Starting phenix.real_space_refine on Thu Jul 2 05:24:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lqx_63308/07_2026/9lqx_63308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lqx_63308/07_2026/9lqx_63308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lqx_63308/07_2026/9lqx_63308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lqx_63308/07_2026/9lqx_63308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lqx_63308/07_2026/9lqx_63308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lqx_63308/07_2026/9lqx_63308.map" } resolution = 2.7 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= 0.003 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 P 3 5.49 5 S 60 5.16 5 C 4598 2.51 5 N 1001 2.21 5 O 1137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6799 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2150 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2186 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 922 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 943 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 252 Unusual residues: {'CLR': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 346 Unusual residues: {'CLR': 7, 'PCF': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 1.64, per 1000 atoms: 0.24 Number of scatterers: 6799 At special positions: 0 Unit cell: (62.31, 115.32, 105.09, 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 60 16.00 P 3 15.00 O 1137 8.00 N 1001 7.00 C 4598 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 102 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 33 " - pdb=" SG CYS D 110 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 110 " distance=2.03 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: 0.52 Conformation dependent library (CDL) restraints added in 317.6 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 58.2% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 29 through 55 Processing helix chain 'A' and resid 64 through 80 Processing helix chain 'A' and resid 81 through 91 Processing helix chain 'A' and resid 98 through 132 Processing helix chain 'A' and resid 146 through 161 Processing helix chain 'A' and resid 161 through 167 Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.621A pdb=" N ASN A 175 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 176' Processing helix chain 'A' and resid 193 through 229 removed outlier: 3.561A pdb=" N TRP A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 244 through 273 removed outlier: 3.760A pdb=" N SER A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 280 through 301 removed outlier: 3.559A pdb=" N PHE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 304 through 313 Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.714A pdb=" N MET A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 54 Processing helix chain 'B' and resid 62 through 80 removed outlier: 4.193A pdb=" N ILE B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 91 Processing helix chain 'B' and resid 98 through 132 Processing helix chain 'B' and resid 146 through 161 removed outlier: 3.536A pdb=" N LEU B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.923A pdb=" N ASN B 175 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 176' Processing helix chain 'B' and resid 193 through 229 removed outlier: 3.534A pdb=" N TRP B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) Proline residue: B 213 - end of helix Processing helix chain 'B' and resid 244 through 273 Proline residue: B 263 - end of helix Processing helix chain 'B' and resid 280 through 301 Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 304 through 313 Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'C' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 Processing sheet with id=AA2, first strand: chain 'B' and resid 168 through 171 Processing sheet with id=AA3, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'D' and resid 11 through 13 removed outlier: 7.520A pdb=" N MET D 34 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 11 through 13 Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 4.170A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET C 82 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.842A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET C 34 " --> pdb=" O MET C 51 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1191 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: 1.04 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 929 1.31 - 1.44: 1959 1.44 - 1.56: 3908 1.56 - 1.69: 115 1.69 - 1.82: 92 Bond restraints: 7003 Sorted by residual: bond pdb=" C21 PCF B 403 " pdb=" O21 PCF B 403 " ideal model delta sigma weight residual 1.334 1.438 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C21 PCF B 402 " pdb=" O21 PCF B 402 " ideal model delta sigma weight residual 1.334 1.436 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C21 PCF B 401 " pdb=" O21 PCF B 401 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C31 PCF B 401 " pdb=" O31 PCF B 401 " ideal model delta sigma weight residual 1.329 1.419 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C31 PCF B 402 " pdb=" O31 PCF B 402 " ideal model delta sigma weight residual 1.329 1.419 -0.090 2.00e-02 2.50e+03 2.01e+01 ... (remaining 6998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 9441 4.51 - 9.02: 147 9.02 - 13.53: 10 13.53 - 18.04: 0 18.04 - 22.55: 3 Bond angle restraints: 9601 Sorted by residual: angle pdb=" O12 PCF B 402 " pdb=" P PCF B 402 " pdb=" O14 PCF B 402 " ideal model delta sigma weight residual 123.69 101.14 22.55 3.00e+00 1.11e-01 5.65e+01 angle pdb=" O12 PCF B 403 " pdb=" P PCF B 403 " pdb=" O14 PCF B 403 " ideal model delta sigma weight residual 123.69 101.43 22.26 3.00e+00 1.11e-01 5.51e+01 angle pdb=" O12 PCF B 401 " pdb=" P PCF B 401 " pdb=" O14 PCF B 401 " ideal model delta sigma weight residual 123.69 101.44 22.25 3.00e+00 1.11e-01 5.50e+01 angle pdb=" N GLY C 42 " pdb=" CA GLY C 42 " pdb=" C GLY C 42 " ideal model delta sigma weight residual 114.40 108.67 5.73 1.11e+00 8.12e-01 2.66e+01 angle pdb=" C22 CLR A 403 " pdb=" C23 CLR A 403 " pdb=" C24 CLR A 403 " ideal model delta sigma weight residual 111.95 102.27 9.68 3.00e+00 1.11e-01 1.04e+01 ... (remaining 9596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.58: 4618 32.58 - 65.17: 238 65.17 - 97.75: 6 97.75 - 130.33: 2 130.33 - 162.91: 1 Dihedral angle restraints: 4865 sinusoidal: 2530 harmonic: 2335 Sorted by residual: dihedral pdb=" CB CYS C 33 " pdb=" SG CYS C 33 " pdb=" SG CYS C 110 " pdb=" CB CYS C 110 " ideal model delta sinusoidal sigma weight residual -86.00 -33.95 -52.05 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS D 33 " pdb=" SG CYS D 33 " pdb=" SG CYS D 110 " pdb=" CB CYS D 110 " ideal model delta sinusoidal sigma weight residual -86.00 -34.97 -51.03 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" O21 PCF B 403 " pdb=" C2 PCF B 403 " pdb=" C3 PCF B 403 " pdb=" O31 PCF B 403 " ideal model delta sinusoidal sigma weight residual 59.47 -103.44 162.91 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 4862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 954 0.070 - 0.139: 97 0.139 - 0.208: 33 0.208 - 0.277: 32 0.277 - 0.347: 16 Chirality restraints: 1132 Sorted by residual: chirality pdb=" C17 CLR A 405 " pdb=" C13 CLR A 405 " pdb=" C16 CLR A 405 " pdb=" C20 CLR A 405 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C17 CLR A 403 " pdb=" C13 CLR A 403 " pdb=" C16 CLR A 403 " pdb=" C20 CLR A 403 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C17 CLR A 407 " pdb=" C13 CLR A 407 " pdb=" C16 CLR A 407 " pdb=" C20 CLR A 407 " both_signs ideal model delta sigma weight residual False 2.55 2.89 -0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 1129 not shown) Planarity restraints: 1060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 39 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C GLN D 39 " 0.061 2.00e-02 2.50e+03 pdb=" O GLN D 39 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA D 40 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 86 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO C 87 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 87 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 87 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 291 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO A 292 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.021 5.00e-02 4.00e+02 ... (remaining 1057 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1082 2.76 - 3.30: 6318 3.30 - 3.83: 11843 3.83 - 4.37: 13661 4.37 - 4.90: 24018 Nonbonded interactions: 56922 Sorted by model distance: nonbonded pdb=" OG1 THR B 206 " pdb=" NZ LYS B 268 " model vdw 2.229 3.120 nonbonded pdb=" O SER C 27 " pdb=" ND2 ASN C 76 " model vdw 2.290 3.120 nonbonded pdb=" NH2 ARG A 91 " pdb=" OD2 ASP A 94 " model vdw 2.290 3.120 nonbonded pdb=" OG SER D 17 " pdb=" OD1 ASN D 83 " model vdw 2.294 3.040 nonbonded pdb=" O PHE B 39 " pdb=" OG1 THR B 43 " model vdw 2.300 3.040 ... (remaining 56917 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 28 through 323 or resid 403 through 409)) selection = (chain 'B' and (resid 28 through 56 or resid 61 through 134 or (resid 145 and (n \ ame N or name CA or name C or name O or name CB )) or resid 146 through 323 or r \ esid 404 through 410)) } ncs_group { reference = (chain 'C' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB )) or resid 4 through 42 or (resid 43 through 44 and (name N \ or name CA or name C or name O or name CB )) or resid 45 or (resid 46 and (name \ N or name CA or name C or name O or name CB )) or resid 47 through 67 or (resid \ 68 and (name N or name CA or name C or name O or name CB )) or resid 69 through \ 70 or (resid 71 through 72 and (name N or name CA or name C or name O or name C \ B )) or resid 73 through 85 or (resid 86 and (name N or name CA or name C or nam \ e O or name CB )) or resid 87 through 121 or (resid 122 and (name N or name CA o \ r name C or name O or name CB )) or resid 123 through 126 or (resid 127 and (nam \ e N or name CA or name C or name O or name CB )) or resid 128 through 129)) selection = (chain 'D' and (resid 1 through 11 or (resid 12 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 62 or (resid 63 and (nam \ e N or name CA or name C or name O or name CB )) or resid 64 through 65 or (resi \ d 66 and (name N or name CA or name C or name O or name CB )) or resid 67 throug \ h 84 or (resid 85 through 86 and (name N or name CA or name C or name O or name \ CB )) or resid 87 through 129)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.580 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 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 : 0.009 0.104 7009 Z= 0.465 Angle : 1.246 22.547 9613 Z= 0.531 Chirality : 0.075 0.347 1132 Planarity : 0.004 0.049 1060 Dihedral : 16.444 162.913 3351 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.64 % Allowed : 3.05 % Favored : 96.31 % Rotamer: Outliers : 0.61 % Allowed : 22.87 % Favored : 76.52 % 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: 0.57 (0.31), residues: 786 helix: 1.87 (0.25), residues: 445 sheet: -0.78 (0.52), residues: 105 loop : -2.04 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 127 TYR 0.012 0.001 TYR A 88 PHE 0.012 0.001 PHE B 78 TRP 0.008 0.001 TRP B 85 HIS 0.001 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00909 / 0.46 ( 7003) covalent geometry : angle 1.24653 / 0.53 ( 9601) SS BOND : bond 0.00132 / 0.08 ( 6) SS BOND : angle 1.02574 / 0.58 ( 12) hydrogen bonds : bond 0.14105 / 9.70 ( 407) hydrogen bonds : angle 5.92355 / 4.55 ( 1191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 THR cc_start: 0.8336 (m) cc_final: 0.7986 (p) REVERT: A 187 MET cc_start: 0.6341 (mpt) cc_final: 0.5752 (mmm) REVERT: A 198 GLU cc_start: 0.7171 (tt0) cc_final: 0.6874 (tt0) REVERT: A 272 MET cc_start: 0.7563 (mmt) cc_final: 0.7217 (mtm) REVERT: B 126 ASP cc_start: 0.7330 (t0) cc_final: 0.7026 (t0) REVERT: B 172 ASP cc_start: 0.7854 (t0) cc_final: 0.7602 (t70) REVERT: B 288 MET cc_start: 0.8277 (mtm) cc_final: 0.8045 (mtm) REVERT: B 323 MET cc_start: 0.2688 (ttt) cc_final: 0.2438 (tpp) REVERT: D 34 MET cc_start: 0.7368 (mtp) cc_final: 0.7081 (mtp) REVERT: C 20 LEU cc_start: 0.7133 (mp) cc_final: 0.6301 (mt) outliers start: 4 outliers final: 2 residues processed: 128 average time/residue: 0.4504 time to fit residues: 61.2813 Evaluate side-chains 92 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain C residue 105 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN B 175 ASN D 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.204015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.160339 restraints weight = 6993.409| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.72 r_work: 0.3562 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7009 Z= 0.142 Angle : 0.658 8.512 9613 Z= 0.311 Chirality : 0.041 0.153 1132 Planarity : 0.005 0.046 1060 Dihedral : 12.670 158.765 2077 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.69 % Favored : 96.06 % Rotamer: Outliers : 4.27 % Allowed : 20.27 % Favored : 75.46 % 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: 0.83 (0.30), residues: 786 helix: 2.02 (0.25), residues: 447 sheet: -0.37 (0.51), residues: 101 loop : -1.98 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 245 TYR 0.013 0.001 TYR C 109 PHE 0.017 0.002 PHE D 67 TRP 0.010 0.001 TRP A 85 HIS 0.004 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 7003) covalent geometry : angle 0.65643 / 0.31 ( 9601) SS BOND : bond 0.00263 / 0.19 ( 6) SS BOND : angle 1.37297 / 0.77 ( 12) hydrogen bonds : bond 0.04763 / 3.16 ( 407) hydrogen bonds : angle 4.74224 / 3.56 ( 1191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 43 THR cc_start: 0.8378 (m) cc_final: 0.7906 (p) REVERT: A 187 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.5702 (mmm) REVERT: A 198 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7116 (tt0) REVERT: A 272 MET cc_start: 0.7764 (mmt) cc_final: 0.7412 (mtm) REVERT: B 126 ASP cc_start: 0.7595 (t0) cc_final: 0.7326 (t0) REVERT: B 272 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7279 (mtt) REVERT: B 288 MET cc_start: 0.8362 (mtm) cc_final: 0.8052 (mtm) REVERT: B 323 MET cc_start: 0.2754 (ttt) cc_final: 0.2451 (tpp) REVERT: D 34 MET cc_start: 0.8032 (mtp) cc_final: 0.7818 (mtp) REVERT: C 20 LEU cc_start: 0.6823 (mp) cc_final: 0.6079 (mt) REVERT: C 48 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8203 (m) REVERT: C 81 GLN cc_start: 0.6165 (OUTLIER) cc_final: 0.5487 (tp40) outliers start: 28 outliers final: 8 residues processed: 105 average time/residue: 0.4747 time to fit residues: 52.7652 Evaluate side-chains 97 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 105 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN C 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.192084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.150202 restraints weight = 7063.526| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.65 r_work: 0.3427 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7009 Z= 0.221 Angle : 0.750 10.041 9613 Z= 0.360 Chirality : 0.045 0.159 1132 Planarity : 0.006 0.049 1060 Dihedral : 12.731 155.593 2077 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.94 % Favored : 95.80 % Rotamer: Outliers : 4.27 % Allowed : 19.66 % Favored : 76.07 % 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: 0.46 (0.30), residues: 786 helix: 1.61 (0.24), residues: 444 sheet: -0.70 (0.47), residues: 113 loop : -1.78 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 55 TYR 0.025 0.002 TYR B 293 PHE 0.022 0.002 PHE B 110 TRP 0.021 0.002 TRP A 51 HIS 0.004 0.002 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 ( 7003) covalent geometry : angle 0.74829 / 0.36 ( 9601) SS BOND : bond 0.00396 / 0.25 ( 6) SS BOND : angle 1.58965 / 0.85 ( 12) hydrogen bonds : bond 0.05797 / 3.93 ( 407) hydrogen bonds : angle 4.86650 / 3.58 ( 1191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.7950 (m-30) cc_final: 0.7673 (m-30) REVERT: A 187 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.5939 (tpt) REVERT: B 126 ASP cc_start: 0.7638 (t0) cc_final: 0.7402 (t70) REVERT: B 272 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7325 (mtt) REVERT: B 288 MET cc_start: 0.8448 (mtm) cc_final: 0.8111 (mtm) REVERT: B 323 MET cc_start: 0.2622 (ttt) cc_final: 0.2348 (tpp) REVERT: D 55 ARG cc_start: 0.5375 (OUTLIER) cc_final: 0.5029 (mpt-90) REVERT: D 82 MET cc_start: 0.2378 (OUTLIER) cc_final: 0.2005 (mmm) REVERT: D 94 TYR cc_start: 0.6415 (m-80) cc_final: 0.5264 (m-10) REVERT: C 20 LEU cc_start: 0.7382 (mp) cc_final: 0.6675 (mt) REVERT: C 48 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8128 (m) REVERT: C 81 GLN cc_start: 0.6294 (OUTLIER) cc_final: 0.5421 (tt0) outliers start: 28 outliers final: 11 residues processed: 110 average time/residue: 0.4576 time to fit residues: 53.5306 Evaluate side-chains 103 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 105 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 68 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.194916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.150499 restraints weight = 6984.281| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.79 r_work: 0.3527 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7009 Z= 0.124 Angle : 0.585 8.005 9613 Z= 0.283 Chirality : 0.038 0.119 1132 Planarity : 0.004 0.044 1060 Dihedral : 12.029 154.468 2077 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.82 % Favored : 95.93 % Rotamer: Outliers : 2.44 % Allowed : 20.73 % Favored : 76.83 % 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: 0.90 (0.30), residues: 786 helix: 1.94 (0.25), residues: 446 sheet: -0.15 (0.50), residues: 109 loop : -1.77 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 315 TYR 0.012 0.001 TYR D 105 PHE 0.012 0.001 PHE B 78 TRP 0.008 0.001 TRP A 195 HIS 0.002 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 7003) covalent geometry : angle 0.58410 / 0.28 ( 9601) SS BOND : bond 0.00197 / 0.13 ( 6) SS BOND : angle 1.16325 / 0.61 ( 12) hydrogen bonds : bond 0.04540 / 3.01 ( 407) hydrogen bonds : angle 4.46561 / 3.31 ( 1191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7917 (mt) cc_final: 0.7705 (tp) REVERT: A 187 MET cc_start: 0.6496 (OUTLIER) cc_final: 0.5975 (tpt) REVERT: B 126 ASP cc_start: 0.7559 (t0) cc_final: 0.7299 (t70) REVERT: B 272 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7299 (mtt) REVERT: B 288 MET cc_start: 0.8344 (mtm) cc_final: 0.8017 (mtm) REVERT: D 82 MET cc_start: 0.2096 (OUTLIER) cc_final: 0.1882 (mmm) REVERT: C 20 LEU cc_start: 0.7223 (mp) cc_final: 0.6592 (mt) outliers start: 16 outliers final: 6 residues processed: 93 average time/residue: 0.3715 time to fit residues: 36.7216 Evaluate side-chains 94 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 105 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 0.0980 chunk 67 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.194461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.150957 restraints weight = 7116.692| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.54 r_work: 0.3461 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7009 Z= 0.145 Angle : 0.614 8.423 9613 Z= 0.294 Chirality : 0.039 0.135 1132 Planarity : 0.005 0.043 1060 Dihedral : 11.967 154.003 2077 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.82 % Favored : 95.93 % Rotamer: Outliers : 2.90 % Allowed : 20.73 % Favored : 76.37 % 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: 0.94 (0.30), residues: 786 helix: 1.96 (0.25), residues: 446 sheet: -0.07 (0.51), residues: 109 loop : -1.77 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 91 TYR 0.016 0.001 TYR B 293 PHE 0.013 0.002 PHE B 78 TRP 0.009 0.001 TRP A 51 HIS 0.002 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 7003) covalent geometry : angle 0.61242 / 0.29 ( 9601) SS BOND : bond 0.00266 / 0.16 ( 6) SS BOND : angle 1.23864 / 0.66 ( 12) hydrogen bonds : bond 0.04775 / 3.20 ( 407) hydrogen bonds : angle 4.38402 / 3.27 ( 1191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7737 (tp) REVERT: A 187 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.5992 (tpt) REVERT: B 126 ASP cc_start: 0.7597 (t0) cc_final: 0.7258 (t70) REVERT: B 272 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7326 (mtt) REVERT: B 288 MET cc_start: 0.8409 (mtm) cc_final: 0.8129 (mtm) REVERT: D 55 ARG cc_start: 0.4998 (OUTLIER) cc_final: 0.4647 (mmt-90) REVERT: D 82 MET cc_start: 0.1933 (OUTLIER) cc_final: 0.1576 (mmm) REVERT: C 20 LEU cc_start: 0.7278 (mp) cc_final: 0.6681 (mt) REVERT: C 81 GLN cc_start: 0.6004 (OUTLIER) cc_final: 0.5219 (tt0) outliers start: 19 outliers final: 9 residues processed: 98 average time/residue: 0.3945 time to fit residues: 41.3547 Evaluate side-chains 101 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 105 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 64 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN B 175 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.195306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.153339 restraints weight = 7181.604| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.68 r_work: 0.3521 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7009 Z= 0.125 Angle : 0.576 7.894 9613 Z= 0.279 Chirality : 0.038 0.122 1132 Planarity : 0.004 0.042 1060 Dihedral : 11.677 152.693 2077 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.20 % Favored : 95.55 % Rotamer: Outliers : 2.74 % Allowed : 21.04 % Favored : 76.22 % 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: 1.08 (0.31), residues: 786 helix: 2.09 (0.25), residues: 446 sheet: 0.09 (0.51), residues: 109 loop : -1.82 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 91 TYR 0.011 0.001 TYR B 293 PHE 0.012 0.001 PHE C 37 TRP 0.008 0.001 TRP A 195 HIS 0.002 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 7003) covalent geometry : angle 0.57461 / 0.28 ( 9601) SS BOND : bond 0.00231 / 0.14 ( 6) SS BOND : angle 1.11800 / 0.59 ( 12) hydrogen bonds : bond 0.04437 / 2.94 ( 407) hydrogen bonds : angle 4.25845 / 3.18 ( 1191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7979 (mt) cc_final: 0.7744 (tp) REVERT: A 187 MET cc_start: 0.6367 (OUTLIER) cc_final: 0.5922 (tpt) REVERT: B 126 ASP cc_start: 0.7605 (t0) cc_final: 0.7243 (t70) REVERT: B 272 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7293 (mtt) REVERT: B 288 MET cc_start: 0.8375 (mtm) cc_final: 0.8113 (mtm) REVERT: B 323 MET cc_start: 0.3264 (ttp) cc_final: 0.2512 (tpp) REVERT: D 55 ARG cc_start: 0.5071 (OUTLIER) cc_final: 0.4683 (mmt-90) REVERT: D 82 MET cc_start: 0.2293 (OUTLIER) cc_final: 0.2053 (mmm) REVERT: D 94 TYR cc_start: 0.6546 (m-80) cc_final: 0.5119 (m-10) REVERT: C 20 LEU cc_start: 0.7256 (mp) cc_final: 0.6703 (mt) outliers start: 18 outliers final: 9 residues processed: 93 average time/residue: 0.4169 time to fit residues: 41.2980 Evaluate side-chains 94 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 105 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN C 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.194480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.151692 restraints weight = 7062.124| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.61 r_work: 0.3478 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7009 Z= 0.129 Angle : 0.584 8.184 9613 Z= 0.282 Chirality : 0.038 0.130 1132 Planarity : 0.004 0.041 1060 Dihedral : 11.588 152.149 2077 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.94 % Favored : 95.80 % Rotamer: Outliers : 3.20 % Allowed : 20.27 % Favored : 76.52 % 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: 1.13 (0.31), residues: 786 helix: 2.13 (0.25), residues: 446 sheet: 0.14 (0.51), residues: 107 loop : -1.79 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 45 TYR 0.012 0.001 TYR B 293 PHE 0.013 0.001 PHE B 78 TRP 0.008 0.001 TRP A 85 HIS 0.002 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 7003) covalent geometry : angle 0.58284 / 0.28 ( 9601) SS BOND : bond 0.00228 / 0.14 ( 6) SS BOND : angle 1.10419 / 0.59 ( 12) hydrogen bonds : bond 0.04503 / 3.00 ( 407) hydrogen bonds : angle 4.23523 / 3.17 ( 1191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7832 (tp) REVERT: A 187 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.6085 (tpt) REVERT: B 126 ASP cc_start: 0.7666 (t0) cc_final: 0.7302 (t70) REVERT: B 272 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7335 (mtt) REVERT: B 288 MET cc_start: 0.8452 (mtm) cc_final: 0.8175 (mtm) REVERT: B 323 MET cc_start: 0.3171 (ttp) cc_final: 0.2500 (tpp) REVERT: D 21 SER cc_start: 0.6436 (m) cc_final: 0.6194 (t) REVERT: D 55 ARG cc_start: 0.5129 (OUTLIER) cc_final: 0.4658 (mmt-90) REVERT: D 82 MET cc_start: 0.2126 (OUTLIER) cc_final: 0.1905 (mmm) REVERT: D 94 TYR cc_start: 0.6534 (m-80) cc_final: 0.5107 (m-10) REVERT: C 20 LEU cc_start: 0.7249 (mp) cc_final: 0.6689 (mt) outliers start: 21 outliers final: 12 residues processed: 99 average time/residue: 0.4071 time to fit residues: 43.0893 Evaluate side-chains 102 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 105 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.194410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150569 restraints weight = 7125.118| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.52 r_work: 0.3509 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7009 Z= 0.129 Angle : 0.581 8.067 9613 Z= 0.282 Chirality : 0.038 0.127 1132 Planarity : 0.004 0.041 1060 Dihedral : 11.435 151.122 2077 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.82 % Favored : 95.93 % Rotamer: Outliers : 3.20 % Allowed : 20.58 % Favored : 76.22 % 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: 1.16 (0.31), residues: 786 helix: 2.13 (0.25), residues: 446 sheet: 0.21 (0.51), residues: 107 loop : -1.75 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 45 TYR 0.012 0.001 TYR D 105 PHE 0.012 0.001 PHE B 78 TRP 0.009 0.001 TRP A 195 HIS 0.002 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 7003) covalent geometry : angle 0.58046 / 0.28 ( 9601) SS BOND : bond 0.00240 / 0.14 ( 6) SS BOND : angle 1.09696 / 0.59 ( 12) hydrogen bonds : bond 0.04469 / 2.96 ( 407) hydrogen bonds : angle 4.21663 / 3.15 ( 1191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7771 (tp) REVERT: A 187 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5999 (tpt) REVERT: B 126 ASP cc_start: 0.7605 (t0) cc_final: 0.7238 (t70) REVERT: B 272 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7282 (mtt) REVERT: B 288 MET cc_start: 0.8398 (mtm) cc_final: 0.8120 (mtm) REVERT: D 55 ARG cc_start: 0.5124 (OUTLIER) cc_final: 0.4618 (mmt-90) REVERT: D 82 MET cc_start: 0.2143 (OUTLIER) cc_final: 0.1668 (mmm) REVERT: C 20 LEU cc_start: 0.7268 (mt) cc_final: 0.6642 (mt) outliers start: 21 outliers final: 13 residues processed: 98 average time/residue: 0.4013 time to fit residues: 42.1184 Evaluate side-chains 102 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 105 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 17 optimal weight: 0.0470 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN C 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.194982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151448 restraints weight = 7114.584| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.64 r_work: 0.3522 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7009 Z= 0.124 Angle : 0.577 8.107 9613 Z= 0.279 Chirality : 0.037 0.126 1132 Planarity : 0.004 0.041 1060 Dihedral : 11.273 150.751 2077 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.82 % Favored : 95.93 % Rotamer: Outliers : 2.90 % Allowed : 21.04 % Favored : 76.07 % 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: 1.21 (0.31), residues: 786 helix: 2.15 (0.25), residues: 446 sheet: 0.40 (0.51), residues: 105 loop : -1.75 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 100 TYR 0.012 0.001 TYR D 105 PHE 0.012 0.001 PHE B 78 TRP 0.009 0.001 TRP A 195 HIS 0.002 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 7003) covalent geometry : angle 0.57599 / 0.28 ( 9601) SS BOND : bond 0.00231 / 0.13 ( 6) SS BOND : angle 1.09832 / 0.59 ( 12) hydrogen bonds : bond 0.04391 / 2.91 ( 407) hydrogen bonds : angle 4.18866 / 3.13 ( 1191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7713 (tp) REVERT: A 187 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.6000 (tpt) REVERT: B 126 ASP cc_start: 0.7576 (t0) cc_final: 0.7209 (t70) REVERT: B 272 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7255 (mtt) REVERT: B 288 MET cc_start: 0.8366 (mtm) cc_final: 0.8094 (mtm) REVERT: D 55 ARG cc_start: 0.5086 (OUTLIER) cc_final: 0.4603 (mmt-90) REVERT: D 82 MET cc_start: 0.2132 (OUTLIER) cc_final: 0.1638 (mmm) REVERT: C 20 LEU cc_start: 0.7269 (mt) cc_final: 0.6626 (mt) outliers start: 19 outliers final: 13 residues processed: 97 average time/residue: 0.3376 time to fit residues: 35.0474 Evaluate side-chains 101 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 105 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.196684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154579 restraints weight = 7041.983| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.55 r_work: 0.3526 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7009 Z= 0.115 Angle : 0.565 8.624 9613 Z= 0.273 Chirality : 0.037 0.133 1132 Planarity : 0.004 0.040 1060 Dihedral : 10.956 150.305 2077 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.82 % Favored : 95.93 % Rotamer: Outliers : 2.29 % Allowed : 21.95 % Favored : 75.76 % 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: 1.33 (0.31), residues: 786 helix: 2.22 (0.25), residues: 447 sheet: 0.38 (0.52), residues: 99 loop : -1.57 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 100 TYR 0.011 0.001 TYR D 105 PHE 0.012 0.001 PHE C 37 TRP 0.009 0.001 TRP A 195 HIS 0.001 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7003) covalent geometry : angle 0.56374 / 0.27 ( 9601) SS BOND : bond 0.00210 / 0.12 ( 6) SS BOND : angle 1.05219 / 0.57 ( 12) hydrogen bonds : bond 0.04215 / 2.78 ( 407) hydrogen bonds : angle 4.12217 / 3.08 ( 1191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8004 (mt) cc_final: 0.7753 (tp) REVERT: A 187 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5999 (tpt) REVERT: B 126 ASP cc_start: 0.7571 (t0) cc_final: 0.7184 (t70) REVERT: B 244 ARG cc_start: 0.6369 (OUTLIER) cc_final: 0.5694 (ptp-110) REVERT: B 272 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7258 (mtt) REVERT: B 288 MET cc_start: 0.8375 (mtm) cc_final: 0.8074 (mtm) REVERT: D 55 ARG cc_start: 0.5145 (OUTLIER) cc_final: 0.4601 (mmt-90) REVERT: D 82 MET cc_start: 0.2085 (OUTLIER) cc_final: 0.1611 (mmm) REVERT: C 20 LEU cc_start: 0.7241 (mt) cc_final: 0.6615 (mt) outliers start: 15 outliers final: 10 residues processed: 93 average time/residue: 0.3891 time to fit residues: 38.6412 Evaluate side-chains 96 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 55 ARG Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 105 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.196310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.154215 restraints weight = 7103.360| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.62 r_work: 0.3522 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7009 Z= 0.113 Angle : 0.574 9.243 9613 Z= 0.277 Chirality : 0.037 0.137 1132 Planarity : 0.004 0.040 1060 Dihedral : 10.824 150.215 2077 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.82 % Favored : 95.93 % Rotamer: Outliers : 2.13 % Allowed : 22.71 % Favored : 75.15 % 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: 1.36 (0.31), residues: 786 helix: 2.23 (0.25), residues: 447 sheet: 0.46 (0.53), residues: 99 loop : -1.55 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 100 TYR 0.011 0.001 TYR D 105 PHE 0.013 0.001 PHE C 37 TRP 0.008 0.001 TRP A 195 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7003) covalent geometry : angle 0.57257 / 0.28 ( 9601) SS BOND : bond 0.00385 / 0.29 ( 6) SS BOND : angle 1.22973 / 0.80 ( 12) hydrogen bonds : bond 0.04187 / 2.77 ( 407) hydrogen bonds : angle 4.14597 / 3.10 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2428.06 seconds wall clock time: 42 minutes 6.72 seconds (2526.72 seconds total)