Starting phenix.real_space_refine on Mon Jan 13 18:28:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ve0_43160/01_2025/8ve0_43160.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ve0_43160/01_2025/8ve0_43160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ve0_43160/01_2025/8ve0_43160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ve0_43160/01_2025/8ve0_43160.map" model { file = "/net/cci-nas-00/data/ceres_data/8ve0_43160/01_2025/8ve0_43160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ve0_43160/01_2025/8ve0_43160.cif" } resolution = 3.1 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= 0.002 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 7 5.16 5 C 2281 2.51 5 N 588 2.21 5 O 651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3527 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 863 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 875 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 108} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 878 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 867 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'1WZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'1WZ:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'1WZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'1WZ:plan-4': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.10, per 1000 atoms: 0.88 Number of scatterers: 3527 At special positions: 0 Unit cell: (77.556, 68.002, 61.82, 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 7 16.00 O 651 8.00 N 588 7.00 C 2281 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 479.8 milliseconds 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 876 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 5 sheets defined 8.4% alpha, 44.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 74 through 83 removed outlier: 4.113A pdb=" N TYR A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 83 removed outlier: 4.006A pdb=" N TYR B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'D' and resid 74 through 83 removed outlier: 3.984A pdb=" N TYR D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 82 " --> pdb=" O TYR D 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.577A pdb=" N VAL A 14 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.204A pdb=" N MET A 13 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA A 109 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS A 15 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A 111 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N MET B 13 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA B 109 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS B 15 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU B 111 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 17 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 48 removed outlier: 6.596A pdb=" N VAL A 32 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A 46 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 30 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE A 68 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 67 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL B 94 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA A 91 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N GLU B 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 93 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N HIS B 90 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE A 95 " --> pdb=" O HIS B 88 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N HIS B 88 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 67 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE B 68 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 30 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER B 46 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 32 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.333A pdb=" N MET C 13 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ALA C 109 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS C 15 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU C 111 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 17 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET D 13 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ALA D 109 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS D 15 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU D 111 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU D 17 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 4.153A 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: 5.657A pdb=" N ARG C 34 " --> pdb=" O PRO C 43 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA C 29 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE C 68 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N HIS C 88 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE D 95 " --> pdb=" O HIS C 88 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N HIS C 90 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL D 93 " --> pdb=" O HIS C 90 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N GLU C 92 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA D 91 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N VAL C 94 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU D 89 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE D 68 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ARG D 34 " --> pdb=" O PRO D 43 " (cutoff:3.500A) 135 hydrogen bonds defined for protein. 375 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: 0.96 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 559 1.31 - 1.44: 1036 1.44 - 1.56: 2017 1.56 - 1.68: 2 1.68 - 1.81: 10 Bond restraints: 3624 Sorted by residual: bond pdb=" CAH 1WZ C 201 " pdb=" CAR 1WZ C 201 " ideal model delta sigma weight residual 1.461 1.570 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" CAH 1WZ B 201 " pdb=" CAR 1WZ B 201 " ideal model delta sigma weight residual 1.461 1.569 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" CAV 1WZ B 201 " pdb=" NAW 1WZ B 201 " ideal model delta sigma weight residual 1.376 1.473 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" CAV 1WZ C 201 " pdb=" NAW 1WZ C 201 " ideal model delta sigma weight residual 1.376 1.472 -0.096 2.00e-02 2.50e+03 2.33e+01 bond pdb=" CAI 1WZ B 201 " pdb=" CAS 1WZ B 201 " ideal model delta sigma weight residual 1.464 1.548 -0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 3619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 4877 2.05 - 4.10: 72 4.10 - 6.16: 4 6.16 - 8.21: 2 8.21 - 10.26: 2 Bond angle restraints: 4957 Sorted by residual: angle pdb=" CAH 1WZ B 201 " pdb=" CAI 1WZ B 201 " pdb=" CAS 1WZ B 201 " ideal model delta sigma weight residual 126.24 115.98 10.26 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CAH 1WZ C 201 " pdb=" CAI 1WZ C 201 " pdb=" CAS 1WZ C 201 " ideal model delta sigma weight residual 126.24 116.06 10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CA LYS C 15 " pdb=" CB LYS C 15 " pdb=" CG LYS C 15 " ideal model delta sigma weight residual 114.10 108.33 5.77 2.00e+00 2.50e-01 8.32e+00 angle pdb=" CB LYS C 80 " pdb=" CG LYS C 80 " pdb=" CD LYS C 80 " ideal model delta sigma weight residual 111.30 117.06 -5.76 2.30e+00 1.89e-01 6.27e+00 angle pdb=" N GLY C 67 " pdb=" CA GLY C 67 " pdb=" C GLY C 67 " ideal model delta sigma weight residual 110.29 113.46 -3.17 1.28e+00 6.10e-01 6.12e+00 ... (remaining 4952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 1914 16.46 - 32.92: 135 32.92 - 49.38: 32 49.38 - 65.84: 8 65.84 - 82.30: 6 Dihedral angle restraints: 2095 sinusoidal: 737 harmonic: 1358 Sorted by residual: dihedral pdb=" CA LYS B 15 " pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " pdb=" CD LYS B 15 " ideal model delta sinusoidal sigma weight residual -180.00 -126.43 -53.57 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N LYS C 15 " pdb=" CA LYS C 15 " pdb=" CB LYS C 15 " pdb=" CG LYS C 15 " ideal model delta sinusoidal sigma weight residual -180.00 -129.56 -50.44 3 1.50e+01 4.44e-03 8.90e+00 dihedral pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " pdb=" CD LYS B 15 " pdb=" CE LYS B 15 " ideal model delta sinusoidal sigma weight residual 60.00 10.16 49.84 3 1.50e+01 4.44e-03 8.83e+00 ... (remaining 2092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 331 0.026 - 0.052: 126 0.052 - 0.078: 39 0.078 - 0.104: 32 0.104 - 0.130: 37 Chirality restraints: 565 Sorted by residual: chirality pdb=" CA ILE A 73 " pdb=" N ILE A 73 " pdb=" C ILE A 73 " pdb=" CB ILE A 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-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 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE B 73 " pdb=" N ILE B 73 " pdb=" C ILE B 73 " pdb=" CB ILE B 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 562 not shown) Planarity restraints: 627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 112 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO D 113 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 113 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 113 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 112 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO B 113 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 23 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO C 24 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 24 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 24 " 0.015 5.00e-02 4.00e+02 ... (remaining 624 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 552 2.77 - 3.30: 3069 3.30 - 3.83: 5878 3.83 - 4.37: 6612 4.37 - 4.90: 12422 Nonbonded interactions: 28533 Sorted by model distance: nonbonded pdb=" OD2 ASP A 74 " pdb=" OG SER A 77 " model vdw 2.234 3.040 nonbonded pdb=" O VAL B 65 " pdb=" OH TYR B 69 " model vdw 2.238 3.040 nonbonded pdb=" OD2 ASP D 18 " pdb=" OH TYR D 78 " model vdw 2.256 3.040 nonbonded pdb=" OG SER A 117 " pdb=" OAG 1WZ C 201 " model vdw 2.310 3.040 nonbonded pdb=" OE2 GLU C 89 " pdb=" OG1 THR D 96 " model vdw 2.329 3.040 ... (remaining 28528 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 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 62 or (resid 63 and ( \ name N or name CA or name C or name O or name CB )) or resid 64 or (resid 65 thr \ ough 66 and (name N or name CA or name C or name O or name CB )) or resid 67 thr \ ough 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) or \ resid 78 through 91 or (resid 92 and (name N or name CA or name C or name O or \ name CB )) or resid 93 through 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 103 or (resid 104 and (na \ me N or name CA or name C or name O or name CB )) or resid 105 through 122 or (r \ esid 123 and (name N or name CA or name C or name O or name CB )) or resid 124)) \ selection = (chain 'B' and (resid 10 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 37 or (resid 38 through \ 40 and (name N or name CA or name C or name O or name CB )) or resid 41 or (res \ id 42 and (name N or name CA or name C or name O or name CB )) or resid 43 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 50 or (resid 51 and (name N or name CA or name C or name O or na \ me CB )) or resid 52 through 58 or (resid 59 through 63 and (name N or name CA o \ r name C or name O or name CB )) or resid 64 or (resid 65 through 66 and (name N \ or name CA or name C or name O or name CB )) or resid 67 through 76 or (resid 7 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 78 through 9 \ 8 or (resid 99 through 100 and (name N or name CA or name C or name O or name CB \ )) or resid 101 through 103 or (resid 104 and (name N or name CA or name C or n \ ame O or name CB )) or resid 105 through 122 or (resid 123 and (name N or name C \ A or name C or name O or name CB )) or resid 124)) selection = (chain 'C' 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 25 or (resid 26 through 27 and (na \ me N or name CA or name C or name O or name CB )) or resid 28 through 37 or (res \ id 38 through 40 and (name N or name CA or name C or name O or name CB )) or res \ id 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or r \ esid 43 through 58 or (resid 59 through 63 and (name N or name CA or name C or n \ ame O or name CB )) or resid 64 through 91 or (resid 92 and (name N or name CA o \ r name C or name O or name CB )) or resid 93 through 95 or (resid 96 through 97 \ and (name N or name CA or name C or name O or name CB )) or resid 98 or (resid 9 \ 9 through 100 and (name N or name CA or name C or name O or name CB )) or resid \ 101 through 103 or (resid 104 and (name N or name CA or name C or name O or name \ CB )) or resid 105 through 122 or (resid 123 and (name N or name CA or name C o \ r name O or name CB )) or resid 124)) selection = (chain 'D' 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 25 or (resid 26 through 27 and (na \ me N or name CA or name C or name O or name CB )) or resid 28 through 37 or (res \ id 38 through 40 and (name N or name CA or name C or name O or name CB )) or res \ id 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or r \ esid 43 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 50 or (resid 51 and (name N or name CA or name C or \ name O or name CB )) or resid 52 through 58 or (resid 59 through 63 and (name N \ or name CA or name C or name O or name CB )) or resid 64 through 65 or (resid 6 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 67 through 7 \ 6 or (resid 77 and (name N or name CA or name C or name O or name CB )) or resid \ 78 through 95 or (resid 96 through 97 and (name N or name CA or name C or name \ O or name CB )) or resid 98 or (resid 99 through 100 and (name N or name CA or n \ ame C or name O or name CB )) or resid 101 through 124)) } 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.390 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 3624 Z= 0.396 Angle : 0.621 10.259 4957 Z= 0.318 Chirality : 0.045 0.130 565 Planarity : 0.004 0.040 627 Dihedral : 13.407 82.301 1219 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 0.57 % Allowed : 0.00 % Favored : 99.43 % 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: 1.74 (0.38), residues: 458 helix: 0.66 (0.86), residues: 34 sheet: 2.28 (0.33), residues: 240 loop : -0.36 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.002 0.000 HIS D 90 PHE 0.009 0.001 PHE A 64 TYR 0.017 0.001 TYR B 78 ARG 0.004 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.317 Fit side-chains REVERT: C 44 PHE cc_start: 0.8001 (t80) cc_final: 0.7721 (t80) outliers start: 2 outliers final: 0 residues processed: 94 average time/residue: 0.1818 time to fit residues: 20.3370 Evaluate side-chains 77 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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: 7.9990 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.154758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.131099 restraints weight = 4954.979| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.66 r_work: 0.3574 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3624 Z= 0.208 Angle : 0.531 5.029 4957 Z= 0.278 Chirality : 0.047 0.139 565 Planarity : 0.004 0.031 627 Dihedral : 5.768 66.325 503 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.14 % Allowed : 9.69 % Favored : 89.17 % 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: 1.68 (0.38), residues: 458 helix: 1.41 (0.92), residues: 36 sheet: 2.44 (0.33), residues: 232 loop : -0.78 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 79 HIS 0.002 0.001 HIS A 88 PHE 0.009 0.002 PHE B 44 TYR 0.010 0.001 TYR B 116 ARG 0.003 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.411 Fit side-chains REVERT: C 44 PHE cc_start: 0.8097 (t80) cc_final: 0.7736 (t80) REVERT: D 54 GLU cc_start: 0.6105 (pm20) cc_final: 0.5905 (pm20) outliers start: 4 outliers final: 4 residues processed: 85 average time/residue: 0.1951 time to fit residues: 19.7135 Evaluate side-chains 83 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.154230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.130802 restraints weight = 4910.073| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.65 r_work: 0.3570 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3624 Z= 0.193 Angle : 0.491 4.365 4957 Z= 0.257 Chirality : 0.047 0.142 565 Planarity : 0.004 0.034 627 Dihedral : 5.418 63.152 503 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.99 % Allowed : 13.39 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.38), residues: 458 helix: 1.60 (0.95), residues: 36 sheet: 2.31 (0.33), residues: 226 loop : -0.89 (0.37), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 79 HIS 0.002 0.001 HIS C 56 PHE 0.008 0.001 PHE A 64 TYR 0.009 0.001 TYR D 116 ARG 0.001 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.339 Fit side-chains REVERT: C 44 PHE cc_start: 0.8111 (t80) cc_final: 0.7730 (t80) outliers start: 7 outliers final: 5 residues processed: 85 average time/residue: 0.2030 time to fit residues: 20.3570 Evaluate side-chains 80 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 12 optimal weight: 0.3980 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.150365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126781 restraints weight = 5014.040| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.67 r_work: 0.3511 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3624 Z= 0.305 Angle : 0.554 5.940 4957 Z= 0.287 Chirality : 0.049 0.145 565 Planarity : 0.005 0.059 627 Dihedral : 5.700 61.951 503 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.99 % Allowed : 15.67 % Favored : 82.34 % 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: 1.17 (0.39), residues: 458 helix: 1.56 (0.95), residues: 36 sheet: 1.97 (0.34), residues: 227 loop : -0.95 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.003 0.001 HIS B 31 PHE 0.011 0.002 PHE A 64 TYR 0.010 0.002 TYR D 116 ARG 0.001 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.375 Fit side-chains REVERT: C 44 PHE cc_start: 0.8138 (t80) cc_final: 0.7726 (t80) REVERT: D 54 GLU cc_start: 0.6186 (pm20) cc_final: 0.5916 (pm20) REVERT: D 84 ILE cc_start: 0.8070 (mt) cc_final: 0.7846 (mt) outliers start: 7 outliers final: 6 residues processed: 86 average time/residue: 0.1920 time to fit residues: 19.4889 Evaluate side-chains 80 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.151905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.128490 restraints weight = 5042.280| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.69 r_work: 0.3534 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3624 Z= 0.217 Angle : 0.503 4.831 4957 Z= 0.261 Chirality : 0.047 0.142 565 Planarity : 0.005 0.063 627 Dihedral : 5.507 59.676 503 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.28 % Allowed : 18.23 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.39), residues: 458 helix: 1.47 (0.94), residues: 36 sheet: 1.90 (0.34), residues: 227 loop : -0.99 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 79 HIS 0.002 0.001 HIS D 88 PHE 0.008 0.001 PHE A 64 TYR 0.010 0.001 TYR D 116 ARG 0.002 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.352 Fit side-chains REVERT: C 44 PHE cc_start: 0.8141 (t80) cc_final: 0.7710 (t80) REVERT: D 54 GLU cc_start: 0.6212 (pm20) cc_final: 0.5880 (pm20) outliers start: 8 outliers final: 5 residues processed: 82 average time/residue: 0.1931 time to fit residues: 18.8147 Evaluate side-chains 79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.148669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.125704 restraints weight = 5147.683| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.59 r_work: 0.3499 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3624 Z= 0.436 Angle : 0.634 7.064 4957 Z= 0.328 Chirality : 0.051 0.151 565 Planarity : 0.006 0.073 627 Dihedral : 6.167 67.725 503 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.13 % Allowed : 18.52 % Favored : 78.35 % 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: 0.69 (0.39), residues: 458 helix: 1.28 (0.92), residues: 36 sheet: 1.63 (0.35), residues: 216 loop : -1.07 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 79 HIS 0.005 0.001 HIS B 31 PHE 0.014 0.002 PHE A 64 TYR 0.011 0.002 TYR B 116 ARG 0.003 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.427 Fit side-chains REVERT: B 17 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8139 (mt) REVERT: C 44 PHE cc_start: 0.8197 (t80) cc_final: 0.7735 (t80) REVERT: D 84 ILE cc_start: 0.8192 (mt) cc_final: 0.7946 (mt) outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 0.1847 time to fit residues: 18.5424 Evaluate side-chains 83 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.153322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.130321 restraints weight = 4937.819| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.64 r_work: 0.3563 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3624 Z= 0.155 Angle : 0.486 4.614 4957 Z= 0.252 Chirality : 0.047 0.140 565 Planarity : 0.005 0.063 627 Dihedral : 5.316 55.945 503 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.28 % Allowed : 20.23 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.38), residues: 458 helix: 1.38 (0.93), residues: 36 sheet: 1.78 (0.35), residues: 213 loop : -1.01 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 79 HIS 0.001 0.000 HIS C 56 PHE 0.006 0.001 PHE A 64 TYR 0.009 0.001 TYR D 116 ARG 0.002 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.393 Fit side-chains REVERT: C 44 PHE cc_start: 0.8186 (t80) cc_final: 0.7732 (t80) REVERT: D 54 GLU cc_start: 0.6198 (pm20) cc_final: 0.5971 (pm20) outliers start: 8 outliers final: 4 residues processed: 84 average time/residue: 0.2089 time to fit residues: 20.6237 Evaluate side-chains 80 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 20 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.149300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.126442 restraints weight = 5010.457| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.60 r_work: 0.3504 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3624 Z= 0.292 Angle : 0.558 6.171 4957 Z= 0.290 Chirality : 0.049 0.147 565 Planarity : 0.005 0.068 627 Dihedral : 5.610 56.852 503 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.56 % Allowed : 20.23 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.39), residues: 458 helix: 1.23 (0.93), residues: 36 sheet: 1.62 (0.35), residues: 209 loop : -1.03 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.003 0.001 HIS B 31 PHE 0.010 0.002 PHE A 64 TYR 0.010 0.002 TYR D 116 ARG 0.002 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.423 Fit side-chains REVERT: C 44 PHE cc_start: 0.8188 (t80) cc_final: 0.7738 (t80) REVERT: D 54 GLU cc_start: 0.6170 (pm20) cc_final: 0.5904 (pm20) REVERT: D 84 ILE cc_start: 0.8128 (mt) cc_final: 0.7892 (mt) outliers start: 9 outliers final: 5 residues processed: 85 average time/residue: 0.1963 time to fit residues: 19.8580 Evaluate side-chains 80 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 74 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 21 optimal weight: 0.0570 chunk 40 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.153323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.130446 restraints weight = 4910.463| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.59 r_work: 0.3556 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3624 Z= 0.170 Angle : 0.508 6.659 4957 Z= 0.263 Chirality : 0.047 0.142 565 Planarity : 0.005 0.062 627 Dihedral : 5.207 56.627 503 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.71 % Allowed : 21.37 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.38), residues: 458 helix: 1.33 (0.95), residues: 36 sheet: 1.74 (0.34), residues: 213 loop : -0.99 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 79 HIS 0.002 0.000 HIS D 88 PHE 0.006 0.001 PHE A 64 TYR 0.010 0.001 TYR D 116 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.390 Fit side-chains REVERT: C 44 PHE cc_start: 0.8188 (t80) cc_final: 0.7718 (t80) REVERT: D 54 GLU cc_start: 0.6152 (pm20) cc_final: 0.5867 (pm20) REVERT: D 89 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7243 (mt-10) outliers start: 6 outliers final: 4 residues processed: 87 average time/residue: 0.2106 time to fit residues: 21.6650 Evaluate side-chains 82 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 20 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 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 = 0.3913 r_free = 0.3913 target = 0.147060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.124343 restraints weight = 4974.614| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.56 r_work: 0.3474 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3624 Z= 0.397 Angle : 0.652 8.209 4957 Z= 0.335 Chirality : 0.051 0.158 565 Planarity : 0.006 0.071 627 Dihedral : 5.984 63.886 503 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.71 % Allowed : 21.37 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.39), residues: 458 helix: 1.12 (0.92), residues: 36 sheet: 1.50 (0.35), residues: 221 loop : -1.15 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 79 HIS 0.004 0.001 HIS D 90 PHE 0.014 0.002 PHE B 33 TYR 0.012 0.002 TYR C 69 ARG 0.006 0.001 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.384 Fit side-chains REVERT: C 44 PHE cc_start: 0.8217 (t80) cc_final: 0.7741 (t80) REVERT: D 54 GLU cc_start: 0.6239 (pm20) cc_final: 0.5947 (pm20) REVERT: D 84 ILE cc_start: 0.8217 (mt) cc_final: 0.7988 (mt) REVERT: D 89 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7432 (mt-10) outliers start: 6 outliers final: 5 residues processed: 85 average time/residue: 0.1942 time to fit residues: 19.5623 Evaluate side-chains 84 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 74 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 15 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 5 optimal weight: 0.0170 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.154049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.131137 restraints weight = 4982.423| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.61 r_work: 0.3566 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3624 Z= 0.157 Angle : 0.535 7.216 4957 Z= 0.272 Chirality : 0.048 0.166 565 Planarity : 0.005 0.060 627 Dihedral : 5.268 61.981 503 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.85 % Allowed : 22.51 % Favored : 76.64 % 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: 0.61 (0.38), residues: 458 helix: 0.96 (1.01), residues: 33 sheet: 1.63 (0.34), residues: 213 loop : -1.05 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 79 HIS 0.002 0.001 HIS B 90 PHE 0.005 0.001 PHE D 44 TYR 0.010 0.001 TYR D 116 ARG 0.004 0.000 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2061.74 seconds wall clock time: 37 minutes 26.44 seconds (2246.44 seconds total)