Starting phenix.real_space_refine on Sat Aug 3 09:37:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r34_18860/08_2024/8r34_18860.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r34_18860/08_2024/8r34_18860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r34_18860/08_2024/8r34_18860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r34_18860/08_2024/8r34_18860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r34_18860/08_2024/8r34_18860.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r34_18860/08_2024/8r34_18860.cif" } resolution = 2.62 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= 0.075 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 S 52 5.16 5 Na 4 4.78 5 C 5174 2.51 5 N 1136 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 381": "OD1" <-> "OD2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A ASP 835": "OD1" <-> "OD2" Residue "A PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 381": "OD1" <-> "OD2" Residue "B PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B ASP 480": "OD1" <-> "OD2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 572": "OD1" <-> "OD2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B ASP 757": "OD1" <-> "OD2" Residue "B ASP 795": "OD1" <-> "OD2" Residue "B PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7762 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3651 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 20, 'TRANS': 464} Chain breaks: 1 Chain: "B" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3651 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 20, 'TRANS': 464} Chain breaks: 1 Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 199 Unusual residues: {' NA': 2, '3PH': 4, 'PO4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 199 Unusual residues: {' NA': 2, '3PH': 4, 'PO4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Time building chain proxies: 5.33, per 1000 atoms: 0.69 Number of scatterers: 7762 At special positions: 0 Unit cell: (93.725, 93.725, 74.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 10 15.00 Na 4 11.00 O 1386 8.00 N 1136 7.00 C 5174 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: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 80.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.662A pdb=" N PHE A 409 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 410 " --> pdb=" O LYS A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 411 through 430 Processing helix chain 'A' and resid 435 through 455 removed outlier: 3.592A pdb=" N ALA A 443 " --> pdb=" O HIS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 473 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 485 through 498 removed outlier: 3.634A pdb=" N ALA A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TRP A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 518 removed outlier: 3.506A pdb=" N TYR A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 533 removed outlier: 3.739A pdb=" N TRP A 527 " --> pdb=" O VAL A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 555 removed outlier: 3.751A pdb=" N TRP A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 567 Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 578 through 596 Processing helix chain 'A' and resid 603 through 614 Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 619 through 646 removed outlier: 3.509A pdb=" N VAL A 626 " --> pdb=" O GLN A 622 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 664 through 683 Processing helix chain 'A' and resid 684 through 686 No H-bonds generated for 'chain 'A' and resid 684 through 686' Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.564A pdb=" N ILE A 697 " --> pdb=" O SER A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 707 removed outlier: 3.903A pdb=" N ILE A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 Processing helix chain 'A' and resid 720 through 741 removed outlier: 3.568A pdb=" N VAL A 724 " --> pdb=" O PRO A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 removed outlier: 3.804A pdb=" N LYS A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 755 " --> pdb=" O GLN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 775 removed outlier: 3.699A pdb=" N THR A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 796 Proline residue: A 788 - end of helix Processing helix chain 'A' and resid 801 through 814 Processing helix chain 'A' and resid 824 through 832 removed outlier: 3.545A pdb=" N SER A 832 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 852 removed outlier: 3.566A pdb=" N VAL A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 874 removed outlier: 3.919A pdb=" N VAL A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.707A pdb=" N PHE B 409 " --> pdb=" O PRO B 406 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 410 " --> pdb=" O LYS B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 410' Processing helix chain 'B' and resid 411 through 430 Processing helix chain 'B' and resid 435 through 455 removed outlier: 3.592A pdb=" N ALA B 443 " --> pdb=" O HIS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 473 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 485 through 496 removed outlier: 3.651A pdb=" N ALA B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 518 Processing helix chain 'B' and resid 519 through 533 removed outlier: 3.523A pdb=" N SER B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP B 527 " --> pdb=" O VAL B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 555 removed outlier: 3.749A pdb=" N TRP B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 567 Processing helix chain 'B' and resid 567 through 572 Processing helix chain 'B' and resid 578 through 596 Processing helix chain 'B' and resid 603 through 614 Processing helix chain 'B' and resid 615 through 617 No H-bonds generated for 'chain 'B' and resid 615 through 617' Processing helix chain 'B' and resid 619 through 646 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 664 through 683 Processing helix chain 'B' and resid 684 through 686 No H-bonds generated for 'chain 'B' and resid 684 through 686' Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 693 through 698 removed outlier: 3.573A pdb=" N ILE B 697 " --> pdb=" O SER B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 707 removed outlier: 3.901A pdb=" N ILE B 702 " --> pdb=" O ALA B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 Processing helix chain 'B' and resid 720 through 741 removed outlier: 3.575A pdb=" N VAL B 724 " --> pdb=" O PRO B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 755 removed outlier: 3.754A pdb=" N LYS B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 775 removed outlier: 3.723A pdb=" N THR B 775 " --> pdb=" O LEU B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 796 Proline residue: B 788 - end of helix Processing helix chain 'B' and resid 801 through 814 Processing helix chain 'B' and resid 824 through 832 removed outlier: 3.565A pdb=" N SER B 832 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 852 removed outlier: 3.553A pdb=" N VAL B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 874 removed outlier: 3.881A pdb=" N VAL B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR B 867 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER B 872 " --> pdb=" O GLY B 868 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1524 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: 2.04 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1168 1.33 - 1.45: 1899 1.45 - 1.57: 4685 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 7846 Sorted by residual: bond pdb=" O3 PO4 B 902 " pdb=" P PO4 B 902 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.46e+00 bond pdb=" O3 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" O4 PO4 B 902 " pdb=" P PO4 B 902 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" O4 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" O2 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.39e+00 ... (remaining 7841 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.25: 221 106.25 - 113.19: 4358 113.19 - 120.13: 2927 120.13 - 127.07: 2988 127.07 - 134.01: 80 Bond angle restraints: 10574 Sorted by residual: angle pdb=" C PHE A 656 " pdb=" N LYS A 657 " pdb=" CA LYS A 657 " ideal model delta sigma weight residual 121.61 127.22 -5.61 1.39e+00 5.18e-01 1.63e+01 angle pdb=" C ILE A 786 " pdb=" N ILE A 787 " pdb=" CA ILE A 787 " ideal model delta sigma weight residual 120.24 122.76 -2.52 6.30e-01 2.52e+00 1.60e+01 angle pdb=" C ILE B 786 " pdb=" N ILE B 787 " pdb=" CA ILE B 787 " ideal model delta sigma weight residual 120.24 122.54 -2.30 6.30e-01 2.52e+00 1.34e+01 angle pdb=" C ILE A 699 " pdb=" N ILE A 700 " pdb=" CA ILE A 700 " ideal model delta sigma weight residual 120.33 123.20 -2.87 8.00e-01 1.56e+00 1.29e+01 angle pdb=" C ILE B 699 " pdb=" N ILE B 700 " pdb=" CA ILE B 700 " ideal model delta sigma weight residual 120.33 123.07 -2.74 8.00e-01 1.56e+00 1.17e+01 ... (remaining 10569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 3923 17.40 - 34.80: 543 34.80 - 52.19: 193 52.19 - 69.59: 78 69.59 - 86.99: 11 Dihedral angle restraints: 4748 sinusoidal: 1966 harmonic: 2782 Sorted by residual: dihedral pdb=" CA GLU A 755 " pdb=" C GLU A 755 " pdb=" N ASN A 756 " pdb=" CA ASN A 756 " ideal model delta harmonic sigma weight residual 180.00 -161.14 -18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CG ARG A 850 " pdb=" CD ARG A 850 " pdb=" NE ARG A 850 " pdb=" CZ ARG A 850 " ideal model delta sinusoidal sigma weight residual 180.00 -136.60 -43.40 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CA LYS A 735 " pdb=" CB LYS A 735 " pdb=" CG LYS A 735 " pdb=" CD LYS A 735 " ideal model delta sinusoidal sigma weight residual -180.00 -120.22 -59.78 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 786 0.033 - 0.066: 357 0.066 - 0.099: 97 0.099 - 0.132: 20 0.132 - 0.164: 2 Chirality restraints: 1262 Sorted by residual: chirality pdb=" CG LEU A 408 " pdb=" CB LEU A 408 " pdb=" CD1 LEU A 408 " pdb=" CD2 LEU A 408 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CG LEU B 408 " pdb=" CB LEU B 408 " pdb=" CD1 LEU B 408 " pdb=" CD2 LEU B 408 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ASN A 756 " pdb=" N ASN A 756 " pdb=" C ASN A 756 " pdb=" CB ASN A 756 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1259 not shown) Planarity restraints: 1226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 719 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.15e+00 pdb=" N PRO B 720 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 720 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 720 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 643 " 0.013 2.00e-02 2.50e+03 1.29e-02 2.91e+00 pdb=" CG PHE B 643 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 643 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 643 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 643 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 643 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 643 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 719 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 720 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 720 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 720 " -0.023 5.00e-02 4.00e+02 ... (remaining 1223 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 260 2.71 - 3.26: 7715 3.26 - 3.81: 12757 3.81 - 4.35: 17570 4.35 - 4.90: 28579 Nonbonded interactions: 66881 Sorted by model distance: nonbonded pdb=" O LEU B 860 " pdb=" OG1 THR B 864 " model vdw 2.167 3.040 nonbonded pdb=" O LEU A 860 " pdb=" OG1 THR A 864 " model vdw 2.202 3.040 nonbonded pdb=" O ILE B 601 " pdb=" O HOH B1001 " model vdw 2.223 3.040 nonbonded pdb=" O ILE A 601 " pdb=" O HOH A1001 " model vdw 2.227 3.040 nonbonded pdb=" O MET A 648 " pdb=" OG1 THR A 651 " model vdw 2.244 3.040 ... (remaining 66876 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 378 through 876 or resid 903 or resid 905 through 907)) selection = (chain 'B' and (resid 378 through 876 or resid 903 or resid 905 through 907)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.070 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 0.062 7846 Z= 0.248 Angle : 0.647 5.608 10574 Z= 0.392 Chirality : 0.040 0.164 1262 Planarity : 0.005 0.044 1226 Dihedral : 19.662 86.987 2956 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.41 % Allowed : 24.94 % Favored : 72.66 % 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: 0.34 (0.27), residues: 962 helix: 0.71 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.99 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 639 HIS 0.004 0.001 HIS B 439 PHE 0.030 0.002 PHE B 643 TYR 0.013 0.001 TYR B 841 ARG 0.001 0.000 ARG A 836 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.852 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 105 average time/residue: 1.1881 time to fit residues: 132.8037 Evaluate side-chains 102 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.8077 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7846 Z= 0.308 Angle : 0.606 5.834 10574 Z= 0.310 Chirality : 0.042 0.139 1262 Planarity : 0.005 0.044 1226 Dihedral : 16.686 84.704 1377 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.68 % Allowed : 22.41 % Favored : 72.91 % 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: 0.74 (0.26), residues: 962 helix: 0.99 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.86 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 553 HIS 0.005 0.002 HIS B 439 PHE 0.031 0.002 PHE B 643 TYR 0.012 0.002 TYR B 841 ARG 0.003 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 92 time to evaluate : 0.874 Fit side-chains REVERT: A 431 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.5956 (tptt) REVERT: B 537 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6748 (ptp-170) REVERT: B 735 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7122 (tttm) REVERT: B 801 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6508 (mttt) REVERT: B 850 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7164 (mpt180) outliers start: 37 outliers final: 14 residues processed: 113 average time/residue: 1.1223 time to fit residues: 135.1641 Evaluate side-chains 108 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 735 LYS Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7846 Z= 0.199 Angle : 0.529 5.389 10574 Z= 0.270 Chirality : 0.039 0.132 1262 Planarity : 0.004 0.041 1226 Dihedral : 16.115 80.479 1368 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.05 % Allowed : 21.77 % Favored : 74.18 % 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: 1.38 (0.27), residues: 962 helix: 1.48 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.74 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 553 HIS 0.003 0.001 HIS B 439 PHE 0.027 0.001 PHE B 643 TYR 0.009 0.001 TYR B 841 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 89 time to evaluate : 0.913 Fit side-chains REVERT: A 431 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.5948 (tptt) REVERT: B 407 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.6997 (mtmm) REVERT: B 537 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6747 (ptp-170) REVERT: B 801 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6464 (mttt) REVERT: B 850 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7194 (mpt180) outliers start: 32 outliers final: 14 residues processed: 106 average time/residue: 1.2015 time to fit residues: 135.3146 Evaluate side-chains 103 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 407 LYS Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8034 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7846 Z= 0.182 Angle : 0.512 5.313 10574 Z= 0.259 Chirality : 0.039 0.129 1262 Planarity : 0.004 0.038 1226 Dihedral : 15.613 79.176 1366 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.67 % Allowed : 21.65 % Favored : 74.68 % 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: 1.69 (0.27), residues: 962 helix: 1.72 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.65 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 553 HIS 0.003 0.001 HIS B 439 PHE 0.025 0.001 PHE B 643 TYR 0.008 0.001 TYR B 841 ARG 0.002 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 87 time to evaluate : 0.897 Fit side-chains REVERT: A 431 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.5958 (tptt) REVERT: B 537 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6737 (ptp-170) REVERT: B 801 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6415 (mttt) REVERT: B 850 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7170 (mpt180) outliers start: 29 outliers final: 9 residues processed: 99 average time/residue: 1.3491 time to fit residues: 141.5350 Evaluate side-chains 98 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 850 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.0470 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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: 0.8021 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7846 Z= 0.167 Angle : 0.497 5.310 10574 Z= 0.250 Chirality : 0.038 0.126 1262 Planarity : 0.004 0.036 1226 Dihedral : 14.579 80.586 1358 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.67 % Allowed : 22.15 % Favored : 74.18 % 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: 1.97 (0.27), residues: 962 helix: 1.91 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.52 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 553 HIS 0.003 0.001 HIS B 439 PHE 0.024 0.001 PHE A 643 TYR 0.008 0.001 TYR B 841 ARG 0.001 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 82 time to evaluate : 0.850 Fit side-chains REVERT: A 431 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.5946 (tptt) REVERT: B 537 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6680 (ptp-170) REVERT: B 611 SER cc_start: 0.7885 (OUTLIER) cc_final: 0.7605 (p) REVERT: B 801 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6412 (mttt) REVERT: B 850 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7113 (mpt180) outliers start: 29 outliers final: 8 residues processed: 95 average time/residue: 1.2074 time to fit residues: 121.9996 Evaluate side-chains 94 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 850 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.0060 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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: 0.8028 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7846 Z= 0.180 Angle : 0.508 5.340 10574 Z= 0.254 Chirality : 0.039 0.131 1262 Planarity : 0.004 0.037 1226 Dihedral : 14.118 82.480 1358 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.29 % Allowed : 22.78 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.27), residues: 962 helix: 1.94 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.48 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 553 HIS 0.003 0.001 HIS B 439 PHE 0.025 0.001 PHE B 643 TYR 0.008 0.001 TYR B 841 ARG 0.001 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 80 time to evaluate : 0.760 Fit side-chains REVERT: A 431 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.5959 (tptt) REVERT: B 537 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6674 (ptp-170) REVERT: B 611 SER cc_start: 0.7971 (OUTLIER) cc_final: 0.7681 (p) REVERT: B 801 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6495 (mttt) REVERT: B 850 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7114 (mpt180) outliers start: 26 outliers final: 12 residues processed: 95 average time/residue: 1.2245 time to fit residues: 123.8376 Evaluate side-chains 97 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 0.0670 chunk 55 optimal weight: 0.3980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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: 0.8012 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7846 Z= 0.157 Angle : 0.495 5.302 10574 Z= 0.247 Chirality : 0.038 0.128 1262 Planarity : 0.004 0.035 1226 Dihedral : 13.601 84.910 1358 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.29 % Allowed : 22.41 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.27), residues: 962 helix: 2.07 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.44 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 553 HIS 0.003 0.001 HIS B 439 PHE 0.024 0.001 PHE A 643 TYR 0.008 0.001 TYR B 518 ARG 0.001 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 84 time to evaluate : 0.807 Fit side-chains REVERT: A 431 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.5953 (tptt) REVERT: B 648 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7237 (ptm) outliers start: 26 outliers final: 8 residues processed: 95 average time/residue: 1.1808 time to fit residues: 119.2492 Evaluate side-chains 93 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 84 optimal weight: 0.0070 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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: 0.8024 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7846 Z= 0.175 Angle : 0.503 5.341 10574 Z= 0.252 Chirality : 0.039 0.126 1262 Planarity : 0.004 0.036 1226 Dihedral : 13.380 87.077 1354 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.90 % Allowed : 24.43 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.27), residues: 962 helix: 2.14 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -0.33 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 PHE 0.025 0.001 PHE A 643 TYR 0.008 0.001 TYR B 841 ARG 0.007 0.001 ARG B 836 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.913 Fit side-chains REVERT: A 431 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.5968 (tptt) outliers start: 15 outliers final: 7 residues processed: 91 average time/residue: 1.2097 time to fit residues: 117.1749 Evaluate side-chains 89 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8033 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7846 Z= 0.194 Angle : 0.515 5.386 10574 Z= 0.258 Chirality : 0.039 0.129 1262 Planarity : 0.004 0.036 1226 Dihedral : 13.372 89.562 1354 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.65 % Allowed : 24.94 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.27), residues: 962 helix: 2.09 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -0.34 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 553 HIS 0.003 0.002 HIS B 439 PHE 0.027 0.001 PHE B 643 TYR 0.008 0.001 TYR B 841 ARG 0.004 0.000 ARG B 836 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.935 Fit side-chains REVERT: A 431 LYS cc_start: 0.6971 (OUTLIER) cc_final: 0.5990 (tptt) REVERT: B 611 SER cc_start: 0.7980 (OUTLIER) cc_final: 0.7695 (p) REVERT: B 875 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7479 (mmmt) outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 1.2452 time to fit residues: 118.7240 Evaluate side-chains 89 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 875 LYS 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: 60.9583 > 50: distance: 66 - 83: 33.174 distance: 70 - 89: 19.924 distance: 76 - 98: 19.179 distance: 79 - 83: 33.054 distance: 80 - 106: 30.678 distance: 83 - 84: 14.842 distance: 84 - 85: 21.154 distance: 84 - 87: 32.944 distance: 85 - 86: 20.515 distance: 85 - 89: 17.320 distance: 86 - 114: 28.738 distance: 87 - 88: 6.110 distance: 89 - 90: 7.267 distance: 90 - 91: 10.964 distance: 90 - 93: 24.328 distance: 91 - 92: 15.362 distance: 91 - 98: 10.282 distance: 93 - 94: 19.563 distance: 94 - 95: 30.696 distance: 95 - 96: 13.779 distance: 95 - 97: 37.395 distance: 98 - 99: 6.929 distance: 99 - 100: 23.860 distance: 99 - 102: 22.865 distance: 100 - 101: 5.783 distance: 100 - 106: 15.638 distance: 102 - 103: 23.931 distance: 102 - 104: 25.829 distance: 103 - 105: 29.653 distance: 106 - 107: 24.361 distance: 107 - 108: 34.043 distance: 107 - 110: 12.507 distance: 108 - 109: 28.752 distance: 108 - 114: 35.028 distance: 110 - 111: 42.531 distance: 111 - 112: 11.796 distance: 111 - 113: 29.074 distance: 114 - 115: 46.366 distance: 115 - 116: 23.717 distance: 115 - 118: 32.828 distance: 116 - 117: 41.203 distance: 116 - 119: 30.540 distance: 119 - 120: 17.193 distance: 120 - 121: 41.764 distance: 120 - 123: 41.401 distance: 121 - 122: 23.588 distance: 121 - 124: 23.002 distance: 124 - 125: 17.188 distance: 125 - 126: 21.010 distance: 125 - 128: 39.756 distance: 126 - 127: 18.739 distance: 126 - 132: 27.603 distance: 128 - 129: 45.550 distance: 129 - 130: 48.283 distance: 130 - 131: 33.974 distance: 132 - 133: 22.984 distance: 133 - 134: 19.298 distance: 133 - 136: 21.017 distance: 134 - 135: 15.127 distance: 134 - 146: 10.333 distance: 136 - 137: 25.186 distance: 137 - 138: 14.674 distance: 137 - 139: 25.304 distance: 138 - 140: 21.811 distance: 139 - 141: 44.451 distance: 139 - 142: 32.277 distance: 140 - 141: 36.783 distance: 141 - 143: 13.868 distance: 142 - 144: 12.456 distance: 143 - 145: 18.936 distance: 144 - 145: 28.946 distance: 146 - 147: 35.240 distance: 147 - 148: 29.182 distance: 147 - 150: 28.067 distance: 148 - 149: 25.063 distance: 148 - 152: 27.000 distance: 149 - 173: 22.809 distance: 150 - 151: 36.220 distance: 152 - 153: 27.123 distance: 153 - 156: 16.342 distance: 154 - 155: 38.092 distance: 154 - 158: 20.251 distance: 155 - 181: 19.984 distance: 156 - 157: 25.784