7976 (mt) REVERT: E 592 ASN cc_start: 0.7984 (m-40) cc_final: 0.7681 (m110) REVERT: E 640 ARG cc_start: 0.5027 (mpp-170) cc_final: 0.3569 (mmp-170) REVERT: E 670 ASN cc_start: 0.7502 (p0) cc_final: 0.7291 (p0) REVERT: E 685 ARG cc_start: 0.6789 (mmp-170) cc_final: 0.6501 (tpt170) REVERT: E 732 LYS cc_start: 0.7022 (tptp) cc_final: 0.6387 (mptt) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.1842 time to fit residues: 19.5278 Evaluate side-chains 70 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.7883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3378 Z= 0.240 Angle : 0.777 8.700 4580 Z= 0.364 Chirality : 0.047 0.168 549 Planarity : 0.005 0.049 578 Dihedral : 5.417 18.749 439 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: -3.48 (0.38), residues: 405 helix: -2.69 (0.42), residues: 123 sheet: -2.21 (0.65), residues: 48 loop : -2.13 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 647 HIS 0.005 0.001 HIS E 694 PHE 0.010 0.002 PHE E 490 TYR 0.011 0.002 TYR E 689 ARG 0.011 0.001 ARG E 605 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 475 TRP cc_start: 0.8492 (m-10) cc_final: 0.8022 (m-10) REVERT: E 521 LEU cc_start: 0.8529 (tt) cc_final: 0.8147 (mt) REVERT: E 532 ASN cc_start: 0.5781 (m-40) cc_final: 0.5187 (m-40) REVERT: E 555 LEU cc_start: 0.7005 (tp) cc_final: 0.6744 (tp) REVERT: E 592 ASN cc_start: 0.8145 (m-40) cc_final: 0.7785 (m110) REVERT: E 647 TRP cc_start: 0.8262 (p90) cc_final: 0.7889 (p-90) REVERT: E 668 TYR cc_start: 0.5009 (m-10) cc_final: 0.4752 (m-10) REVERT: E 732 LYS cc_start: 0.7287 (tptp) cc_final: 0.6711 (mptt) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1648 time to fit residues: 16.8095 Evaluate side-chains 64 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 7.9990 chunk 30 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.8316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3378 Z= 0.244 Angle : 0.776 7.986 4580 Z= 0.374 Chirality : 0.047 0.141 549 Planarity : 0.005 0.051 578 Dihedral : 5.528 19.753 439 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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 (0.38), residues: 405 helix: -2.75 (0.42), residues: 123 sheet: -2.36 (0.63), residues: 48 loop : -2.24 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 647 HIS 0.006 0.001 HIS E 694 PHE 0.013 0.002 PHE E 433 TYR 0.020 0.002 TYR E 689 ARG 0.004 0.001 ARG E 640 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 430 LEU cc_start: 0.8564 (pp) cc_final: 0.8334 (pp) REVERT: E 474 LEU cc_start: 0.8702 (tt) cc_final: 0.8257 (tt) REVERT: E 475 TRP cc_start: 0.8239 (m-10) cc_final: 0.7974 (m-10) REVERT: E 521 LEU cc_start: 0.8560 (tt) cc_final: 0.8109 (mt) REVERT: E 532 ASN cc_start: 0.5955 (m-40) cc_final: 0.5340 (m-40) REVERT: E 592 ASN cc_start: 0.8047 (m-40) cc_final: 0.7715 (m110) REVERT: E 635 PHE cc_start: 0.8568 (m-80) cc_final: 0.8308 (m-10) REVERT: E 647 TRP cc_start: 0.8298 (p90) cc_final: 0.7983 (p-90) REVERT: E 670 ASN cc_start: 0.7490 (p0) cc_final: 0.7152 (p0) REVERT: E 674 ILE cc_start: 0.7625 (mm) cc_final: 0.6967 (tp) REVERT: E 732 LYS cc_start: 0.7382 (tptp) cc_final: 0.6866 (mptt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1718 time to fit residues: 16.6976 Evaluate side-chains 62 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.0030 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 0.0870 overall best weight: 0.2946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 694 HIS ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.8431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3378 Z= 0.174 Angle : 0.711 8.783 4580 Z= 0.339 Chirality : 0.045 0.154 549 Planarity : 0.004 0.041 578 Dihedral : 5.012 18.075 439 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -3.63 (0.37), residues: 405 helix: -2.75 (0.39), residues: 130 sheet: -2.40 (0.63), residues: 48 loop : -2.20 (0.39), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP E 411 HIS 0.006 0.001 HIS E 522 PHE 0.015 0.002 PHE E 433 TYR 0.016 0.002 TYR E 689 ARG 0.015 0.001 ARG E 688 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 477 TYR cc_start: 0.7457 (m-80) cc_final: 0.7165 (m-80) REVERT: E 517 THR cc_start: 0.8356 (p) cc_final: 0.8136 (p) REVERT: E 521 LEU cc_start: 0.8488 (tt) cc_final: 0.8047 (mt) REVERT: E 532 ASN cc_start: 0.5781 (m-40) cc_final: 0.5237 (m-40) REVERT: E 592 ASN cc_start: 0.7826 (m-40) cc_final: 0.7410 (m110) REVERT: E 670 ASN cc_start: 0.7453 (p0) cc_final: 0.7172 (p0) REVERT: E 729 GLN cc_start: 0.4719 (mp-120) cc_final: 0.3286 (tp-100) REVERT: E 732 LYS cc_start: 0.7386 (tptp) cc_final: 0.6955 (mptt) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1746 time to fit residues: 18.2651 Evaluate side-chains 66 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 575 ASN ** E 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 moved from start: 0.8697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3378 Z= 0.188 Angle : 0.738 8.163 4580 Z= 0.351 Chirality : 0.047 0.197 549 Planarity : 0.005 0.044 578 Dihedral : 5.134 18.107 439 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: -3.27 (0.39), residues: 405 helix: -2.68 (0.41), residues: 123 sheet: -2.07 (0.66), residues: 48 loop : -1.89 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.006 TRP E 411 HIS 0.003 0.001 HIS E 522 PHE 0.021 0.002 PHE E 682 TYR 0.018 0.002 TYR E 668 ARG 0.007 0.001 ARG E 688 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 521 LEU cc_start: 0.8586 (tt) cc_final: 0.8182 (mt) REVERT: E 532 ASN cc_start: 0.5789 (m-40) cc_final: 0.5285 (m-40) REVERT: E 592 ASN cc_start: 0.7881 (m-40) cc_final: 0.7487 (m110) REVERT: E 597 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7681 (mm-30) REVERT: E 670 ASN cc_start: 0.7332 (p0) cc_final: 0.7072 (p0) REVERT: E 674 ILE cc_start: 0.7696 (mm) cc_final: 0.7040 (tp) REVERT: E 729 GLN cc_start: 0.4759 (mp-120) cc_final: 0.3380 (tp-100) REVERT: E 732 LYS cc_start: 0.7407 (tptp) cc_final: 0.7072 (mptt) REVERT: E 766 LEU cc_start: 0.5944 (tp) cc_final: 0.5631 (tt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1438 time to fit residues: 14.1937 Evaluate side-chains 58 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 61.75 > 50: distance: 60 - 67: 11.404 distance: 67 - 68: 15.803 distance: 68 - 69: 11.743 distance: 68 - 71: 10.768 distance: 69 - 70: 19.120 distance: 69 - 75: 11.070 distance: 71 - 72: 20.892 distance: 72 - 73: 26.129 distance: 72 - 74: 11.363 distance: 75 - 76: 42.468 distance: 76 - 77: 13.932 distance: 76 - 79: 16.168 distance: 77 - 78: 8.690 distance: 77 - 86: 39.045 distance: 79 - 80: 40.530 distance: 81 - 82: 8.998 distance: 83 - 84: 12.453 distance: 83 - 85: 27.861 distance: 86 - 87: 16.594 distance: 87 - 88: 20.168 distance: 88 - 89: 14.298 distance: 88 - 90: 24.629 distance: 90 - 91: 13.549 distance: 91 - 92: 5.818 distance: 91 - 94: 22.313 distance: 92 - 93: 30.270 distance: 92 - 98: 10.781 distance: 94 - 95: 4.616 distance: 95 - 96: 6.607 distance: 98 - 99: 15.351 distance: 99 - 100: 9.184 distance: 99 - 102: 12.292 distance: 100 - 101: 24.783 distance: 100 - 109: 15.884 distance: 102 - 103: 15.351 distance: 103 - 104: 18.796 distance: 104 - 105: 10.544 distance: 105 - 106: 27.953 distance: 106 - 107: 12.620 distance: 106 - 108: 3.485 distance: 109 - 110: 22.024 distance: 110 - 111: 16.348 distance: 110 - 113: 3.718 distance: 111 - 112: 14.706 distance: 111 - 117: 29.059 distance: 113 - 114: 12.656 distance: 114 - 115: 40.970 distance: 114 - 116: 27.839 distance: 117 - 118: 14.062 distance: 118 - 119: 20.233 distance: 119 - 120: 4.924 distance: 119 - 126: 23.740 distance: 121 - 122: 11.197 distance: 122 - 123: 35.403 distance: 123 - 124: 4.773 distance: 123 - 125: 5.556 distance: 126 - 127: 9.560 distance: 127 - 128: 16.123 distance: 127 - 130: 18.054 distance: 128 - 129: 22.013 distance: 128 - 132: 22.967 distance: 130 - 131: 16.461 distance: 132 - 133: 17.665 distance: 133 - 134: 40.691 distance: 133 - 136: 10.389 distance: 134 - 135: 4.435 distance: 134 - 140: 48.716 distance: 136 - 137: 19.093 distance: 137 - 138: 9.068 distance: 137 - 139: 19.299 distance: 140 - 141: 14.860 distance: 140 - 146: 5.994 distance: 141 - 142: 33.426 distance: 142 - 143: 13.072 distance: 142 - 147: 22.094 distance: 144 - 145: 3.081 distance: 145 - 146: 8.083