Starting phenix.real_space_refine on Wed Mar 5 17:10:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ve2_43162/03_2025/8ve2_43162.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ve2_43162/03_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_43162/03_2025/8ve2_43162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ve2_43162/03_2025/8ve2_43162.map" model { file = "/net/cci-nas-00/data/ceres_data/8ve2_43162/03_2025/8ve2_43162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ve2_43162/03_2025/8ve2_43162.cif" } resolution = 3.3 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= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLU:plan': 10, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 5} 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: {'GLU:plan': 8, 'HIS:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 5} 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: {'ARG:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 10, 'ASP:plan': 5} 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: {'GLU:plan': 10, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 73 Time building chain proxies: 2.98, per 1000 atoms: 0.96 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: 0.75 Conformation dependent library (CDL) restraints added in 445.6 milliseconds 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: 0.46 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: 0.85 Time building geometry restraints manager: 0.92 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.410 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.630 ------------------------------------------------------------------------------- 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= 0.164 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 (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: 1.60 (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 TRP 0.021 0.001 TRP C 79 HIS 0.003 0.001 HIS C 88 PHE 0.009 0.001 PHE C 64 TYR 0.008 0.001 TYR D 116 ARG 0.004 0.001 ARG A 34 *********************** 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 : 0.340 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: 0.2057 time to fit residues: 14.1012 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 : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 0.4980 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.167687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.135754 restraints weight = 4889.404| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 3.89 r_work: 0.3857 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3196 Z= 0.232 Angle : 0.546 6.156 4418 Z= 0.285 Chirality : 0.048 0.145 531 Planarity : 0.005 0.044 564 Dihedral : 3.857 17.447 489 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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 (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: 1.31 (0.39), residues: 457 helix: 0.48 (0.80), residues: 40 sheet: 1.52 (0.35), residues: 217 loop : 0.29 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 79 HIS 0.002 0.001 HIS C 31 PHE 0.011 0.001 PHE B 44 TYR 0.016 0.002 TYR D 78 ARG 0.003 0.001 ARG A 34 *********************** 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 64 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.354 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 59 average time/residue: 0.2089 time to fit residues: 14.3611 Evaluate side-chains 58 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 23 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 22 optimal weight: 0.2980 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.166307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.134781 restraints weight = 4865.537| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 3.83 r_work: 0.3847 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1819 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= 0.216 Angle : 0.532 6.968 4418 Z= 0.269 Chirality : 0.047 0.142 531 Planarity : 0.005 0.046 564 Dihedral : 3.841 16.951 489 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 5.05 % Allowed : 12.84 % 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 (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: 1.09 (0.39), residues: 457 helix: 0.59 (0.79), residues: 40 sheet: 1.28 (0.35), residues: 221 loop : 0.19 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 79 HIS 0.002 0.001 HIS D 31 PHE 0.020 0.001 PHE B 44 TYR 0.014 0.001 TYR D 78 ARG 0.003 0.000 ARG A 34 *********************** 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 68 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.318 Fit side-chains REVERT: A 34 ARG cc_start: 0.7870 (ttt-90) cc_final: 0.7484 (tpt90) REVERT: B 34 ARG cc_start: 0.7667 (tmt170) cc_final: 0.7436 (ttt-90) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 0.2082 time to fit residues: 14.2419 Evaluate side-chains 64 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 12 LEU 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 1 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.169292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.137795 restraints weight = 4872.654| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.84 r_work: 0.3887 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2038 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= 0.149 Angle : 0.492 6.062 4418 Z= 0.246 Chirality : 0.046 0.134 531 Planarity : 0.005 0.046 564 Dihedral : 3.500 14.669 489 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.67 % Allowed : 14.68 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.39), residues: 457 helix: 0.69 (0.80), residues: 40 sheet: 1.25 (0.35), residues: 223 loop : 0.25 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 79 HIS 0.002 0.001 HIS D 90 PHE 0.008 0.001 PHE B 44 TYR 0.015 0.001 TYR D 78 ARG 0.003 0.000 ARG A 34 *********************** 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: 8 poor density : 58 time to evaluate : 0.316 Fit side-chains REVERT: A 34 ARG cc_start: 0.7817 (ttt-90) cc_final: 0.7491 (tpt90) outliers start: 8 outliers final: 8 residues processed: 59 average time/residue: 0.2205 time to fit residues: 14.9335 Evaluate side-chains 62 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 110 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 31 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 0.0040 chunk 42 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 overall best weight: 3.7998 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.161199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.128202 restraints weight = 4985.043| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.91 r_work: 0.3643 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3196 Z= 0.382 Angle : 0.603 6.161 4418 Z= 0.311 Chirality : 0.049 0.146 531 Planarity : 0.006 0.052 564 Dihedral : 4.325 17.866 489 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 6.42 % Allowed : 14.22 % Favored : 79.36 % 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: 0.56 (0.39), residues: 457 helix: 0.48 (0.78), residues: 40 sheet: 0.71 (0.35), residues: 222 loop : 0.09 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 79 HIS 0.002 0.001 HIS D 31 PHE 0.015 0.002 PHE C 33 TYR 0.022 0.002 TYR D 78 ARG 0.002 0.000 ARG A 34 *********************** 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 68 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.361 Fit side-chains REVERT: A 34 ARG cc_start: 0.7949 (ttt-90) cc_final: 0.7544 (tpt90) outliers start: 14 outliers final: 13 residues processed: 58 average time/residue: 0.1981 time to fit residues: 13.4813 Evaluate side-chains 66 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 D residue 110 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 7.9990 chunk 16 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.0000 chunk 5 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- 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 = 0.4375 r_free = 0.4375 target = 0.168717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.136780 restraints weight = 5025.245| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 3.88 r_work: 0.3734 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3196 Z= 0.145 Angle : 0.505 6.634 4418 Z= 0.251 Chirality : 0.046 0.134 531 Planarity : 0.005 0.048 564 Dihedral : 3.569 15.438 489 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.96 % Allowed : 16.06 % Favored : 77.98 % 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: 0.77 (0.39), residues: 457 helix: 0.66 (0.80), residues: 40 sheet: 0.91 (0.35), residues: 223 loop : 0.13 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 79 HIS 0.002 0.001 HIS D 90 PHE 0.006 0.001 PHE B 33 TYR 0.021 0.001 TYR D 78 ARG 0.003 0.000 ARG A 34 *********************** 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 70 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.364 Fit side-chains REVERT: A 34 ARG cc_start: 0.7851 (ttt-90) cc_final: 0.7554 (tpt90) outliers start: 13 outliers final: 11 residues processed: 62 average time/residue: 0.2148 time to fit residues: 15.7973 Evaluate side-chains 66 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 0.0010 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- 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 = 0.4359 r_free = 0.4359 target = 0.167267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.135500 restraints weight = 4924.082| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.83 r_work: 0.3721 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2600 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= 0.186 Angle : 0.511 6.169 4418 Z= 0.257 Chirality : 0.046 0.135 531 Planarity : 0.005 0.051 564 Dihedral : 3.618 16.572 489 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 5.96 % Allowed : 17.43 % Favored : 76.61 % 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: 0.78 (0.40), residues: 457 helix: 0.77 (0.81), residues: 40 sheet: 0.90 (0.35), residues: 223 loop : 0.13 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 79 HIS 0.001 0.000 HIS D 90 PHE 0.006 0.001 PHE B 33 TYR 0.016 0.002 TYR D 78 ARG 0.003 0.000 ARG A 103 *********************** 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 67 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.311 Fit side-chains REVERT: A 34 ARG cc_start: 0.7863 (ttt-90) cc_final: 0.7537 (tpt90) outliers start: 13 outliers final: 12 residues processed: 58 average time/residue: 0.1840 time to fit residues: 12.5242 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 : 0.351 ------------------------------------------------------------------------------- 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 B residue 121 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 9 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 4 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4402 r_free = 0.4402 target = 0.171290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.140063 restraints weight = 4926.115| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.78 r_work: 0.3779 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3196 Z= 0.132 Angle : 0.485 6.568 4418 Z= 0.240 Chirality : 0.046 0.128 531 Planarity : 0.005 0.055 564 Dihedral : 3.278 14.215 489 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.50 % Allowed : 18.35 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.40), residues: 457 helix: 0.95 (0.84), residues: 40 sheet: 0.95 (0.35), residues: 223 loop : 0.21 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 79 HIS 0.002 0.000 HIS D 90 PHE 0.004 0.001 PHE C 87 TYR 0.017 0.001 TYR D 78 ARG 0.003 0.001 ARG A 103 *********************** 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 66 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.309 Fit side-chains REVERT: A 34 ARG cc_start: 0.7803 (ttt-90) cc_final: 0.7525 (tpt90) outliers start: 12 outliers final: 11 residues processed: 58 average time/residue: 0.1935 time to fit residues: 13.1834 Evaluate side-chains 64 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 12 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 118 THR Chi-restraints excluded: chain B residue 121 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 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.4352 r_free = 0.4352 target = 0.166658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.134965 restraints weight = 4933.528| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.82 r_work: 0.3714 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3196 Z= 0.206 Angle : 0.512 6.194 4418 Z= 0.259 Chirality : 0.046 0.135 531 Planarity : 0.005 0.053 564 Dihedral : 3.555 16.253 489 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 5.50 % Allowed : 18.35 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.40), residues: 457 helix: 0.86 (0.82), residues: 40 sheet: 0.88 (0.35), residues: 223 loop : 0.20 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 79 HIS 0.001 0.000 HIS D 31 PHE 0.007 0.001 PHE B 33 TYR 0.017 0.002 TYR B 116 ARG 0.003 0.000 ARG A 103 *********************** 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 65 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.352 Fit side-chains REVERT: A 34 ARG cc_start: 0.7863 (ttt-90) cc_final: 0.7546 (tpt90) outliers start: 12 outliers final: 12 residues processed: 58 average time/residue: 0.1925 time to fit residues: 13.1799 Evaluate side-chains 64 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 10 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.156031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.123232 restraints weight = 4999.285| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 3.90 r_work: 0.3588 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.047 3196 Z= 0.594 Angle : 0.712 6.777 4418 Z= 0.379 Chirality : 0.052 0.173 531 Planarity : 0.006 0.054 564 Dihedral : 5.029 21.666 489 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 6.42 % Allowed : 17.89 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.38), residues: 457 helix: 0.07 (0.79), residues: 40 sheet: 0.02 (0.35), residues: 207 loop : -0.26 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 79 HIS 0.005 0.001 HIS D 31 PHE 0.024 0.003 PHE C 33 TYR 0.019 0.003 TYR D 69 ARG 0.002 0.001 ARG D 21 ********************** 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 64 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.351 Fit side-chains REVERT: A 34 ARG cc_start: 0.8003 (ttt-90) cc_final: 0.7577 (tpt90) outliers start: 14 outliers final: 14 residues processed: 58 average time/residue: 0.1881 time to fit residues: 13.1502 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 : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 8 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4352 r_free = 0.4352 target = 0.165326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.132569 restraints weight = 4869.154| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.88 r_work: 0.3849 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3196 Z= 0.161 Angle : 0.529 7.877 4418 Z= 0.263 Chirality : 0.047 0.132 531 Planarity : 0.005 0.058 564 Dihedral : 3.734 17.600 489 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 5.50 % Allowed : 19.72 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.38), residues: 457 helix: 0.49 (0.81), residues: 40 sheet: 0.33 (0.34), residues: 221 loop : -0.11 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 79 HIS 0.003 0.001 HIS D 90 PHE 0.008 0.001 PHE C 87 TYR 0.016 0.001 TYR D 78 ARG 0.003 0.001 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2044.60 seconds wall clock time: 35 minutes 41.86 seconds (2141.86 seconds total)