Starting phenix.real_space_refine on Sun Aug 24 13:28:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6l3t_0825/08_2025/6l3t_0825_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l3t_0825/08_2025/6l3t_0825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6l3t_0825/08_2025/6l3t_0825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l3t_0825/08_2025/6l3t_0825.map" model { file = "/net/cci-nas-00/data/ceres_data/6l3t_0825/08_2025/6l3t_0825_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l3t_0825/08_2025/6l3t_0825_trim.cif" } resolution = 2.34 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= 0.006 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: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 6540 2.51 5 N 1638 2.21 5 O 1890 1.98 5 H 9588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19722 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "B" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "C" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "D" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "E" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "F" Number of atoms: 3184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3184 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Chain breaks: 1 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Time building chain proxies: 4.06, per 1000 atoms: 0.21 Number of scatterers: 19722 At special positions: 0 Unit cell: (112.391, 121.813, 93.547, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 O 1890 8.00 N 1638 7.00 C 6540 6.00 H 9588 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.04 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.04 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 169 " distance=2.04 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.04 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 169 " distance=2.04 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 180 " distance=2.04 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 169 " distance=2.04 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 180 " distance=2.04 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 169 " distance=2.04 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: 2.02 Conformation dependent library (CDL) restraints added in 556.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 76.6% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.625A pdb=" N ALA A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 23 through 45 removed outlier: 3.516A pdb=" N VAL A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 85 through 104 removed outlier: 3.843A pdb=" N GLU A 104 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 160 removed outlier: 3.606A pdb=" N LEU A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 212 Processing helix chain 'A' and resid 214 through 220 removed outlier: 3.927A pdb=" N ARG A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 14 removed outlier: 3.625A pdb=" N ALA B 11 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 23 through 45 removed outlier: 3.517A pdb=" N VAL B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Proline residue: B 41 - end of helix Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 85 through 104 removed outlier: 3.844A pdb=" N GLU B 104 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 160 removed outlier: 3.606A pdb=" N LEU B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 212 Processing helix chain 'B' and resid 214 through 220 removed outlier: 3.927A pdb=" N ARG B 220 " --> pdb=" O GLY B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.626A pdb=" N ALA C 11 " --> pdb=" O ARG C 7 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 23 through 45 removed outlier: 3.516A pdb=" N VAL C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) Proline residue: C 41 - end of helix Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 85 Processing helix chain 'C' and resid 85 through 104 removed outlier: 3.844A pdb=" N GLU C 104 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 160 removed outlier: 3.607A pdb=" N LEU C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 212 Processing helix chain 'C' and resid 214 through 220 removed outlier: 3.927A pdb=" N ARG C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 14 removed outlier: 3.625A pdb=" N ALA D 11 " --> pdb=" O ARG D 7 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 23 through 45 removed outlier: 3.516A pdb=" N VAL D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) Proline residue: D 41 - end of helix Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 85 Processing helix chain 'D' and resid 85 through 104 removed outlier: 3.844A pdb=" N GLU D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 160 removed outlier: 3.607A pdb=" N LEU D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 212 Processing helix chain 'D' and resid 214 through 220 removed outlier: 3.927A pdb=" N ARG D 220 " --> pdb=" O GLY D 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 14 removed outlier: 3.625A pdb=" N ALA E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 23 through 45 removed outlier: 3.516A pdb=" N VAL E 27 " --> pdb=" O LEU E 23 " (cutoff:3.500A) Proline residue: E 41 - end of helix Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 85 Processing helix chain 'E' and resid 85 through 104 removed outlier: 3.844A pdb=" N GLU E 104 " --> pdb=" O ILE E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 160 removed outlier: 3.607A pdb=" N LEU E 134 " --> pdb=" O SER E 130 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 212 Processing helix chain 'E' and resid 214 through 220 removed outlier: 3.927A pdb=" N ARG E 220 " --> pdb=" O GLY E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 14 removed outlier: 3.626A pdb=" N ALA F 11 " --> pdb=" O ARG F 7 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 23 through 45 removed outlier: 3.516A pdb=" N VAL F 27 " --> pdb=" O LEU F 23 " (cutoff:3.500A) Proline residue: F 41 - end of helix Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 104 removed outlier: 3.617A pdb=" N VAL F 86 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Proline residue: F 87 - end of helix removed outlier: 3.843A pdb=" N GLU F 104 " --> pdb=" O ILE F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 160 removed outlier: 3.608A pdb=" N LEU F 134 " --> pdb=" O SER F 130 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP F 135 " --> pdb=" O LEU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 212 Processing helix chain 'F' and resid 214 through 220 removed outlier: 3.926A pdb=" N ARG F 220 " --> pdb=" O GLY F 216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AA5, first strand: chain 'E' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'F' and resid 51 through 53 684 hydrogen bonds defined for protein. 2034 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: 4.39 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9576 1.03 - 1.23: 27 1.23 - 1.43: 4377 1.43 - 1.62: 5748 1.62 - 1.82: 84 Bond restraints: 19812 Sorted by residual: bond pdb=" CCJ LMN C 301 " pdb=" OBV LMN C 301 " ideal model delta sigma weight residual 1.378 1.466 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CCJ LMN E 301 " pdb=" OBV LMN E 301 " ideal model delta sigma weight residual 1.378 1.465 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" CCJ LMN F 301 " pdb=" OBV LMN F 301 " ideal model delta sigma weight residual 1.378 1.465 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" CCJ LMN D 301 " pdb=" OBV LMN D 301 " ideal model delta sigma weight residual 1.378 1.465 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" CCJ LMN A 301 " pdb=" OBV LMN A 301 " ideal model delta sigma weight residual 1.378 1.465 -0.087 2.00e-02 2.50e+03 1.89e+01 ... (remaining 19807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 34298 2.15 - 4.30: 1083 4.30 - 6.45: 142 6.45 - 8.60: 15 8.60 - 10.74: 12 Bond angle restraints: 35550 Sorted by residual: angle pdb=" C GLU E 172 " pdb=" N PRO E 173 " pdb=" CA PRO E 173 " ideal model delta sigma weight residual 127.00 137.74 -10.74 2.40e+00 1.74e-01 2.00e+01 angle pdb=" C GLU F 172 " pdb=" N PRO F 173 " pdb=" CA PRO F 173 " ideal model delta sigma weight residual 127.00 137.73 -10.73 2.40e+00 1.74e-01 2.00e+01 angle pdb=" C GLU C 172 " pdb=" N PRO C 173 " pdb=" CA PRO C 173 " ideal model delta sigma weight residual 127.00 137.73 -10.73 2.40e+00 1.74e-01 2.00e+01 angle pdb=" C GLU A 172 " pdb=" N PRO A 173 " pdb=" CA PRO A 173 " ideal model delta sigma weight residual 127.00 137.71 -10.71 2.40e+00 1.74e-01 1.99e+01 angle pdb=" C GLU D 172 " pdb=" N PRO D 173 " pdb=" CA PRO D 173 " ideal model delta sigma weight residual 127.00 137.69 -10.69 2.40e+00 1.74e-01 1.98e+01 ... (remaining 35545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.02: 8824 19.02 - 38.04: 618 38.04 - 57.06: 308 57.06 - 76.07: 96 76.07 - 95.09: 48 Dihedral angle restraints: 9894 sinusoidal: 5592 harmonic: 4302 Sorted by residual: dihedral pdb=" CAZ LMN D 301 " pdb=" CBB LMN D 301 " pdb=" CBD LMN D 301 " pdb=" CBF LMN D 301 " ideal model delta sinusoidal sigma weight residual 180.29 85.20 95.09 1 3.00e+01 1.11e-03 1.16e+01 dihedral pdb=" CAZ LMN A 301 " pdb=" CBB LMN A 301 " pdb=" CBD LMN A 301 " pdb=" CBF LMN A 301 " ideal model delta sinusoidal sigma weight residual 180.29 85.23 95.06 1 3.00e+01 1.11e-03 1.16e+01 dihedral pdb=" CAZ LMN C 301 " pdb=" CBB LMN C 301 " pdb=" CBD LMN C 301 " pdb=" CBF LMN C 301 " ideal model delta sinusoidal sigma weight residual 180.29 85.24 95.05 1 3.00e+01 1.11e-03 1.16e+01 ... (remaining 9891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1213 0.046 - 0.092: 277 0.092 - 0.138: 66 0.138 - 0.184: 16 0.184 - 0.230: 6 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CCV LMN A 301 " pdb=" CCR LMN A 301 " pdb=" CCT LMN A 301 " pdb=" OAU LMN A 301 " both_signs ideal model delta sigma weight residual False 2.28 2.51 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CCV LMN B 301 " pdb=" CCR LMN B 301 " pdb=" CCT LMN B 301 " pdb=" OAU LMN B 301 " both_signs ideal model delta sigma weight residual False 2.28 2.51 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CCV LMN F 301 " pdb=" CCR LMN F 301 " pdb=" CCT LMN F 301 " pdb=" OAU LMN F 301 " both_signs ideal model delta sigma weight residual False 2.28 2.51 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1575 not shown) Planarity restraints: 2784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 171 " -0.060 9.50e-02 1.11e+02 2.31e-02 3.41e+00 pdb=" NE ARG C 171 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG C 171 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG C 171 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 171 " -0.024 2.00e-02 2.50e+03 pdb="HH11 ARG C 171 " -0.008 2.00e-02 2.50e+03 pdb="HH12 ARG C 171 " 0.005 2.00e-02 2.50e+03 pdb="HH21 ARG C 171 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG C 171 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 171 " -0.060 9.50e-02 1.11e+02 2.30e-02 3.39e+00 pdb=" NE ARG D 171 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D 171 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG D 171 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 171 " -0.024 2.00e-02 2.50e+03 pdb="HH11 ARG D 171 " -0.009 2.00e-02 2.50e+03 pdb="HH12 ARG D 171 " 0.005 2.00e-02 2.50e+03 pdb="HH21 ARG D 171 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 171 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 171 " 0.059 9.50e-02 1.11e+02 2.27e-02 3.35e+00 pdb=" NE ARG A 171 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 171 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 171 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 171 " 0.025 2.00e-02 2.50e+03 pdb="HH11 ARG A 171 " 0.008 2.00e-02 2.50e+03 pdb="HH12 ARG A 171 " -0.005 2.00e-02 2.50e+03 pdb="HH21 ARG A 171 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 171 " -0.010 2.00e-02 2.50e+03 ... (remaining 2781 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 3930 2.31 - 2.88: 39980 2.88 - 3.45: 46658 3.45 - 4.03: 65707 4.03 - 4.60: 98027 Nonbonded interactions: 254302 Sorted by model distance: nonbonded pdb=" HE2 HIS F 54 " pdb=" OD1 ASN F 181 " model vdw 1.734 2.450 nonbonded pdb=" HE2 HIS B 54 " pdb=" OD1 ASN B 181 " model vdw 1.734 2.450 nonbonded pdb=" HE2 HIS E 54 " pdb=" OD1 ASN E 181 " model vdw 1.734 2.450 nonbonded pdb=" HE2 HIS D 54 " pdb=" OD1 ASN D 181 " model vdw 1.734 2.450 nonbonded pdb=" HE2 HIS C 54 " pdb=" OD1 ASN C 181 " model vdw 1.734 2.450 ... (remaining 254297 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.570 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 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 : 0.010 0.088 10242 Z= 0.442 Angle : 1.071 10.744 13908 Z= 0.475 Chirality : 0.047 0.230 1578 Planarity : 0.006 0.038 1650 Dihedral : 18.398 95.092 4194 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.61 % Allowed : 4.82 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -3.24 (0.20), residues: 1182 helix: -1.92 (0.14), residues: 870 sheet: -0.67 (0.58), residues: 60 loop : -2.55 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG C 171 TYR 0.007 0.002 TYR B 44 PHE 0.018 0.002 PHE F 31 TRP 0.011 0.002 TRP D 103 HIS 0.005 0.002 HIS B 69 Details of bonding type rmsd covalent geometry : bond 0.00985 (10224) covalent geometry : angle 1.07068 (13872) SS BOND : bond 0.00499 ( 18) SS BOND : angle 1.33646 ( 36) hydrogen bonds : bond 0.28579 ( 684) hydrogen bonds : angle 7.49876 ( 2034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.581 Fit side-chains REVERT: A 132 ARG cc_start: 0.7484 (mtp85) cc_final: 0.6866 (tpm170) REVERT: A 220 ARG cc_start: 0.3992 (OUTLIER) cc_final: 0.3482 (pmt100) REVERT: B 4 ARG cc_start: 0.7095 (tpt-90) cc_final: 0.6868 (tmm-80) REVERT: B 132 ARG cc_start: 0.7547 (mtp85) cc_final: 0.6882 (tpm170) REVERT: B 220 ARG cc_start: 0.3965 (OUTLIER) cc_final: 0.3574 (ptt-90) REVERT: C 132 ARG cc_start: 0.7480 (mtp85) cc_final: 0.6905 (tpm170) REVERT: C 171 ARG cc_start: 0.6788 (mmm-85) cc_final: 0.6438 (ttt180) REVERT: C 220 ARG cc_start: 0.4026 (OUTLIER) cc_final: 0.3532 (pmt100) REVERT: D 132 ARG cc_start: 0.7458 (mtp85) cc_final: 0.6845 (tpm170) REVERT: D 220 ARG cc_start: 0.4035 (OUTLIER) cc_final: 0.3680 (ptt-90) REVERT: E 4 ARG cc_start: 0.7072 (tpt-90) cc_final: 0.6842 (tmm-80) REVERT: E 132 ARG cc_start: 0.7548 (mtp85) cc_final: 0.6870 (tpm170) REVERT: E 220 ARG cc_start: 0.4016 (OUTLIER) cc_final: 0.3590 (ptt-90) REVERT: F 132 ARG cc_start: 0.7471 (mtp85) cc_final: 0.6870 (tpm170) REVERT: F 220 ARG cc_start: 0.4009 (OUTLIER) cc_final: 0.3601 (pmt100) outliers start: 36 outliers final: 9 residues processed: 191 average time/residue: 2.0189 time to fit residues: 403.7550 Evaluate side-chains 155 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.152100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.111790 restraints weight = 23349.877| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.17 r_work: 0.2927 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10242 Z= 0.177 Angle : 0.686 6.909 13908 Z= 0.349 Chirality : 0.037 0.114 1578 Planarity : 0.006 0.045 1650 Dihedral : 13.486 86.916 2124 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.61 % Allowed : 9.44 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.54 (0.25), residues: 1182 helix: 1.20 (0.17), residues: 912 sheet: -0.95 (0.51), residues: 60 loop : -2.90 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 4 TYR 0.006 0.001 TYR D 97 PHE 0.010 0.002 PHE A 94 TRP 0.003 0.001 TRP F 101 HIS 0.004 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00315 (10224) covalent geometry : angle 0.68620 (13872) SS BOND : bond 0.00193 ( 18) SS BOND : angle 0.58012 ( 36) hydrogen bonds : bond 0.09104 ( 684) hydrogen bonds : angle 4.47341 ( 2034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 4 ARG cc_start: 0.6517 (tpp80) cc_final: 0.6137 (tmm-80) REVERT: B 4 ARG cc_start: 0.6346 (tpt-90) cc_final: 0.5858 (tmm-80) REVERT: B 132 ARG cc_start: 0.7507 (mtp85) cc_final: 0.6169 (tpt170) REVERT: C 4 ARG cc_start: 0.5966 (OUTLIER) cc_final: 0.5723 (tmm-80) REVERT: C 47 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7774 (mt-10) REVERT: C 132 ARG cc_start: 0.7520 (mtp85) cc_final: 0.6183 (tpt170) REVERT: E 4 ARG cc_start: 0.6429 (tpt-90) cc_final: 0.5889 (tmm-80) REVERT: E 132 ARG cc_start: 0.7529 (mtp85) cc_final: 0.6180 (tpt170) REVERT: F 4 ARG cc_start: 0.6233 (tpp80) cc_final: 0.5854 (tmm-80) REVERT: F 47 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7711 (mt-10) outliers start: 16 outliers final: 7 residues processed: 144 average time/residue: 2.0399 time to fit residues: 308.0254 Evaluate side-chains 138 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain C residue 4 ARG Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 4 ARG Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain F residue 104 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.148110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.107226 restraints weight = 23223.822| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.18 r_work: 0.2853 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10242 Z= 0.190 Angle : 0.657 4.430 13908 Z= 0.331 Chirality : 0.038 0.122 1578 Planarity : 0.005 0.034 1650 Dihedral : 11.587 72.700 2094 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.51 % Allowed : 9.94 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.42 (0.25), residues: 1182 helix: 1.92 (0.17), residues: 906 sheet: -0.30 (0.53), residues: 60 loop : -3.07 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 75 TYR 0.012 0.002 TYR D 97 PHE 0.017 0.002 PHE D 31 TRP 0.006 0.001 TRP F 101 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00378 (10224) covalent geometry : angle 0.65625 (13872) SS BOND : bond 0.00486 ( 18) SS BOND : angle 0.94456 ( 36) hydrogen bonds : bond 0.09481 ( 684) hydrogen bonds : angle 4.25333 ( 2034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.601 Fit side-chains REVERT: A 4 ARG cc_start: 0.6714 (tpp80) cc_final: 0.6328 (tmm-80) REVERT: A 220 ARG cc_start: 0.3418 (OUTLIER) cc_final: 0.2891 (pmt100) REVERT: B 4 ARG cc_start: 0.6626 (tpt-90) cc_final: 0.6199 (tmm-80) REVERT: B 132 ARG cc_start: 0.7593 (mtp85) cc_final: 0.6209 (tpt170) REVERT: B 220 ARG cc_start: 0.3500 (OUTLIER) cc_final: 0.2926 (pmt100) REVERT: C 171 ARG cc_start: 0.6389 (mmm-85) cc_final: 0.5888 (ttt180) REVERT: C 220 ARG cc_start: 0.3446 (OUTLIER) cc_final: 0.2918 (pmt100) REVERT: D 4 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.5630 (ttm-80) REVERT: D 104 GLU cc_start: 0.5181 (OUTLIER) cc_final: 0.4948 (mm-30) REVERT: D 220 ARG cc_start: 0.3488 (OUTLIER) cc_final: 0.2952 (pmt100) REVERT: E 4 ARG cc_start: 0.6665 (tpt-90) cc_final: 0.6205 (tmm-80) REVERT: E 132 ARG cc_start: 0.7603 (mtp85) cc_final: 0.6223 (tpt170) REVERT: E 220 ARG cc_start: 0.3515 (OUTLIER) cc_final: 0.3020 (ptt-90) REVERT: F 4 ARG cc_start: 0.6515 (tpp80) cc_final: 0.6140 (tmm-80) REVERT: F 162 GLN cc_start: 0.8486 (pt0) cc_final: 0.8093 (pt0) REVERT: F 171 ARG cc_start: 0.6388 (mmm-85) cc_final: 0.5900 (ttt180) REVERT: F 220 ARG cc_start: 0.3463 (OUTLIER) cc_final: 0.2961 (pmt100) outliers start: 25 outliers final: 14 residues processed: 161 average time/residue: 1.8859 time to fit residues: 318.5868 Evaluate side-chains 156 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 4 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 63 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.146709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.105860 restraints weight = 23146.764| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.18 r_work: 0.2832 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10242 Z= 0.204 Angle : 0.688 4.880 13908 Z= 0.347 Chirality : 0.040 0.119 1578 Planarity : 0.005 0.029 1650 Dihedral : 11.490 62.636 2094 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.41 % Allowed : 9.84 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.67 (0.25), residues: 1182 helix: 2.06 (0.17), residues: 906 sheet: 0.15 (0.54), residues: 60 loop : -2.96 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 4 TYR 0.014 0.003 TYR D 97 PHE 0.015 0.002 PHE F 31 TRP 0.007 0.001 TRP D 103 HIS 0.004 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00416 (10224) covalent geometry : angle 0.68688 (13872) SS BOND : bond 0.00566 ( 18) SS BOND : angle 1.09649 ( 36) hydrogen bonds : bond 0.09736 ( 684) hydrogen bonds : angle 4.20716 ( 2034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.559 Fit side-chains REVERT: A 4 ARG cc_start: 0.6785 (tpp80) cc_final: 0.6406 (tmm-80) REVERT: A 220 ARG cc_start: 0.3399 (OUTLIER) cc_final: 0.2846 (pmt100) REVERT: B 4 ARG cc_start: 0.6649 (tpt-90) cc_final: 0.6284 (tmm-80) REVERT: B 132 ARG cc_start: 0.7673 (mtp85) cc_final: 0.6287 (tpt170) REVERT: B 220 ARG cc_start: 0.3463 (OUTLIER) cc_final: 0.2970 (ptt-90) REVERT: C 132 ARG cc_start: 0.7663 (mtp85) cc_final: 0.6340 (tpt170) REVERT: C 171 ARG cc_start: 0.6422 (mmm-85) cc_final: 0.5929 (ttt180) REVERT: C 220 ARG cc_start: 0.3436 (OUTLIER) cc_final: 0.2928 (pmt100) REVERT: D 4 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.5722 (ttm-80) REVERT: D 220 ARG cc_start: 0.3427 (OUTLIER) cc_final: 0.2912 (pmt100) REVERT: E 4 ARG cc_start: 0.6624 (tpt-90) cc_final: 0.6256 (tmm-80) REVERT: E 132 ARG cc_start: 0.7674 (mtp85) cc_final: 0.6290 (tpt170) REVERT: E 220 ARG cc_start: 0.3434 (OUTLIER) cc_final: 0.2915 (ptt-90) REVERT: F 4 ARG cc_start: 0.6660 (tpp80) cc_final: 0.6305 (tmm-80) REVERT: F 162 GLN cc_start: 0.8481 (pt0) cc_final: 0.8100 (pt0) REVERT: F 171 ARG cc_start: 0.6408 (mmm-85) cc_final: 0.5937 (ttt180) REVERT: F 220 ARG cc_start: 0.3442 (OUTLIER) cc_final: 0.2968 (pmt100) outliers start: 34 outliers final: 8 residues processed: 170 average time/residue: 2.0234 time to fit residues: 360.4204 Evaluate side-chains 151 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 4 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.148298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.107589 restraints weight = 22981.410| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.17 r_work: 0.2857 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10242 Z= 0.171 Angle : 0.621 4.688 13908 Z= 0.314 Chirality : 0.037 0.114 1578 Planarity : 0.004 0.028 1650 Dihedral : 10.615 68.047 2082 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.51 % Allowed : 11.65 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.03 (0.25), residues: 1182 helix: 2.34 (0.17), residues: 906 sheet: 0.43 (0.56), residues: 60 loop : -3.00 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 4 TYR 0.011 0.002 TYR A 97 PHE 0.013 0.002 PHE B 51 TRP 0.005 0.001 TRP F 101 HIS 0.003 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00333 (10224) covalent geometry : angle 0.62038 (13872) SS BOND : bond 0.00416 ( 18) SS BOND : angle 0.90420 ( 36) hydrogen bonds : bond 0.08737 ( 684) hydrogen bonds : angle 4.09388 ( 2034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.574 Fit side-chains REVERT: A 4 ARG cc_start: 0.6768 (tpp80) cc_final: 0.6399 (tmm-80) REVERT: B 4 ARG cc_start: 0.6644 (tpt-90) cc_final: 0.6308 (tmm-80) REVERT: B 132 ARG cc_start: 0.7588 (mtp85) cc_final: 0.6232 (tpt170) REVERT: C 104 GLU cc_start: 0.5228 (OUTLIER) cc_final: 0.4930 (mm-30) REVERT: E 4 ARG cc_start: 0.6654 (tpt-90) cc_final: 0.6286 (tmm-80) REVERT: E 132 ARG cc_start: 0.7573 (mtp85) cc_final: 0.6224 (tpt170) REVERT: F 4 ARG cc_start: 0.6679 (tpp80) cc_final: 0.6347 (tmm-80) REVERT: F 162 GLN cc_start: 0.8482 (pt0) cc_final: 0.8088 (pt0) outliers start: 15 outliers final: 10 residues processed: 151 average time/residue: 1.9811 time to fit residues: 313.9964 Evaluate side-chains 148 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 104 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.151044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110713 restraints weight = 23118.639| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.17 r_work: 0.2903 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 10242 Z= 0.137 Angle : 0.546 4.811 13908 Z= 0.279 Chirality : 0.034 0.104 1578 Planarity : 0.004 0.027 1650 Dihedral : 9.768 77.863 2082 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.41 % Allowed : 12.35 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.47 (0.25), residues: 1182 helix: 2.70 (0.17), residues: 906 sheet: 0.70 (0.59), residues: 60 loop : -3.11 (0.35), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 132 TYR 0.009 0.001 TYR B 156 PHE 0.010 0.001 PHE E 51 TRP 0.005 0.001 TRP F 101 HIS 0.004 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00253 (10224) covalent geometry : angle 0.54541 (13872) SS BOND : bond 0.00242 ( 18) SS BOND : angle 0.65724 ( 36) hydrogen bonds : bond 0.07274 ( 684) hydrogen bonds : angle 3.91349 ( 2034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.564 Fit side-chains REVERT: A 4 ARG cc_start: 0.6683 (tpp80) cc_final: 0.6344 (tmm-80) REVERT: B 4 ARG cc_start: 0.6620 (tpt-90) cc_final: 0.6253 (tmm-80) REVERT: B 220 ARG cc_start: 0.3357 (OUTLIER) cc_final: 0.2910 (ptt-90) REVERT: C 104 GLU cc_start: 0.5298 (OUTLIER) cc_final: 0.5008 (mm-30) REVERT: D 220 ARG cc_start: 0.3303 (OUTLIER) cc_final: 0.2791 (pmt100) REVERT: E 4 ARG cc_start: 0.6642 (tpt-90) cc_final: 0.6256 (tmm-80) REVERT: E 220 ARG cc_start: 0.3328 (OUTLIER) cc_final: 0.2879 (ptt-90) REVERT: F 4 ARG cc_start: 0.6616 (tpp80) cc_final: 0.6301 (tmm-80) REVERT: F 162 GLN cc_start: 0.8473 (pt0) cc_final: 0.8080 (pt0) outliers start: 14 outliers final: 6 residues processed: 149 average time/residue: 1.8349 time to fit residues: 286.8035 Evaluate side-chains 145 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 58 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.147195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.106330 restraints weight = 23016.107| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.18 r_work: 0.3025 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10242 Z= 0.211 Angle : 0.682 4.783 13908 Z= 0.342 Chirality : 0.039 0.122 1578 Planarity : 0.005 0.028 1650 Dihedral : 10.391 75.237 2079 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.71 % Allowed : 11.95 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.30 (0.25), residues: 1182 helix: 2.52 (0.17), residues: 906 sheet: 0.86 (0.59), residues: 60 loop : -2.94 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 132 TYR 0.016 0.003 TYR A 97 PHE 0.016 0.002 PHE C 31 TRP 0.010 0.001 TRP A 103 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00435 (10224) covalent geometry : angle 0.68088 (13872) SS BOND : bond 0.00580 ( 18) SS BOND : angle 1.13916 ( 36) hydrogen bonds : bond 0.09455 ( 684) hydrogen bonds : angle 4.11230 ( 2034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.592 Fit side-chains REVERT: A 4 ARG cc_start: 0.6901 (tpp80) cc_final: 0.6586 (tmm-80) REVERT: A 220 ARG cc_start: 0.3389 (OUTLIER) cc_final: 0.3090 (mtm-85) REVERT: B 4 ARG cc_start: 0.6760 (tpt-90) cc_final: 0.6456 (tmm-80) REVERT: B 132 ARG cc_start: 0.7650 (mtp85) cc_final: 0.6390 (tpt170) REVERT: B 220 ARG cc_start: 0.3440 (OUTLIER) cc_final: 0.2986 (ptt-90) REVERT: C 104 GLU cc_start: 0.5487 (OUTLIER) cc_final: 0.4889 (mm-30) REVERT: C 220 ARG cc_start: 0.3460 (OUTLIER) cc_final: 0.3010 (pmt100) REVERT: D 220 ARG cc_start: 0.3440 (OUTLIER) cc_final: 0.2903 (pmt100) REVERT: E 4 ARG cc_start: 0.6818 (tpt-90) cc_final: 0.6492 (tmm-80) REVERT: E 132 ARG cc_start: 0.7634 (mtp85) cc_final: 0.6391 (tpt170) REVERT: E 220 ARG cc_start: 0.3432 (OUTLIER) cc_final: 0.2959 (ptt-90) REVERT: F 4 ARG cc_start: 0.6814 (tpp80) cc_final: 0.6509 (tmm-80) REVERT: F 162 GLN cc_start: 0.8467 (pt0) cc_final: 0.8091 (pt0) REVERT: F 220 ARG cc_start: 0.3484 (OUTLIER) cc_final: 0.3050 (pmt100) outliers start: 17 outliers final: 6 residues processed: 153 average time/residue: 2.0116 time to fit residues: 322.7960 Evaluate side-chains 150 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 112 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.148411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.107709 restraints weight = 23048.839| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.18 r_work: 0.3071 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10242 Z= 0.170 Angle : 0.611 4.856 13908 Z= 0.310 Chirality : 0.037 0.115 1578 Planarity : 0.004 0.029 1650 Dihedral : 10.261 82.628 2079 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.61 % Allowed : 12.25 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.40 (0.25), residues: 1182 helix: 2.60 (0.17), residues: 906 sheet: 0.84 (0.60), residues: 60 loop : -2.95 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 15 TYR 0.012 0.002 TYR A 97 PHE 0.013 0.002 PHE D 31 TRP 0.008 0.001 TRP A 103 HIS 0.003 0.001 HIS D 98 Details of bonding type rmsd covalent geometry : bond 0.00333 (10224) covalent geometry : angle 0.60959 (13872) SS BOND : bond 0.00425 ( 18) SS BOND : angle 0.93143 ( 36) hydrogen bonds : bond 0.08547 ( 684) hydrogen bonds : angle 4.03093 ( 2034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.6876 (tpp80) cc_final: 0.6568 (tmm-80) REVERT: A 220 ARG cc_start: 0.3348 (OUTLIER) cc_final: 0.3044 (mtm-85) REVERT: B 4 ARG cc_start: 0.6752 (tpt-90) cc_final: 0.6446 (tmm-80) REVERT: B 220 ARG cc_start: 0.3329 (OUTLIER) cc_final: 0.2886 (ptt-90) REVERT: C 104 GLU cc_start: 0.5464 (OUTLIER) cc_final: 0.4910 (mp0) REVERT: C 131 LEU cc_start: 0.8207 (tp) cc_final: 0.7999 (mt) REVERT: C 132 ARG cc_start: 0.7621 (ptm160) cc_final: 0.6302 (tpt170) REVERT: C 220 ARG cc_start: 0.3406 (OUTLIER) cc_final: 0.2956 (pmt100) REVERT: D 220 ARG cc_start: 0.3343 (OUTLIER) cc_final: 0.2824 (pmt100) REVERT: E 4 ARG cc_start: 0.6766 (tpt-90) cc_final: 0.6438 (tmm-80) REVERT: E 220 ARG cc_start: 0.3314 (OUTLIER) cc_final: 0.2860 (ptt-90) REVERT: F 4 ARG cc_start: 0.6784 (tpp80) cc_final: 0.6487 (tmm-80) REVERT: F 162 GLN cc_start: 0.8461 (pt0) cc_final: 0.8088 (pt0) REVERT: F 220 ARG cc_start: 0.3436 (OUTLIER) cc_final: 0.3065 (pmt100) outliers start: 16 outliers final: 8 residues processed: 156 average time/residue: 2.0227 time to fit residues: 330.8747 Evaluate side-chains 154 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 220 ARG Chi-restraints excluded: chain F residue 69 HIS Chi-restraints excluded: chain F residue 220 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 18 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.150771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.110103 restraints weight = 23089.682| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.18 r_work: 0.2897 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10242 Z= 0.135 Angle : 0.543 4.941 13908 Z= 0.279 Chirality : 0.034 0.101 1578 Planarity : 0.004 0.028 1650 Dihedral : 10.035 88.499 2079 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.20 % Allowed : 12.95 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.67 (0.25), residues: 1182 helix: 2.83 (0.17), residues: 906 sheet: 0.86 (0.60), residues: 60 loop : -3.05 (0.34), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 132 TYR 0.009 0.001 TYR A 156 PHE 0.009 0.001 PHE B 51 TRP 0.005 0.001 TRP D 103 HIS 0.003 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00248 (10224) covalent geometry : angle 0.54267 (13872) SS BOND : bond 0.00226 ( 18) SS BOND : angle 0.65770 ( 36) hydrogen bonds : bond 0.07241 ( 684) hydrogen bonds : angle 3.89601 ( 2034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.6761 (tpp80) cc_final: 0.6427 (tmm-80) REVERT: B 4 ARG cc_start: 0.6644 (tpt-90) cc_final: 0.6285 (tmm-80) REVERT: C 104 GLU cc_start: 0.5354 (OUTLIER) cc_final: 0.5050 (mp0) REVERT: E 4 ARG cc_start: 0.6639 (tpt-90) cc_final: 0.6269 (tmm-80) REVERT: F 4 ARG cc_start: 0.6632 (tpp80) cc_final: 0.6330 (tmm-80) REVERT: F 162 GLN cc_start: 0.8445 (pt0) cc_final: 0.8040 (pt0) outliers start: 12 outliers final: 8 residues processed: 145 average time/residue: 2.0150 time to fit residues: 306.5485 Evaluate side-chains 144 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.150254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.109561 restraints weight = 23251.260| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.18 r_work: 0.2889 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10242 Z= 0.145 Angle : 0.555 4.908 13908 Z= 0.284 Chirality : 0.035 0.107 1578 Planarity : 0.004 0.028 1650 Dihedral : 9.316 85.145 2079 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.80 % Allowed : 13.35 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.75 (0.25), residues: 1182 helix: 2.89 (0.17), residues: 906 sheet: 0.97 (0.61), residues: 60 loop : -3.05 (0.34), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 132 TYR 0.010 0.002 TYR A 97 PHE 0.011 0.001 PHE B 51 TRP 0.006 0.001 TRP A 103 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00277 (10224) covalent geometry : angle 0.55438 (13872) SS BOND : bond 0.00308 ( 18) SS BOND : angle 0.72025 ( 36) hydrogen bonds : bond 0.07579 ( 684) hydrogen bonds : angle 3.89857 ( 2034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.6768 (tpp80) cc_final: 0.6443 (tmm-80) REVERT: B 4 ARG cc_start: 0.6678 (tpt-90) cc_final: 0.6338 (tmm-80) REVERT: C 104 GLU cc_start: 0.5336 (OUTLIER) cc_final: 0.5113 (mp0) REVERT: E 4 ARG cc_start: 0.6673 (tpt-90) cc_final: 0.6319 (tmm-80) REVERT: F 4 ARG cc_start: 0.6654 (tpp80) cc_final: 0.6349 (tmm-80) REVERT: F 162 GLN cc_start: 0.8451 (pt0) cc_final: 0.8049 (pt0) outliers start: 8 outliers final: 7 residues processed: 143 average time/residue: 2.0287 time to fit residues: 304.3303 Evaluate side-chains 143 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain F residue 69 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.150550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.109794 restraints weight = 23169.339| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.18 r_work: 0.2896 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 10242 Z= 0.137 Angle : 0.540 4.880 13908 Z= 0.277 Chirality : 0.034 0.104 1578 Planarity : 0.004 0.028 1650 Dihedral : 8.733 86.329 2079 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.00 % Allowed : 13.15 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.85 (0.25), residues: 1182 helix: 2.98 (0.17), residues: 906 sheet: 1.00 (0.61), residues: 60 loop : -3.06 (0.34), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 15 TYR 0.009 0.001 TYR B 156 PHE 0.010 0.001 PHE E 51 TRP 0.006 0.001 TRP F 103 HIS 0.003 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00259 (10224) covalent geometry : angle 0.53952 (13872) SS BOND : bond 0.00289 ( 18) SS BOND : angle 0.67487 ( 36) hydrogen bonds : bond 0.07301 ( 684) hydrogen bonds : angle 3.86571 ( 2034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9730.87 seconds wall clock time: 165 minutes 21.53 seconds (9921.53 seconds total)