Starting phenix.real_space_refine on Wed Feb 4 01:53:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yq5_39496/02_2026/8yq5_39496.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yq5_39496/02_2026/8yq5_39496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yq5_39496/02_2026/8yq5_39496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yq5_39496/02_2026/8yq5_39496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yq5_39496/02_2026/8yq5_39496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yq5_39496/02_2026/8yq5_39496.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.087 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 35 5.16 5 C 5571 2.51 5 N 1283 2.21 5 O 1369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8258 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1636 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1637 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1651 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1651 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1607 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 20 Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 1.88, per 1000 atoms: 0.23 Number of scatterers: 8258 At special positions: 0 Unit cell: (78.264, 78.264, 121.744, 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 35 16.00 O 1369 8.00 N 1283 7.00 C 5571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 345.2 milliseconds 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 74.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 53 through 67 removed outlier: 3.691A pdb=" N PHE E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR E 59 " --> pdb=" O GLN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 88 Processing helix chain 'E' and resid 90 through 105 Processing helix chain 'E' and resid 109 through 139 Processing helix chain 'E' and resid 141 through 173 removed outlier: 3.536A pdb=" N GLU E 173 " --> pdb=" O ARG E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 208 removed outlier: 3.568A pdb=" N LEU E 208 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 22 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 55 through 67 removed outlier: 4.316A pdb=" N TYR D 59 " --> pdb=" O GLN D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 90 through 104 Processing helix chain 'D' and resid 110 through 139 Processing helix chain 'D' and resid 141 through 174 Processing helix chain 'D' and resid 175 through 208 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 55 through 67 removed outlier: 4.361A pdb=" N TYR C 59 " --> pdb=" O GLN C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 90 through 105 Processing helix chain 'C' and resid 109 through 139 Processing helix chain 'C' and resid 141 through 173 removed outlier: 3.620A pdb=" N GLU C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 208 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 90 through 105 Processing helix chain 'B' and resid 109 through 139 Processing helix chain 'B' and resid 141 through 172 Processing helix chain 'B' and resid 175 through 208 removed outlier: 3.785A pdb=" N LEU B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 53 through 67 removed outlier: 3.797A pdb=" N PHE A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.521A pdb=" N LEU A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 104 Processing helix chain 'A' and resid 110 through 139 Processing helix chain 'A' and resid 141 through 174 Processing helix chain 'A' and resid 175 through 208 removed outlier: 3.831A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 12 through 16 removed outlier: 4.512A pdb=" N VAL E 40 " --> pdb=" O PHE E 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.222A pdb=" N VAL D 40 " --> pdb=" O PHE D 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 12 through 16 removed outlier: 4.278A pdb=" N VAL C 40 " --> pdb=" O PHE C 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 17 removed outlier: 3.622A pdb=" N HIS B 47 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL B 40 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 12 through 17 removed outlier: 4.376A pdb=" N VAL A 40 " --> pdb=" O PHE A 49 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1896 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: 0.92 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2450 1.34 - 1.46: 1515 1.46 - 1.58: 4377 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 8412 Sorted by residual: bond pdb=" CB GLU B 104 " pdb=" CG GLU B 104 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.95e-01 bond pdb=" C11 LMT B 301 " pdb=" C12 LMT B 301 " ideal model delta sigma weight residual 1.522 1.503 0.019 2.00e-02 2.50e+03 8.90e-01 bond pdb=" C8 LMT E 301 " pdb=" C9 LMT E 301 " ideal model delta sigma weight residual 1.531 1.513 0.018 2.00e-02 2.50e+03 8.16e-01 bond pdb=" C11 LMT A 301 " pdb=" C12 LMT A 301 " ideal model delta sigma weight residual 1.522 1.504 0.018 2.00e-02 2.50e+03 7.96e-01 bond pdb=" C11 LMT E 301 " pdb=" C12 LMT E 301 " ideal model delta sigma weight residual 1.522 1.504 0.018 2.00e-02 2.50e+03 7.80e-01 ... (remaining 8407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 11135 1.83 - 3.67: 139 3.67 - 5.50: 54 5.50 - 7.33: 19 7.33 - 9.17: 3 Bond angle restraints: 11350 Sorted by residual: angle pdb=" C6 LMT A 301 " pdb=" C7 LMT A 301 " pdb=" C8 LMT A 301 " ideal model delta sigma weight residual 117.26 108.09 9.17 3.00e+00 1.11e-01 9.34e+00 angle pdb=" C10 LMT B 301 " pdb=" C9 LMT B 301 " pdb=" C8 LMT B 301 " ideal model delta sigma weight residual 116.03 108.22 7.81 3.00e+00 1.11e-01 6.78e+00 angle pdb=" C6 LMT C 301 " pdb=" C7 LMT C 301 " pdb=" C8 LMT C 301 " ideal model delta sigma weight residual 117.26 109.70 7.56 3.00e+00 1.11e-01 6.35e+00 angle pdb=" CB LYS C 140 " pdb=" CG LYS C 140 " pdb=" CD LYS C 140 " ideal model delta sigma weight residual 111.30 117.02 -5.72 2.30e+00 1.89e-01 6.18e+00 angle pdb=" CB LYS A 86 " pdb=" CG LYS A 86 " pdb=" CD LYS A 86 " ideal model delta sigma weight residual 111.30 105.60 5.70 2.30e+00 1.89e-01 6.13e+00 ... (remaining 11345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 4514 16.02 - 32.04: 415 32.04 - 48.06: 85 48.06 - 64.07: 20 64.07 - 80.09: 2 Dihedral angle restraints: 5036 sinusoidal: 2033 harmonic: 3003 Sorted by residual: dihedral pdb=" CB MET A 205 " pdb=" CG MET A 205 " pdb=" SD MET A 205 " pdb=" CE MET A 205 " ideal model delta sinusoidal sigma weight residual 60.00 117.59 -57.59 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA GLU D 173 " pdb=" C GLU D 173 " pdb=" N GLY D 174 " pdb=" CA GLY D 174 " ideal model delta harmonic sigma weight residual 180.00 165.30 14.70 0 5.00e+00 4.00e-02 8.65e+00 dihedral pdb=" CG ARG C 169 " pdb=" CD ARG C 169 " pdb=" NE ARG C 169 " pdb=" CZ ARG C 169 " ideal model delta sinusoidal sigma weight residual 90.00 51.01 38.99 2 1.50e+01 4.44e-03 8.45e+00 ... (remaining 5033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 811 0.027 - 0.053: 341 0.053 - 0.080: 161 0.080 - 0.106: 38 0.106 - 0.133: 23 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA ILE E 39 " pdb=" N ILE E 39 " pdb=" C ILE E 39 " pdb=" CB ILE E 39 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE A 7 " pdb=" N ILE A 7 " pdb=" C ILE A 7 " pdb=" CB ILE A 7 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA ILE C 50 " pdb=" N ILE C 50 " pdb=" C ILE C 50 " pdb=" CB ILE C 50 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1371 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 96 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" CD GLU E 96 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU E 96 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU E 96 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 71 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO A 72 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 71 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO D 72 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 72 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 72 " 0.016 5.00e-02 4.00e+02 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1584 2.78 - 3.31: 7888 3.31 - 3.84: 13423 3.84 - 4.37: 14374 4.37 - 4.90: 26450 Nonbonded interactions: 63719 Sorted by model distance: nonbonded pdb=" OG SER E 27 " pdb=" O PHE E 88 " model vdw 2.248 3.040 nonbonded pdb=" O GLU A 26 " pdb=" NH1 ARG A 31 " model vdw 2.308 3.120 nonbonded pdb=" NH1 ARG B 31 " pdb=" OE1 GLU B 37 " model vdw 2.360 3.120 nonbonded pdb=" NZ LYS A 23 " pdb=" O LEU A 64 " model vdw 2.380 3.120 nonbonded pdb=" NZ LYS E 23 " pdb=" OG SER E 67 " model vdw 2.381 3.120 ... (remaining 63714 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 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 44 or (resid 45 through 46 and (nam \ e N or name CA or name C or name O or name CB )) or resid 47 through 72 or (resi \ d 73 through 74 and (name N or name CA or name C or name O or name CB )) or resi \ d 75 through 82 or (resid 83 through 85 and (name N or name CA or name C or name \ O or name CB )) or resid 86 through 102 or (resid 103 and (name N or name CA or \ name C or name O or name CB )) or resid 104 through 301)) selection = (chain 'B' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 through 33 or (resid 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 36 or (resid 37 and (na \ me N or name CA or name C or name O or name CB )) or resid 38 through 42 or (res \ id 43 through 46 and (name N or name CA or name C or name O or name CB )) or res \ id 47 through 73 or (resid 74 and (name N or name CA or name C or name O or name \ CB )) or resid 75 through 82 or (resid 83 through 85 and (name N or name CA or \ name C or name O or name CB )) or resid 86 through 97 or (resid 98 and (name N o \ r name CA or name C or name O or name CB )) or resid 99 through 102 or (resid 10 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 104 or resid \ 109 through 171 or (resid 172 and (name N or name CA or name C or name O or nam \ e CB )) or resid 173 through 175 or (resid 176 through 177 and (name N or name C \ A or name C or name O or name CB )) or resid 178 through 301)) selection = (chain 'C' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 through 33 or (resid 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 36 or (resid 37 and (na \ me N or name CA or name C or name O or name CB )) or resid 38 through 43 or (res \ id 44 through 46 and (name N or name CA or name C or name O or name CB )) or res \ id 47 through 73 or (resid 74 and (name N or name CA or name C or name O or name \ CB )) or resid 75 through 82 or (resid 83 through 85 and (name N or name CA or \ name C or name O or name CB )) or resid 86 through 97 or (resid 98 and (name N o \ r name CA or name C or name O or name CB )) or resid 99 through 104 or resid 109 \ through 171 or (resid 172 and (name N or name CA or name C or name O or name CB \ )) or resid 173 through 175 or (resid 176 through 177 and (name N or name CA or \ name C or name O or name CB )) or resid 178 through 301)) selection = (chain 'D' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 through 33 or (resid 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 36 or (resid 37 and (na \ me N or name CA or name C or name O or name CB )) or resid 38 through 42 or (res \ id 43 through 46 and (name N or name CA or name C or name O or name CB )) or res \ id 47 through 73 or (resid 74 and (name N or name CA or name C or name O or name \ CB )) or resid 75 through 82 or (resid 83 through 85 and (name N or name CA or \ name C or name O or name CB )) or resid 86 through 97 or (resid 98 and (name N o \ r name CA or name C or name O or name CB )) or resid 99 through 102 or (resid 10 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 104 through \ 171 or (resid 172 and (name N or name CA or name C or name O or name CB )) or re \ sid 173 through 175 or (resid 176 through 177 and (name N or name CA or name C o \ r name O or name CB )) or resid 178 through 301)) selection = (chain 'E' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 through 33 or (resid 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 42 or (resid 43 through \ 46 and (name N or name CA or name C or name O or name CB )) or resid 47 through \ 73 or (resid 74 and (name N or name CA or name C or name O or name CB )) or res \ id 75 through 83 or (resid 84 through 85 and (name N or name CA or name C or nam \ e O or name CB )) or resid 86 through 102 or (resid 103 and (name N or name CA o \ r name C or name O or name CB )) or resid 104 or resid 109 through 171 or (resid \ 172 and (name N or name CA or name C or name O or name CB )) or resid 173 throu \ gh 175 or (resid 176 through 177 and (name N or name CA or name C or name O or n \ ame CB )) or resid 178 through 301)) } 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.890 Find NCS groups from input model: 0.140 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 : 0.003 0.028 8412 Z= 0.149 Angle : 0.651 9.166 11350 Z= 0.323 Chirality : 0.038 0.133 1374 Planarity : 0.003 0.031 1345 Dihedral : 12.881 80.092 3084 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.87 (0.26), residues: 1006 helix: 3.34 (0.17), residues: 746 sheet: None (None), residues: 0 loop : 0.14 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 169 TYR 0.019 0.001 TYR A 82 PHE 0.011 0.001 PHE D 75 TRP 0.012 0.001 TRP C 100 HIS 0.003 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8412) covalent geometry : angle 0.65068 (11350) hydrogen bonds : bond 0.10904 ( 643) hydrogen bonds : angle 4.20168 ( 1896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.248 Fit side-chains REVERT: D 45 LYS cc_start: 0.6390 (mttt) cc_final: 0.5791 (ttpt) REVERT: C 188 LEU cc_start: 0.8718 (tp) cc_final: 0.8516 (tp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.0712 time to fit residues: 17.0019 Evaluate side-chains 136 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 GLN B 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.178826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.146456 restraints weight = 9573.378| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.92 r_work: 0.3556 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8412 Z= 0.178 Angle : 0.538 7.445 11350 Z= 0.277 Chirality : 0.040 0.247 1374 Planarity : 0.003 0.031 1345 Dihedral : 6.429 59.369 1149 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.70 % Allowed : 7.14 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.77 (0.25), residues: 1006 helix: 3.24 (0.17), residues: 749 sheet: None (None), residues: 0 loop : 0.11 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 169 TYR 0.014 0.001 TYR D 24 PHE 0.012 0.002 PHE B 189 TRP 0.008 0.001 TRP D 135 HIS 0.004 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 8412) covalent geometry : angle 0.53807 (11350) hydrogen bonds : bond 0.05773 ( 643) hydrogen bonds : angle 3.72113 ( 1896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 0.297 Fit side-chains REVERT: E 84 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6904 (mm-30) REVERT: C 188 LEU cc_start: 0.8900 (tp) cc_final: 0.8654 (tp) REVERT: B 42 ASP cc_start: 0.7384 (t0) cc_final: 0.6722 (m-30) outliers start: 6 outliers final: 4 residues processed: 160 average time/residue: 0.0970 time to fit residues: 20.6880 Evaluate side-chains 144 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain A residue 173 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 HIS B 46 GLN B 47 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.181135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.146402 restraints weight = 9743.687| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.10 r_work: 0.3512 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8412 Z= 0.160 Angle : 0.500 6.138 11350 Z= 0.261 Chirality : 0.039 0.138 1374 Planarity : 0.003 0.030 1345 Dihedral : 5.778 54.816 1149 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.41 % Allowed : 9.72 % Favored : 88.88 % 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 are not related in a simple way. whole: 3.82 (0.25), residues: 1006 helix: 3.28 (0.17), residues: 747 sheet: None (None), residues: 0 loop : 0.14 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 169 TYR 0.013 0.001 TYR D 24 PHE 0.010 0.002 PHE C 163 TRP 0.008 0.001 TRP A 100 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8412) covalent geometry : angle 0.49954 (11350) hydrogen bonds : bond 0.05435 ( 643) hydrogen bonds : angle 3.67336 ( 1896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.348 Fit side-chains REVERT: E 84 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6801 (mm-30) REVERT: E 96 GLU cc_start: 0.7278 (mp0) cc_final: 0.6881 (mp0) REVERT: E 97 MET cc_start: 0.8125 (mtm) cc_final: 0.7918 (mtp) REVERT: C 188 LEU cc_start: 0.8921 (tp) cc_final: 0.8698 (tp) REVERT: B 46 GLN cc_start: 0.6189 (mp-120) cc_final: 0.5845 (mp10) REVERT: B 99 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7305 (tmm160) outliers start: 12 outliers final: 10 residues processed: 154 average time/residue: 0.0763 time to fit residues: 16.1745 Evaluate side-chains 147 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 207 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN B 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.172923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.140999 restraints weight = 9771.670| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.91 r_work: 0.3488 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 8412 Z= 0.231 Angle : 0.596 8.052 11350 Z= 0.309 Chirality : 0.042 0.309 1374 Planarity : 0.004 0.030 1345 Dihedral : 5.796 52.023 1149 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.87 % Allowed : 12.65 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.25), residues: 1006 helix: 2.93 (0.17), residues: 746 sheet: None (None), residues: 0 loop : -0.06 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 169 TYR 0.016 0.001 TYR D 24 PHE 0.014 0.002 PHE B 189 TRP 0.009 0.001 TRP A 100 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00560 ( 8412) covalent geometry : angle 0.59559 (11350) hydrogen bonds : bond 0.06673 ( 643) hydrogen bonds : angle 3.94402 ( 1896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: E 16 SER cc_start: 0.9088 (m) cc_final: 0.8860 (m) REVERT: E 84 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6793 (mm-30) REVERT: E 96 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: E 97 MET cc_start: 0.8252 (mtm) cc_final: 0.8043 (mtp) REVERT: D 98 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7141 (mm-30) REVERT: D 168 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7062 (tt0) REVERT: C 188 LEU cc_start: 0.8984 (tp) cc_final: 0.8746 (tp) REVERT: A 169 ARG cc_start: 0.7248 (ttt180) cc_final: 0.6957 (ttt180) REVERT: A 175 LYS cc_start: 0.7253 (mttt) cc_final: 0.6819 (mtpp) outliers start: 16 outliers final: 12 residues processed: 160 average time/residue: 0.0874 time to fit residues: 18.9641 Evaluate side-chains 146 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 91 optimal weight: 0.0970 chunk 86 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN B 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.181418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147283 restraints weight = 9816.395| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.07 r_work: 0.3509 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8412 Z= 0.124 Angle : 0.479 7.568 11350 Z= 0.250 Chirality : 0.039 0.135 1374 Planarity : 0.003 0.034 1345 Dihedral : 5.025 49.123 1149 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.29 % Allowed : 14.75 % Favored : 83.96 % 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 are not related in a simple way. whole: 3.95 (0.25), residues: 1006 helix: 3.46 (0.17), residues: 742 sheet: None (None), residues: 0 loop : -0.01 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 99 TYR 0.011 0.001 TYR E 87 PHE 0.008 0.001 PHE C 63 TRP 0.011 0.001 TRP A 100 HIS 0.003 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8412) covalent geometry : angle 0.47853 (11350) hydrogen bonds : bond 0.04742 ( 643) hydrogen bonds : angle 3.53283 ( 1896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.300 Fit side-chains REVERT: E 96 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: E 97 MET cc_start: 0.8271 (mtm) cc_final: 0.8062 (mtp) REVERT: E 169 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7516 (tpp80) REVERT: D 98 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7336 (mm-30) REVERT: D 168 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7011 (tt0) REVERT: C 188 LEU cc_start: 0.8907 (tp) cc_final: 0.8672 (tp) REVERT: B 56 MET cc_start: 0.8716 (mmt) cc_final: 0.8241 (mmt) REVERT: B 102 GLN cc_start: 0.7743 (mt0) cc_final: 0.7195 (pp30) REVERT: A 168 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6812 (tm-30) outliers start: 11 outliers final: 9 residues processed: 149 average time/residue: 0.0785 time to fit residues: 16.2326 Evaluate side-chains 147 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN B 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.176936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.142956 restraints weight = 9839.585| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.06 r_work: 0.3460 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8412 Z= 0.192 Angle : 0.559 10.805 11350 Z= 0.283 Chirality : 0.041 0.405 1374 Planarity : 0.003 0.032 1345 Dihedral : 5.206 49.885 1149 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.52 % Allowed : 17.21 % Favored : 81.26 % 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 are not related in a simple way. whole: 3.60 (0.25), residues: 1006 helix: 3.20 (0.17), residues: 746 sheet: None (None), residues: 0 loop : -0.17 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 99 TYR 0.013 0.001 TYR D 24 PHE 0.014 0.002 PHE A 124 TRP 0.009 0.001 TRP A 100 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 8412) covalent geometry : angle 0.55893 (11350) hydrogen bonds : bond 0.05871 ( 643) hydrogen bonds : angle 3.74550 ( 1896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: E 16 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8827 (m) REVERT: E 24 TYR cc_start: 0.8005 (m-10) cc_final: 0.7684 (m-10) REVERT: E 96 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: E 97 MET cc_start: 0.8259 (mtm) cc_final: 0.8018 (mtp) REVERT: D 116 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7069 (mm) REVERT: D 168 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7051 (tt0) REVERT: C 188 LEU cc_start: 0.8967 (tp) cc_final: 0.8745 (tp) REVERT: B 99 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7159 (tmm160) REVERT: B 102 GLN cc_start: 0.7736 (mt0) cc_final: 0.7209 (pp30) REVERT: A 169 ARG cc_start: 0.7170 (ttt180) cc_final: 0.6961 (ttt180) REVERT: A 175 LYS cc_start: 0.7215 (mttt) cc_final: 0.6879 (mmmm) outliers start: 13 outliers final: 10 residues processed: 146 average time/residue: 0.0964 time to fit residues: 19.1950 Evaluate side-chains 147 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN B 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.180558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146238 restraints weight = 9831.227| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.08 r_work: 0.3492 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8412 Z= 0.136 Angle : 0.500 9.640 11350 Z= 0.258 Chirality : 0.040 0.355 1374 Planarity : 0.003 0.036 1345 Dihedral : 4.806 48.825 1149 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.64 % Allowed : 16.74 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.89 (0.25), residues: 1006 helix: 3.44 (0.17), residues: 743 sheet: None (None), residues: 0 loop : -0.13 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 99 TYR 0.009 0.001 TYR E 87 PHE 0.008 0.001 PHE A 163 TRP 0.012 0.001 TRP A 100 HIS 0.003 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8412) covalent geometry : angle 0.50006 (11350) hydrogen bonds : bond 0.04883 ( 643) hydrogen bonds : angle 3.57364 ( 1896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.325 Fit side-chains REVERT: E 24 TYR cc_start: 0.7969 (m-10) cc_final: 0.7649 (m-10) REVERT: E 96 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6906 (mp0) REVERT: E 97 MET cc_start: 0.8254 (mtm) cc_final: 0.7994 (mtp) REVERT: E 169 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7529 (tpp80) REVERT: D 98 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7125 (mm-30) REVERT: D 168 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7016 (tt0) REVERT: C 188 LEU cc_start: 0.8933 (tp) cc_final: 0.8696 (tp) REVERT: B 46 GLN cc_start: 0.6896 (mm-40) cc_final: 0.6662 (tt0) REVERT: B 102 GLN cc_start: 0.7735 (mt0) cc_final: 0.7216 (pp30) outliers start: 14 outliers final: 11 residues processed: 146 average time/residue: 0.0905 time to fit residues: 18.0881 Evaluate side-chains 144 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.176746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.145056 restraints weight = 9595.155| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.88 r_work: 0.3518 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8412 Z= 0.145 Angle : 0.508 8.202 11350 Z= 0.260 Chirality : 0.040 0.319 1374 Planarity : 0.003 0.034 1345 Dihedral : 4.736 48.120 1149 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.87 % Allowed : 16.98 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.89 (0.25), residues: 1006 helix: 3.40 (0.17), residues: 746 sheet: None (None), residues: 0 loop : -0.06 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 169 TYR 0.010 0.001 TYR D 24 PHE 0.017 0.001 PHE A 124 TRP 0.010 0.001 TRP A 100 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8412) covalent geometry : angle 0.50819 (11350) hydrogen bonds : bond 0.05015 ( 643) hydrogen bonds : angle 3.59732 ( 1896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.347 Fit side-chains REVERT: E 24 TYR cc_start: 0.7952 (m-10) cc_final: 0.7632 (m-10) REVERT: E 96 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: E 97 MET cc_start: 0.8242 (mtm) cc_final: 0.7974 (mtp) REVERT: D 116 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7060 (mm) REVERT: D 168 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6992 (tt0) REVERT: C 188 LEU cc_start: 0.8914 (tp) cc_final: 0.8683 (tp) REVERT: B 46 GLN cc_start: 0.6908 (mm-40) cc_final: 0.6668 (tt0) REVERT: B 102 GLN cc_start: 0.7715 (mt0) cc_final: 0.7224 (pp30) REVERT: A 169 ARG cc_start: 0.7185 (ttt180) cc_final: 0.6960 (ttt180) outliers start: 16 outliers final: 11 residues processed: 149 average time/residue: 0.0853 time to fit residues: 17.3940 Evaluate side-chains 155 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.0970 chunk 45 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.175729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144245 restraints weight = 9660.937| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.87 r_work: 0.3509 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8412 Z= 0.160 Angle : 0.539 8.936 11350 Z= 0.276 Chirality : 0.040 0.296 1374 Planarity : 0.003 0.033 1345 Dihedral : 4.760 47.932 1149 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.76 % Allowed : 17.80 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.81 (0.25), residues: 1006 helix: 3.35 (0.17), residues: 745 sheet: None (None), residues: 0 loop : -0.11 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 169 TYR 0.011 0.001 TYR D 24 PHE 0.009 0.001 PHE A 163 TRP 0.013 0.001 TRP C 100 HIS 0.002 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8412) covalent geometry : angle 0.53893 (11350) hydrogen bonds : bond 0.05251 ( 643) hydrogen bonds : angle 3.67082 ( 1896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.240 Fit side-chains REVERT: E 16 SER cc_start: 0.9017 (OUTLIER) cc_final: 0.8812 (m) REVERT: E 96 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: E 97 MET cc_start: 0.8237 (mtm) cc_final: 0.7965 (mtp) REVERT: D 116 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6950 (mm) REVERT: D 168 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7018 (tt0) REVERT: D 169 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6615 (mtt180) REVERT: C 188 LEU cc_start: 0.8932 (tp) cc_final: 0.8705 (tp) REVERT: B 102 GLN cc_start: 0.7705 (mt0) cc_final: 0.7241 (pp30) REVERT: A 175 LYS cc_start: 0.7141 (mttt) cc_final: 0.6897 (mmmm) outliers start: 15 outliers final: 10 residues processed: 153 average time/residue: 0.0892 time to fit residues: 18.5950 Evaluate side-chains 146 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.177344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145829 restraints weight = 9542.819| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.87 r_work: 0.3545 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8412 Z= 0.137 Angle : 0.514 8.220 11350 Z= 0.265 Chirality : 0.039 0.289 1374 Planarity : 0.003 0.035 1345 Dihedral : 4.640 47.234 1149 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.64 % Allowed : 17.68 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.93 (0.25), residues: 1006 helix: 3.43 (0.17), residues: 746 sheet: None (None), residues: 0 loop : -0.02 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 169 TYR 0.011 0.001 TYR D 82 PHE 0.020 0.001 PHE A 124 TRP 0.011 0.001 TRP C 100 HIS 0.003 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8412) covalent geometry : angle 0.51372 (11350) hydrogen bonds : bond 0.04816 ( 643) hydrogen bonds : angle 3.59443 ( 1896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2012 Ramachandran restraints generated. 1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.299 Fit side-chains REVERT: E 96 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: E 97 MET cc_start: 0.8217 (mtm) cc_final: 0.7941 (mtp) REVERT: D 116 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6892 (mm) REVERT: D 168 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7009 (tt0) REVERT: C 188 LEU cc_start: 0.8915 (tp) cc_final: 0.8681 (tp) REVERT: B 46 GLN cc_start: 0.7042 (mm-40) cc_final: 0.6770 (tt0) REVERT: B 102 GLN cc_start: 0.7718 (mt0) cc_final: 0.7232 (pp30) REVERT: A 134 LEU cc_start: 0.7869 (mp) cc_final: 0.7657 (mt) outliers start: 14 outliers final: 11 residues processed: 144 average time/residue: 0.0866 time to fit residues: 17.0806 Evaluate side-chains 144 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.172656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141067 restraints weight = 9730.269| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.89 r_work: 0.3489 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 8412 Z= 0.206 Angle : 0.598 9.605 11350 Z= 0.304 Chirality : 0.041 0.330 1374 Planarity : 0.003 0.034 1345 Dihedral : 4.969 48.164 1149 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.76 % Allowed : 18.15 % Favored : 80.09 % 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 are not related in a simple way. whole: 3.58 (0.25), residues: 1006 helix: 3.19 (0.17), residues: 745 sheet: None (None), residues: 0 loop : -0.18 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 169 TYR 0.012 0.001 TYR D 24 PHE 0.011 0.002 PHE A 163 TRP 0.012 0.001 TRP A 100 HIS 0.002 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 8412) covalent geometry : angle 0.59782 (11350) hydrogen bonds : bond 0.05930 ( 643) hydrogen bonds : angle 3.81438 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1540.66 seconds wall clock time: 27 minutes 4.44 seconds (1624.44 seconds total)