Starting phenix.real_space_refine on Wed Sep 17 03:54:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ve0_43160/09_2025/8ve0_43160.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ve0_43160/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ve0_43160/09_2025/8ve0_43160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ve0_43160/09_2025/8ve0_43160.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ve0_43160/09_2025/8ve0_43160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ve0_43160/09_2025/8ve0_43160.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 4} 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: {'ASP:plan': 1, 'GLU:plan': 3} 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: {'ASP:plan': 1, 'GLU:plan': 4} 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: {'ASP:plan': 1, 'GLU:plan': 3, 'ARG: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: 1.30, per 1000 atoms: 0.37 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: 0.32 Conformation dependent library (CDL) restraints added in 138.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.14 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: 0.43 Time building geometry restraints manager: 0.42 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.490 Find NCS groups from input model: 0.050 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.870 ------------------------------------------------------------------------------- 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 3626 Z= 0.303 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 : 6.10 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (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 ARG 0.004 0.001 ARG C 103 TYR 0.017 0.001 TYR B 78 PHE 0.009 0.001 PHE A 64 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.000 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 3624) covalent geometry : angle 0.62076 ( 4957) hydrogen bonds : bond 0.22681 ( 133) hydrogen bonds : angle 9.06418 ( 375) Misc. bond : bond 0.04348 ( 2) *********************** 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 : 0.147 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: 0.0785 time to fit residues: 8.7725 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 : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.155752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.132004 restraints weight = 4963.368| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.68 r_work: 0.3589 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3626 Z= 0.124 Angle : 0.521 4.727 4957 Z= 0.272 Chirality : 0.047 0.137 565 Planarity : 0.004 0.031 627 Dihedral : 5.724 66.865 503 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.85 % Allowed : 9.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.38), residues: 458 helix: 1.41 (0.92), residues: 36 sheet: 2.47 (0.33), residues: 232 loop : -0.78 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 103 TYR 0.010 0.001 TYR B 116 PHE 0.009 0.001 PHE B 44 TRP 0.005 0.001 TRP A 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3624) covalent geometry : angle 0.52133 ( 4957) hydrogen bonds : bond 0.03774 ( 133) hydrogen bonds : angle 6.80967 ( 375) Misc. bond : bond 0.00081 ( 2) *********************** 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 85 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.139 Fit side-chains REVERT: C 44 PHE cc_start: 0.8092 (t80) cc_final: 0.7734 (t80) REVERT: D 54 GLU cc_start: 0.6077 (pm20) cc_final: 0.5876 (pm20) outliers start: 3 outliers final: 3 residues processed: 83 average time/residue: 0.0897 time to fit residues: 8.7801 Evaluate side-chains 80 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 13 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.155869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.132316 restraints weight = 4947.077| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.67 r_work: 0.3592 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3626 Z= 0.108 Angle : 0.477 4.086 4957 Z= 0.250 Chirality : 0.047 0.140 565 Planarity : 0.004 0.032 627 Dihedral : 5.372 65.640 503 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.42 % Allowed : 12.82 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.38), residues: 458 helix: 1.59 (0.94), residues: 36 sheet: 2.37 (0.33), residues: 233 loop : -0.89 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 21 TYR 0.009 0.001 TYR D 116 PHE 0.007 0.001 PHE A 64 TRP 0.005 0.001 TRP A 79 HIS 0.002 0.000 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 3624) covalent geometry : angle 0.47748 ( 4957) hydrogen bonds : bond 0.03327 ( 133) hydrogen bonds : angle 6.37025 ( 375) Misc. bond : bond 0.00062 ( 2) *********************** 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 87 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.140 Fit side-chains REVERT: C 44 PHE cc_start: 0.8097 (t80) cc_final: 0.7689 (t80) outliers start: 5 outliers final: 3 residues processed: 84 average time/residue: 0.0940 time to fit residues: 9.2343 Evaluate side-chains 79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain D residue 20 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 12 optimal weight: 0.0170 chunk 3 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.155314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.132150 restraints weight = 4909.697| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.63 r_work: 0.3589 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3626 Z= 0.105 Angle : 0.476 4.336 4957 Z= 0.246 Chirality : 0.047 0.140 565 Planarity : 0.004 0.047 627 Dihedral : 5.146 60.798 503 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.42 % Allowed : 15.67 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.38), residues: 458 helix: 1.68 (0.94), residues: 36 sheet: 2.32 (0.34), residues: 227 loop : -0.90 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 21 TYR 0.010 0.001 TYR D 116 PHE 0.006 0.001 PHE A 64 TRP 0.006 0.001 TRP A 79 HIS 0.002 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3624) covalent geometry : angle 0.47577 ( 4957) hydrogen bonds : bond 0.02923 ( 133) hydrogen bonds : angle 6.08595 ( 375) Misc. bond : bond 0.00049 ( 2) *********************** 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: 5 poor density : 83 time to evaluate : 0.113 Fit side-chains REVERT: C 44 PHE cc_start: 0.8111 (t80) cc_final: 0.7701 (t80) REVERT: D 54 GLU cc_start: 0.6038 (pm20) cc_final: 0.5722 (pm20) outliers start: 5 outliers final: 4 residues processed: 84 average time/residue: 0.0973 time to fit residues: 9.4714 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 : 0.139 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 2 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 0.0770 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 0.0010 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 overall best weight: 0.5944 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.157257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.134162 restraints weight = 5010.714| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.65 r_work: 0.3619 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3626 Z= 0.086 Angle : 0.442 4.599 4957 Z= 0.230 Chirality : 0.046 0.138 565 Planarity : 0.004 0.052 627 Dihedral : 5.014 66.417 503 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.71 % Allowed : 17.09 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.38), residues: 458 helix: 1.44 (0.94), residues: 36 sheet: 2.42 (0.34), residues: 227 loop : -0.87 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 21 TYR 0.010 0.001 TYR D 116 PHE 0.005 0.001 PHE B 44 TRP 0.004 0.001 TRP A 79 HIS 0.001 0.000 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 3624) covalent geometry : angle 0.44206 ( 4957) hydrogen bonds : bond 0.02577 ( 133) hydrogen bonds : angle 5.73471 ( 375) Misc. bond : bond 0.00037 ( 2) *********************** 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 87 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.135 Fit side-chains REVERT: C 44 PHE cc_start: 0.8104 (t80) cc_final: 0.7750 (t80) REVERT: D 54 GLU cc_start: 0.6048 (pm20) cc_final: 0.5669 (pm20) outliers start: 6 outliers final: 4 residues processed: 83 average time/residue: 0.0937 time to fit residues: 9.1081 Evaluate side-chains 79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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 17 LEU Chi-restraints excluded: chain D residue 20 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.152863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.129122 restraints weight = 5010.773| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.69 r_work: 0.3549 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3626 Z= 0.146 Angle : 0.506 5.187 4957 Z= 0.261 Chirality : 0.048 0.143 565 Planarity : 0.004 0.061 627 Dihedral : 5.344 63.068 503 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.13 % Allowed : 16.24 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.39), residues: 458 helix: 1.43 (0.96), residues: 36 sheet: 2.15 (0.34), residues: 227 loop : -0.91 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 21 TYR 0.011 0.001 TYR D 116 PHE 0.008 0.001 PHE A 64 TRP 0.008 0.001 TRP A 79 HIS 0.003 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3624) covalent geometry : angle 0.50587 ( 4957) hydrogen bonds : bond 0.03155 ( 133) hydrogen bonds : angle 6.24515 ( 375) Misc. bond : bond 0.00044 ( 2) *********************** 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 : 0.135 Fit side-chains REVERT: C 44 PHE cc_start: 0.8130 (t80) cc_final: 0.7711 (t80) REVERT: D 54 GLU cc_start: 0.6138 (pm20) cc_final: 0.5935 (pm20) outliers start: 11 outliers final: 6 residues processed: 84 average time/residue: 0.0900 time to fit residues: 8.8909 Evaluate side-chains 79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.090 ------------------------------------------------------------------------------- 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 74 ASP 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 33 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.154443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.130851 restraints weight = 5036.376| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.68 r_work: 0.3573 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3626 Z= 0.111 Angle : 0.477 5.679 4957 Z= 0.248 Chirality : 0.047 0.140 565 Planarity : 0.004 0.061 627 Dihedral : 5.172 63.129 503 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.99 % Allowed : 17.95 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.38), residues: 458 helix: 1.20 (0.93), residues: 36 sheet: 2.15 (0.33), residues: 226 loop : -0.91 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 21 TYR 0.010 0.001 TYR D 116 PHE 0.006 0.001 PHE A 64 TRP 0.007 0.001 TRP A 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3624) covalent geometry : angle 0.47722 ( 4957) hydrogen bonds : bond 0.02756 ( 133) hydrogen bonds : angle 6.03328 ( 375) Misc. bond : bond 0.00038 ( 2) *********************** 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 88 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.144 Fit side-chains REVERT: A 55 LEU cc_start: 0.7196 (mt) cc_final: 0.6996 (mt) REVERT: C 44 PHE cc_start: 0.8143 (t80) cc_final: 0.7727 (t80) REVERT: D 54 GLU cc_start: 0.6164 (pm20) cc_final: 0.5947 (pm20) outliers start: 7 outliers final: 4 residues processed: 85 average time/residue: 0.0978 time to fit residues: 9.6702 Evaluate side-chains 81 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 74 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 0.0370 chunk 31 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 1.2062 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.153726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.130342 restraints weight = 5049.201| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.68 r_work: 0.3570 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3626 Z= 0.118 Angle : 0.494 6.217 4957 Z= 0.255 Chirality : 0.047 0.140 565 Planarity : 0.004 0.063 627 Dihedral : 5.238 65.066 503 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.56 % Allowed : 17.09 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.38), residues: 458 helix: 1.26 (0.94), residues: 36 sheet: 2.12 (0.33), residues: 226 loop : -0.89 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 21 TYR 0.010 0.001 TYR D 116 PHE 0.007 0.001 PHE A 64 TRP 0.007 0.001 TRP A 79 HIS 0.002 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3624) covalent geometry : angle 0.49408 ( 4957) hydrogen bonds : bond 0.02795 ( 133) hydrogen bonds : angle 6.04654 ( 375) Misc. bond : bond 0.00039 ( 2) *********************** 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 85 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.129 Fit side-chains REVERT: C 44 PHE cc_start: 0.8144 (t80) cc_final: 0.7722 (t80) REVERT: D 54 GLU cc_start: 0.6144 (pm20) cc_final: 0.5913 (pm20) outliers start: 9 outliers final: 5 residues processed: 82 average time/residue: 0.1011 time to fit residues: 9.6395 Evaluate side-chains 81 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 17 LEU 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 22 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.151759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.129060 restraints weight = 4936.865| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.55 r_work: 0.3548 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3626 Z= 0.148 Angle : 0.538 6.816 4957 Z= 0.276 Chirality : 0.048 0.144 565 Planarity : 0.005 0.066 627 Dihedral : 5.436 63.995 503 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.56 % Allowed : 17.66 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.39), residues: 458 helix: 1.29 (0.96), residues: 36 sheet: 1.98 (0.33), residues: 226 loop : -1.01 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 34 TYR 0.010 0.002 TYR D 116 PHE 0.009 0.001 PHE A 64 TRP 0.009 0.001 TRP A 79 HIS 0.003 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 3624) covalent geometry : angle 0.53810 ( 4957) hydrogen bonds : bond 0.03091 ( 133) hydrogen bonds : angle 6.30713 ( 375) Misc. bond : bond 0.00040 ( 2) *********************** 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 85 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.140 Fit side-chains REVERT: C 44 PHE cc_start: 0.8168 (t80) cc_final: 0.7735 (t80) REVERT: D 54 GLU cc_start: 0.6153 (pm20) cc_final: 0.5920 (pm20) outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.1020 time to fit residues: 9.5924 Evaluate side-chains 81 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 74 ASP Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.152023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128665 restraints weight = 5064.663| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.64 r_work: 0.3540 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3626 Z= 0.147 Angle : 0.545 7.573 4957 Z= 0.278 Chirality : 0.048 0.146 565 Planarity : 0.005 0.066 627 Dihedral : 5.437 63.743 503 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.71 % Allowed : 18.52 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.39), residues: 458 helix: 1.18 (0.95), residues: 36 sheet: 1.91 (0.34), residues: 226 loop : -1.05 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 104 TYR 0.010 0.001 TYR D 116 PHE 0.009 0.001 PHE A 64 TRP 0.009 0.001 TRP A 79 HIS 0.004 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3624) covalent geometry : angle 0.54511 ( 4957) hydrogen bonds : bond 0.03053 ( 133) hydrogen bonds : angle 6.32377 ( 375) Misc. bond : bond 0.00041 ( 2) ********************** 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 82 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.142 Fit side-chains REVERT: C 44 PHE cc_start: 0.8167 (t80) cc_final: 0.7713 (t80) REVERT: D 54 GLU cc_start: 0.6140 (pm20) cc_final: 0.5911 (pm20) REVERT: D 84 ILE cc_start: 0.8099 (mt) cc_final: 0.7879 (mt) outliers start: 6 outliers final: 6 residues processed: 80 average time/residue: 0.1056 time to fit residues: 9.7977 Evaluate side-chains 82 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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 74 ASP Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.150352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.126954 restraints weight = 5032.035| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.64 r_work: 0.3513 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 : 0.004 0.028 3626 Z= 0.179 Angle : 0.584 7.270 4957 Z= 0.297 Chirality : 0.049 0.145 565 Planarity : 0.005 0.069 627 Dihedral : 5.628 63.090 503 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.99 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.38), residues: 458 helix: 1.21 (0.95), residues: 36 sheet: 1.81 (0.34), residues: 220 loop : -1.17 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 104 TYR 0.011 0.002 TYR C 69 PHE 0.011 0.002 PHE A 64 TRP 0.011 0.002 TRP A 79 HIS 0.004 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 3624) covalent geometry : angle 0.58358 ( 4957) hydrogen bonds : bond 0.03368 ( 133) hydrogen bonds : angle 6.55066 ( 375) Misc. bond : bond 0.00044 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1019.52 seconds wall clock time: 18 minutes 11.07 seconds (1091.07 seconds total)