Starting phenix.real_space_refine on Wed Sep 17 03:21:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ve2_43162/09_2025/8ve2_43162.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ve2_43162/09_2025/8ve2_43162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ve2_43162/09_2025/8ve2_43162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ve2_43162/09_2025/8ve2_43162.map" model { file = "/net/cci-nas-00/data/ceres_data/8ve2_43162/09_2025/8ve2_43162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ve2_43162/09_2025/8ve2_43162.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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 4 5.16 5 C 2047 2.51 5 N 540 2.21 5 O 514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3105 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 795 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 10, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 780 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 8, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 761 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 7, 'TRANS': 108} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 10, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 769 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 10, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 73 Time building chain proxies: 1.13, per 1000 atoms: 0.36 Number of scatterers: 3105 At special positions: 0 Unit cell: (75.87, 70.25, 63.506, 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 4 16.00 O 514 8.00 N 540 7.00 C 2047 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 136.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 874 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 5 sheets defined 8.4% alpha, 51.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'B' and resid 74 through 83 removed outlier: 3.888A pdb=" N TYR B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 82 Processing helix chain 'D' and resid 74 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.855A pdb=" N SER A 23 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N MET A 13 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ALA A 109 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS A 15 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU A 111 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET B 13 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA B 109 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS B 15 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU B 111 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 17 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B 23 " --> pdb=" O ASP B 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.855A pdb=" N SER A 23 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N MET A 13 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ALA A 109 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS A 15 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU A 111 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET B 13 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA B 109 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS B 15 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU B 111 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU B 17 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 14 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 48 removed outlier: 6.882A pdb=" N VAL A 32 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER A 46 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A 30 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE A 68 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL B 94 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA A 91 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N GLU B 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 93 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N HIS B 90 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE A 95 " --> pdb=" O HIS B 88 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N HIS B 88 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE B 68 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG B 34 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 56 removed outlier: 3.571A pdb=" N SER D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG D 104 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL D 14 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 48 removed outlier: 6.749A pdb=" N VAL C 32 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER C 46 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C 30 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE C 68 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL D 94 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA C 91 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLU D 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS D 70 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL D 30 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER D 46 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 32 " --> pdb=" O PHE D 44 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 462 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: 0.31 Time building geometry restraints manager: 0.31 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: 989 1.34 - 1.46: 821 1.46 - 1.58: 1381 1.58 - 1.69: 0 1.69 - 1.81: 5 Bond restraints: 3196 Sorted by residual: bond pdb=" CA PRO B 102 " pdb=" C PRO B 102 " ideal model delta sigma weight residual 1.528 1.520 0.008 9.10e-03 1.21e+04 8.55e-01 bond pdb=" CA GLU C 42 " pdb=" CB GLU C 42 " ideal model delta sigma weight residual 1.524 1.537 -0.012 1.55e-02 4.16e+03 6.47e-01 bond pdb=" CA CYS A 10 " pdb=" CB CYS A 10 " ideal model delta sigma weight residual 1.524 1.537 -0.012 1.55e-02 4.16e+03 6.25e-01 bond pdb=" C GLY B 67 " pdb=" O GLY B 67 " ideal model delta sigma weight residual 1.236 1.227 0.008 1.22e-02 6.72e+03 4.62e-01 bond pdb=" CG PRO D 43 " pdb=" CD PRO D 43 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.05e-01 ... (remaining 3191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 4259 1.27 - 2.53: 120 2.53 - 3.80: 33 3.80 - 5.07: 3 5.07 - 6.33: 3 Bond angle restraints: 4418 Sorted by residual: angle pdb=" N LEU A 58 " pdb=" CA LEU A 58 " pdb=" C LEU A 58 " ideal model delta sigma weight residual 113.12 110.77 2.35 1.25e+00 6.40e-01 3.54e+00 angle pdb=" CA LEU D 12 " pdb=" CB LEU D 12 " pdb=" CG LEU D 12 " ideal model delta sigma weight residual 116.30 122.63 -6.33 3.50e+00 8.16e-02 3.27e+00 angle pdb=" C PRO C 113 " pdb=" N TYR C 114 " pdb=" CA TYR C 114 " ideal model delta sigma weight residual 121.54 124.97 -3.43 1.91e+00 2.74e-01 3.23e+00 angle pdb=" CB ARG B 34 " pdb=" CG ARG B 34 " pdb=" CD ARG B 34 " ideal model delta sigma weight residual 111.30 115.41 -4.11 2.30e+00 1.89e-01 3.19e+00 angle pdb=" C LEU D 111 " pdb=" N SER D 112 " pdb=" CA SER D 112 " ideal model delta sigma weight residual 122.26 125.12 -2.86 1.60e+00 3.91e-01 3.19e+00 ... (remaining 4413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.89: 1617 9.89 - 19.79: 116 19.79 - 29.68: 49 29.68 - 39.57: 16 39.57 - 49.47: 10 Dihedral angle restraints: 1808 sinusoidal: 453 harmonic: 1355 Sorted by residual: dihedral pdb=" CA LEU C 82 " pdb=" C LEU C 82 " pdb=" N GLY C 83 " pdb=" CA GLY C 83 " ideal model delta harmonic sigma weight residual 180.00 164.44 15.56 0 5.00e+00 4.00e-02 9.69e+00 dihedral pdb=" CG ARG D 34 " pdb=" CD ARG D 34 " pdb=" NE ARG D 34 " pdb=" CZ ARG D 34 " ideal model delta sinusoidal sigma weight residual 90.00 130.62 -40.62 2 1.50e+01 4.44e-03 9.04e+00 dihedral pdb=" CB LYS B 76 " pdb=" CG LYS B 76 " pdb=" CD LYS B 76 " pdb=" CE LYS B 76 " ideal model delta sinusoidal sigma weight residual 60.00 109.46 -49.46 3 1.50e+01 4.44e-03 8.78e+00 ... (remaining 1805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 271 0.024 - 0.048: 152 0.048 - 0.072: 36 0.072 - 0.096: 20 0.096 - 0.119: 52 Chirality restraints: 531 Sorted by residual: chirality pdb=" CA VAL A 30 " pdb=" N VAL A 30 " pdb=" C VAL A 30 " pdb=" CB VAL A 30 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CA VAL A 93 " pdb=" N VAL A 93 " pdb=" C VAL A 93 " pdb=" CB VAL A 93 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 528 not shown) Planarity restraints: 564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 112 " 0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO C 113 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 113 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 113 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 85 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO C 86 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 86 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 86 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 42 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO B 43 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 43 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 43 " -0.021 5.00e-02 4.00e+02 ... (remaining 561 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 922 2.82 - 3.34: 2449 3.34 - 3.86: 4862 3.86 - 4.38: 5146 4.38 - 4.90: 9771 Nonbonded interactions: 23150 Sorted by model distance: nonbonded pdb=" NH1 ARG A 34 " pdb=" O LYS A 35 " model vdw 2.295 3.120 nonbonded pdb=" O THR C 60 " pdb=" N PHE C 64 " model vdw 2.428 3.120 nonbonded pdb=" O VAL B 65 " pdb=" OH TYR B 69 " model vdw 2.441 3.040 nonbonded pdb=" O PRO A 11 " pdb=" N TYR A 105 " model vdw 2.479 3.120 nonbonded pdb=" ND2 ASN A 98 " pdb=" O GLY A 101 " model vdw 2.496 3.120 ... (remaining 23145 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 10 and (name N or name CA or name C or name O or name CB \ )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C or name \ O or name CB )) or resid 16 through 19 or (resid 20 through 21 and (name N or na \ me CA or name C or name O or name CB )) or resid 22 through 25 or (resid 26 thro \ ugh 27 and (name N or name CA or name C or name O or name CB )) or resid 28 thro \ ugh 29 or (resid 30 and (name N or name CA or name C or name O or name CB )) or \ resid 31 through 33 or (resid 34 and (name N or name CA or name C or name O or n \ ame CB )) or resid 35 through 48 or (resid 49 through 52 and (name N or name CA \ or name C or name O or name CB )) or (resid 53 through 56 and (name N or name CA \ or name C or name O or name CB )) or resid 57 or (resid 58 through 63 and (name \ N or name CA or name C or name O or name CB )) or resid 64 through 67 or (resid \ 68 and (name N or name CA or name C or name O or name CB )) or resid 69 through \ 74 or (resid 75 through 77 and (name N or name CA or name C or name O or name C \ B )) or resid 78 through 79 or (resid 80 through 82 and (name N or name CA or na \ me C or name O or name CB )) or resid 83 or (resid 84 through 85 and (name N or \ name CA or name C or name O or name CB )) or resid 86 through 87 or (resid 88 th \ rough 89 and (name N or name CA or name C or name O or name CB )) or resid 90 th \ rough 102 or (resid 103 through 104 and (name N or name CA or name C or name O o \ r name CB )) or resid 105 through 123)) selection = (chain 'B' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 19 or (resid 20 through 21 and (na \ me N or name CA or name C or name O or name CB )) or resid 22 through 29 or (res \ id 30 and (name N or name CA or name C or name O or name CB )) or resid 31 throu \ gh 33 or (resid 34 and (name N or name CA or name C or name O or name CB )) or r \ esid 35 through 65 or (resid 66 and (name N or name CA or name C or name O or na \ me CB )) or resid 67 or (resid 68 and (name N or name CA or name C or name O or \ name CB )) or resid 69 through 75 or (resid 76 through 77 and (name N or name CA \ or name C or name O or name CB )) or resid 78 through 87 or (resid 88 through 8 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 90 through 9 \ 3 or (resid 94 and (name N or name CA or name C or name O or name CB )) or resid \ 95 through 102 or (resid 103 through 104 and (name N or name CA or name C or na \ me O or name CB )) or resid 105 through 114 or (resid 115 and (name N or name CA \ or name C or name O or name CB )) or resid 116 through 117 or (resid 118 throug \ h 120 and (name N or name CA or name C or name O or name CB )) or resid 121 thro \ ugh 123)) selection = (chain 'C' and ((resid 10 and (name N or name CA or name C or name O or name CB \ )) or resid 11 through 19 or (resid 20 through 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 29 or (resid 30 and (name N or na \ me CA or name C or name O or name CB )) or resid 31 through 57 or (resid 58 thro \ ugh 63 and (name N or name CA or name C or name O or name CB )) or resid 64 thro \ ugh 81 or (resid 82 and (name N or name CA or name C or name O or name CB )) or \ resid 83 or (resid 84 through 85 and (name N or name CA or name C or name O or n \ ame CB )) or resid 86 through 87 or (resid 88 through 89 and (name N or name CA \ or name C or name O or name CB )) or resid 90 through 93 or (resid 94 and (name \ N or name CA or name C or name O or name CB )) or resid 95 or (resid 96 through \ 97 and (name N or name CA or name C or name O or name CB )) or resid 98 through \ 118 or (resid 119 through 120 and (name N or name CA or name C or name O or name \ CB )) or resid 121 through 122 or (resid 123 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'D' and ((resid 10 and (name N or name CA or name C or name O or name CB \ )) or resid 11 through 14 or (resid 15 and (name N or name CA or name C or name \ O or name CB )) or resid 16 through 20 or (resid 21 and (name N or name CA or na \ me C or name O or name CB )) or resid 22 through 25 or (resid 26 through 27 and \ (name N or name CA or name C or name O or name CB )) or resid 28 through 33 or ( \ resid 34 and (name N or name CA or name C or name O or name CB )) or resid 35 th \ rough 49 or (resid 50 through 52 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 53 through 56 and (name N or name CA or name C or name O or \ name CB )) or resid 57 or (resid 58 through 63 and (name N or name CA or name C \ or name O or name CB )) or resid 64 through 67 or (resid 68 and (name N or name \ CA or name C or name O or name CB )) or resid 69 through 74 or (resid 75 through \ 77 and (name N or name CA or name C or name O or name CB )) or resid 78 through \ 81 or (resid 82 and (name N or name CA or name C or name O or name CB )) or res \ id 83 through 93 or (resid 94 and (name N or name CA or name C or name O or name \ CB )) or resid 95 through 117 or (resid 118 through 120 and (name N or name CA \ or name C or name O or name CB )) or resid 121 through 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.050 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 : 0.002 0.024 3196 Z= 0.126 Angle : 0.571 6.332 4418 Z= 0.311 Chirality : 0.045 0.119 531 Planarity : 0.005 0.051 564 Dihedral : 10.508 49.467 934 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.40), residues: 457 helix: 0.91 (0.84), residues: 40 sheet: 1.77 (0.35), residues: 215 loop : 0.37 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 34 TYR 0.008 0.001 TYR D 116 PHE 0.009 0.001 PHE C 64 TRP 0.021 0.001 TRP C 79 HIS 0.003 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3196) covalent geometry : angle 0.57066 ( 4418) hydrogen bonds : bond 0.23592 ( 143) hydrogen bonds : angle 9.21020 ( 462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.123 Fit side-chains REVERT: A 34 ARG cc_start: 0.7681 (ttt-90) cc_final: 0.7091 (tpt90) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0912 time to fit residues: 6.2676 Evaluate side-chains 57 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.168996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.136912 restraints weight = 4912.730| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.92 r_work: 0.3869 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3196 Z= 0.139 Angle : 0.531 6.409 4418 Z= 0.274 Chirality : 0.047 0.140 531 Planarity : 0.005 0.044 564 Dihedral : 3.807 17.342 489 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.21 % Allowed : 8.26 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.39), residues: 457 helix: 0.46 (0.79), residues: 40 sheet: 1.56 (0.35), residues: 217 loop : 0.31 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.017 0.002 TYR D 78 PHE 0.013 0.001 PHE B 44 TRP 0.015 0.001 TRP C 79 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3196) covalent geometry : angle 0.53137 ( 4418) hydrogen bonds : bond 0.03755 ( 143) hydrogen bonds : angle 6.03259 ( 462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.139 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 0.0963 time to fit residues: 6.6714 Evaluate side-chains 59 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 110 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 9 optimal weight: 0.0040 chunk 35 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 overall best weight: 2.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.165404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.132906 restraints weight = 5020.996| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 3.98 r_work: 0.3661 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3196 Z= 0.213 Angle : 0.565 5.611 4418 Z= 0.294 Chirality : 0.049 0.149 531 Planarity : 0.005 0.046 564 Dihedral : 4.218 17.366 489 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 6.88 % Allowed : 11.01 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.39), residues: 457 helix: 0.40 (0.78), residues: 40 sheet: 1.15 (0.35), residues: 219 loop : 0.10 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.013 0.002 TYR D 78 PHE 0.018 0.002 PHE B 44 TRP 0.016 0.002 TRP C 79 HIS 0.002 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 3196) covalent geometry : angle 0.56496 ( 4418) hydrogen bonds : bond 0.04074 ( 143) hydrogen bonds : angle 5.94120 ( 462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.149 Fit side-chains REVERT: A 34 ARG cc_start: 0.7943 (ttt-90) cc_final: 0.7409 (tpt90) outliers start: 15 outliers final: 12 residues processed: 59 average time/residue: 0.0892 time to fit residues: 6.1825 Evaluate side-chains 68 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 110 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.163448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.131447 restraints weight = 5038.939| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.86 r_work: 0.3651 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3196 Z= 0.239 Angle : 0.573 5.857 4418 Z= 0.301 Chirality : 0.049 0.147 531 Planarity : 0.006 0.049 564 Dihedral : 4.346 17.072 489 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 6.42 % Allowed : 15.14 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.39), residues: 457 helix: 0.32 (0.79), residues: 40 sheet: 0.80 (0.34), residues: 219 loop : -0.11 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.012 0.002 TYR C 116 PHE 0.013 0.002 PHE C 33 TRP 0.015 0.002 TRP C 79 HIS 0.002 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 3196) covalent geometry : angle 0.57300 ( 4418) hydrogen bonds : bond 0.03858 ( 143) hydrogen bonds : angle 5.93674 ( 462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.120 Fit side-chains REVERT: A 34 ARG cc_start: 0.7924 (ttt-90) cc_final: 0.7533 (tpt90) outliers start: 14 outliers final: 12 residues processed: 56 average time/residue: 0.0870 time to fit residues: 5.7351 Evaluate side-chains 63 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain D residue 110 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 26 optimal weight: 0.0020 chunk 19 optimal weight: 6.9990 chunk 22 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 overall best weight: 1.5370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.165892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.133917 restraints weight = 4973.427| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 3.89 r_work: 0.3840 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3196 Z= 0.127 Angle : 0.513 6.697 4418 Z= 0.260 Chirality : 0.047 0.143 531 Planarity : 0.005 0.046 564 Dihedral : 3.767 16.038 489 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 6.42 % Allowed : 16.06 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.39), residues: 457 helix: 0.73 (0.81), residues: 40 sheet: 0.80 (0.35), residues: 221 loop : -0.00 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.011 0.001 TYR D 116 PHE 0.007 0.001 PHE B 33 TRP 0.014 0.001 TRP C 79 HIS 0.002 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3196) covalent geometry : angle 0.51268 ( 4418) hydrogen bonds : bond 0.02996 ( 143) hydrogen bonds : angle 5.52662 ( 462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.119 Fit side-chains REVERT: A 34 ARG cc_start: 0.7815 (ttt-90) cc_final: 0.7505 (tpt90) outliers start: 14 outliers final: 12 residues processed: 63 average time/residue: 0.1021 time to fit residues: 7.3784 Evaluate side-chains 66 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 110 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 40 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.160844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.127601 restraints weight = 5020.592| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.94 r_work: 0.3635 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3196 Z= 0.246 Angle : 0.591 6.106 4418 Z= 0.305 Chirality : 0.049 0.178 531 Planarity : 0.006 0.052 564 Dihedral : 4.271 18.230 489 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 6.88 % Allowed : 17.89 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.39), residues: 457 helix: 0.38 (0.79), residues: 40 sheet: 0.56 (0.35), residues: 217 loop : -0.18 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 34 TYR 0.013 0.002 TYR D 78 PHE 0.014 0.002 PHE C 33 TRP 0.019 0.002 TRP C 79 HIS 0.002 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 3196) covalent geometry : angle 0.59057 ( 4418) hydrogen bonds : bond 0.03801 ( 143) hydrogen bonds : angle 5.89116 ( 462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.122 Fit side-chains REVERT: A 34 ARG cc_start: 0.7913 (ttt-90) cc_final: 0.7543 (tpt90) outliers start: 15 outliers final: 14 residues processed: 57 average time/residue: 0.0996 time to fit residues: 6.5550 Evaluate side-chains 65 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 110 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 14 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 4 optimal weight: 0.0060 overall best weight: 2.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.160633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.127476 restraints weight = 5050.524| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.95 r_work: 0.3775 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3196 Z= 0.208 Angle : 0.563 6.618 4418 Z= 0.290 Chirality : 0.048 0.159 531 Planarity : 0.006 0.053 564 Dihedral : 4.147 18.087 489 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 6.42 % Allowed : 18.35 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.39), residues: 457 helix: 0.38 (0.79), residues: 40 sheet: 0.39 (0.35), residues: 217 loop : -0.20 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.012 0.002 TYR D 116 PHE 0.011 0.001 PHE C 33 TRP 0.020 0.002 TRP C 79 HIS 0.002 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 3196) covalent geometry : angle 0.56344 ( 4418) hydrogen bonds : bond 0.03497 ( 143) hydrogen bonds : angle 5.80221 ( 462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.123 Fit side-chains REVERT: A 34 ARG cc_start: 0.7884 (ttt-90) cc_final: 0.7532 (tpt90) outliers start: 14 outliers final: 14 residues processed: 56 average time/residue: 0.0909 time to fit residues: 5.8641 Evaluate side-chains 63 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 110 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 35 optimal weight: 0.0020 chunk 43 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.162825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.129532 restraints weight = 5068.129| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 3.99 r_work: 0.3806 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3196 Z= 0.141 Angle : 0.528 6.751 4418 Z= 0.268 Chirality : 0.047 0.143 531 Planarity : 0.005 0.049 564 Dihedral : 3.814 17.652 489 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.96 % Allowed : 19.72 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.39), residues: 457 helix: 0.55 (0.80), residues: 40 sheet: 0.38 (0.35), residues: 221 loop : -0.15 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.012 0.001 TYR D 116 PHE 0.007 0.001 PHE B 33 TRP 0.022 0.001 TRP C 79 HIS 0.002 0.000 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3196) covalent geometry : angle 0.52811 ( 4418) hydrogen bonds : bond 0.03058 ( 143) hydrogen bonds : angle 5.57434 ( 462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.122 Fit side-chains REVERT: A 34 ARG cc_start: 0.7837 (ttt-90) cc_final: 0.7521 (tpt90) REVERT: A 103 ARG cc_start: 0.8302 (tpp80) cc_final: 0.7900 (tpp80) outliers start: 13 outliers final: 12 residues processed: 58 average time/residue: 0.1039 time to fit residues: 6.9234 Evaluate side-chains 66 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 110 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 15 optimal weight: 30.0000 chunk 41 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.159916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.126483 restraints weight = 5097.220| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 3.99 r_work: 0.3623 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3196 Z= 0.256 Angle : 0.601 7.019 4418 Z= 0.312 Chirality : 0.049 0.144 531 Planarity : 0.006 0.054 564 Dihedral : 4.294 20.057 489 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.96 % Allowed : 20.64 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.39), residues: 457 helix: 0.22 (0.79), residues: 40 sheet: 0.24 (0.34), residues: 217 loop : -0.30 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 34 TYR 0.012 0.002 TYR C 116 PHE 0.014 0.002 PHE C 33 TRP 0.026 0.002 TRP C 79 HIS 0.002 0.001 HIS D 31 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 3196) covalent geometry : angle 0.60087 ( 4418) hydrogen bonds : bond 0.03768 ( 143) hydrogen bonds : angle 5.93507 ( 462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.127 Fit side-chains REVERT: A 34 ARG cc_start: 0.7918 (ttt-90) cc_final: 0.7542 (tpt90) REVERT: A 103 ARG cc_start: 0.8327 (tpp80) cc_final: 0.7972 (tpp80) outliers start: 13 outliers final: 12 residues processed: 57 average time/residue: 0.1011 time to fit residues: 6.6214 Evaluate side-chains 62 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.164411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.131972 restraints weight = 4999.028| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 3.98 r_work: 0.3801 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3196 Z= 0.139 Angle : 0.541 7.195 4418 Z= 0.273 Chirality : 0.047 0.139 531 Planarity : 0.005 0.056 564 Dihedral : 3.830 18.396 489 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.50 % Allowed : 21.56 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.39), residues: 457 helix: 0.29 (0.79), residues: 40 sheet: 0.28 (0.35), residues: 221 loop : -0.23 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.012 0.001 TYR D 116 PHE 0.007 0.001 PHE C 33 TRP 0.025 0.002 TRP C 79 HIS 0.002 0.000 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3196) covalent geometry : angle 0.54099 ( 4418) hydrogen bonds : bond 0.03047 ( 143) hydrogen bonds : angle 5.60796 ( 462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.118 Fit side-chains REVERT: A 34 ARG cc_start: 0.7853 (ttt-90) cc_final: 0.7530 (tpt90) REVERT: A 103 ARG cc_start: 0.8376 (tpp80) cc_final: 0.7968 (tpp80) REVERT: B 34 ARG cc_start: 0.7693 (tmt170) cc_final: 0.7467 (ttt-90) outliers start: 12 outliers final: 12 residues processed: 58 average time/residue: 0.0977 time to fit residues: 6.5620 Evaluate side-chains 65 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.164921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.132711 restraints weight = 5013.020| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.92 r_work: 0.3810 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3196 Z= 0.140 Angle : 0.539 7.413 4418 Z= 0.271 Chirality : 0.047 0.138 531 Planarity : 0.005 0.055 564 Dihedral : 3.712 17.490 489 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 5.50 % Allowed : 22.02 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.39), residues: 457 helix: 0.39 (0.80), residues: 40 sheet: 0.36 (0.35), residues: 221 loop : -0.21 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.012 0.001 TYR D 116 PHE 0.007 0.001 PHE B 33 TRP 0.027 0.002 TRP C 79 HIS 0.001 0.000 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3196) covalent geometry : angle 0.53912 ( 4418) hydrogen bonds : bond 0.02993 ( 143) hydrogen bonds : angle 5.54787 ( 462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1006.78 seconds wall clock time: 17 minutes 51.25 seconds (1071.25 seconds total)