Starting phenix.real_space_refine on Fri Aug 22 19:38:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dce_30636/08_2025/7dce_30636.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dce_30636/08_2025/7dce_30636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dce_30636/08_2025/7dce_30636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dce_30636/08_2025/7dce_30636.map" model { file = "/net/cci-nas-00/data/ceres_data/7dce_30636/08_2025/7dce_30636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dce_30636/08_2025/7dce_30636.cif" } resolution = 3.8 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= 0.001 sd= 0.011 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 1 5.49 5 S 28 5.16 5 C 4602 2.51 5 N 1161 2.21 5 O 1310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 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: 7102 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1032 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 125} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2837 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 17, 'TRANS': 336} Chain: "H" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1553 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1626 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 207} Chain: "X" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'DLP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.60, per 1000 atoms: 0.23 Number of scatterers: 7102 At special positions: 0 Unit cell: (113.295, 70.965, 117.03, 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 28 16.00 P 1 15.00 O 1310 8.00 N 1161 7.00 C 4602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 185 " distance=2.02 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 195 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 81 " - pdb=" SG CYS L 175 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 198 " 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: 0.42 Conformation dependent library (CDL) restraints added in 285.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1690 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 40.4% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 209 through 230 removed outlier: 3.713A pdb=" N LEU B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 215 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 41 Processing helix chain 'X' and resid 43 through 71 Processing helix chain 'X' and resid 83 through 91 Processing helix chain 'X' and resid 95 through 112 Processing helix chain 'X' and resid 116 through 141 removed outlier: 3.505A pdb=" N LEU X 120 " --> pdb=" O SER X 116 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA X 121 " --> pdb=" O GLU X 117 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 157 Processing helix chain 'X' and resid 160 through 188 Processing helix chain 'X' and resid 195 through 225 Proline residue: X 213 - end of helix Processing helix chain 'X' and resid 228 through 247 Processing helix chain 'X' and resid 257 through 270 removed outlier: 4.160A pdb=" N TYR X 261 " --> pdb=" O SER X 257 " (cutoff:3.500A) Processing helix chain 'X' and resid 283 through 306 Processing helix chain 'X' and resid 315 through 340 removed outlier: 3.859A pdb=" N LEU X 320 " --> pdb=" O LEU X 316 " (cutoff:3.500A) Proline residue: X 321 - end of helix Processing helix chain 'X' and resid 348 through 358 removed outlier: 3.594A pdb=" N ASP X 352 " --> pdb=" O LYS X 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.603A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 157 No H-bonds generated for 'chain 'H' and resid 155 through 157' Processing helix chain 'H' and resid 185 through 190 removed outlier: 4.389A pdb=" N GLY H 189 " --> pdb=" O SER H 185 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 185 through 190' Processing helix chain 'H' and resid 200 through 203 Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'L' and resid 94 through 99 Processing helix chain 'L' and resid 125 through 132 removed outlier: 3.514A pdb=" N LYS L 130 " --> pdb=" O ASP L 126 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER L 131 " --> pdb=" O GLU L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 193 removed outlier: 3.593A pdb=" N HIS L 193 " --> pdb=" O ASP L 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 107 through 109 Processing sheet with id=AA2, first strand: chain 'B' and resid 113 through 117 removed outlier: 6.706A pdb=" N GLU B 114 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ARG B 203 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 116 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLN B 182 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP B 136 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 2 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.811A pdb=" N ALA H 32 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N MET H 33 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE H 49 " --> pdb=" O MET H 33 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP H 35 " --> pdb=" O ILE H 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.221A pdb=" N ILE H 101 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 119 through 123 removed outlier: 6.005A pdb=" N TYR H 175 " --> pdb=" O ASP H 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 119 through 123 removed outlier: 6.005A pdb=" N TYR H 175 " --> pdb=" O ASP H 143 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER H 176 " --> pdb=" O VAL H 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 150 through 153 Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.502A pdb=" N GLN L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 15 removed outlier: 6.452A pdb=" N VAL L 12 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS L 111 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA L 14 " --> pdb=" O LYS L 111 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA L 85 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.505A pdb=" N TYR L 177 " --> pdb=" O ASN L 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 157 through 158 removed outlier: 3.621A pdb=" N LYS L 211 " --> pdb=" O CYS L 198 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1211 1.32 - 1.44: 2012 1.44 - 1.57: 4029 1.57 - 1.69: 2 1.69 - 1.82: 36 Bond restraints: 7290 Sorted by residual: bond pdb=" N PCA H 1 " pdb=" CD PCA H 1 " ideal model delta sigma weight residual 1.345 1.460 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C4 DLP X 501 " pdb=" O4P DLP X 501 " ideal model delta sigma weight residual 1.409 1.454 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" O4P DLP X 501 " pdb=" P DLP X 501 " ideal model delta sigma weight residual 1.649 1.605 0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" CB VAL X 49 " pdb=" CG2 VAL X 49 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.52e+00 bond pdb=" CA ALA X 285 " pdb=" C ALA X 285 " ideal model delta sigma weight residual 1.524 1.498 0.027 1.29e-02 6.01e+03 4.25e+00 ... (remaining 7285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 9618 2.94 - 5.88: 280 5.88 - 8.82: 34 8.82 - 11.76: 9 11.76 - 14.70: 3 Bond angle restraints: 9944 Sorted by residual: angle pdb=" N ALA X 285 " pdb=" CA ALA X 285 " pdb=" C ALA X 285 " ideal model delta sigma weight residual 111.40 103.05 8.35 1.22e+00 6.72e-01 4.68e+01 angle pdb=" N GLY H 98 " pdb=" CA GLY H 98 " pdb=" C GLY H 98 " ideal model delta sigma weight residual 112.37 100.25 12.12 1.84e+00 2.95e-01 4.34e+01 angle pdb=" N TRP X 340 " pdb=" CA TRP X 340 " pdb=" C TRP X 340 " ideal model delta sigma weight residual 111.24 118.00 -6.76 1.29e+00 6.01e-01 2.74e+01 angle pdb=" N ALA H 97 " pdb=" CA ALA H 97 " pdb=" C ALA H 97 " ideal model delta sigma weight residual 107.23 99.23 8.00 1.67e+00 3.59e-01 2.29e+01 angle pdb=" N GLU B 146 " pdb=" CA GLU B 146 " pdb=" C GLU B 146 " ideal model delta sigma weight residual 108.52 115.60 -7.08 1.52e+00 4.33e-01 2.17e+01 ... (remaining 9939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.90: 4016 24.90 - 49.81: 222 49.81 - 74.71: 23 74.71 - 99.62: 9 99.62 - 124.52: 1 Dihedral angle restraints: 4271 sinusoidal: 1635 harmonic: 2636 Sorted by residual: dihedral pdb=" CB CYS L 81 " pdb=" SG CYS L 81 " pdb=" SG CYS L 175 " pdb=" CB CYS L 175 " ideal model delta sinusoidal sigma weight residual -86.00 -126.28 40.28 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" N DLP X 501 " pdb=" C4 DLP X 501 " pdb=" C5 DLP X 501 " pdb=" O4P DLP X 501 " ideal model delta sinusoidal sigma weight residual 288.95 164.43 124.52 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" CB GLU L 199 " pdb=" CG GLU L 199 " pdb=" CD GLU L 199 " pdb=" OE1 GLU L 199 " ideal model delta sinusoidal sigma weight residual 0.00 86.84 -86.84 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 4268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 802 0.056 - 0.112: 253 0.112 - 0.168: 61 0.168 - 0.224: 12 0.224 - 0.280: 5 Chirality restraints: 1133 Sorted by residual: chirality pdb=" CA PRO X 253 " pdb=" N PRO X 253 " pdb=" C PRO X 253 " pdb=" CB PRO X 253 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA LEU X 236 " pdb=" N LEU X 236 " pdb=" C LEU X 236 " pdb=" CB LEU X 236 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA TRP X 212 " pdb=" N TRP X 212 " pdb=" C TRP X 212 " pdb=" CB TRP X 212 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1130 not shown) Planarity restraints: 1234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 DLP X 501 " 0.062 2.00e-02 2.50e+03 1.21e-01 1.46e+02 pdb=" C22 DLP X 501 " -0.158 2.00e-02 2.50e+03 pdb=" C23 DLP X 501 " 0.159 2.00e-02 2.50e+03 pdb=" C24 DLP X 501 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG X 262 " 0.123 9.50e-02 1.11e+02 7.08e-02 2.67e+01 pdb=" NE ARG X 262 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG X 262 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG X 262 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG X 262 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 DLP X 501 " 0.044 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C42 DLP X 501 " -0.047 2.00e-02 2.50e+03 pdb=" C43 DLP X 501 " -0.040 2.00e-02 2.50e+03 pdb=" C44 DLP X 501 " 0.043 2.00e-02 2.50e+03 ... (remaining 1231 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1158 2.76 - 3.29: 6879 3.29 - 3.83: 11876 3.83 - 4.36: 13450 4.36 - 4.90: 23314 Nonbonded interactions: 56677 Sorted by model distance: nonbonded pdb=" OG SER L 125 " pdb=" OE1 GLU L 127 " model vdw 2.220 3.040 nonbonded pdb=" NE2 HIS X 182 " pdb=" OH TYR X 337 " model vdw 2.222 3.120 nonbonded pdb=" NH2 ARG B 184 " pdb=" OE1 GLN B 195 " model vdw 2.256 3.120 nonbonded pdb=" OH TYR X 37 " pdb=" NE2 GLN X 163 " model vdw 2.263 3.120 nonbonded pdb=" OD1 ASP X 12 " pdb=" NH2 ARG X 183 " model vdw 2.287 3.120 ... (remaining 56672 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.760 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 0.115 7296 Z= 0.424 Angle : 1.213 14.698 9956 Z= 0.666 Chirality : 0.060 0.280 1133 Planarity : 0.009 0.121 1234 Dihedral : 14.999 124.523 2563 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.44 % Favored : 92.34 % Rotamer: Outliers : 3.27 % Allowed : 10.07 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % 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: -3.04 (0.24), residues: 901 helix: -2.75 (0.24), residues: 309 sheet: -0.59 (0.29), residues: 259 loop : -2.24 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.086 0.003 ARG X 262 TYR 0.028 0.003 TYR L 98 PHE 0.026 0.003 PHE L 102 TRP 0.053 0.004 TRP X 303 HIS 0.010 0.003 HIS X 232 Details of bonding type rmsd covalent geometry : bond 0.00945 ( 7290) covalent geometry : angle 1.21171 ( 9944) SS BOND : bond 0.00511 ( 6) SS BOND : angle 1.78943 ( 12) hydrogen bonds : bond 0.13483 ( 412) hydrogen bonds : angle 7.97139 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8161 (p0) REVERT: B 123 MET cc_start: 0.9055 (ttp) cc_final: 0.8610 (ttp) REVERT: B 160 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8861 (p) REVERT: B 173 ASN cc_start: 0.8943 (t0) cc_final: 0.8709 (t0) REVERT: B 227 PHE cc_start: 0.8523 (t80) cc_final: 0.8155 (t80) REVERT: X 43 TYR cc_start: 0.7301 (p90) cc_final: 0.6746 (p90) REVERT: X 66 LEU cc_start: 0.9346 (mm) cc_final: 0.9073 (mp) REVERT: X 103 LEU cc_start: 0.9205 (mt) cc_final: 0.8900 (mt) REVERT: X 145 GLN cc_start: 0.8767 (tp40) cc_final: 0.8462 (tp40) REVERT: X 209 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8575 (mp) REVERT: X 233 PHE cc_start: 0.8576 (t80) cc_final: 0.8246 (t80) REVERT: X 259 TRP cc_start: 0.6462 (t60) cc_final: 0.6061 (t-100) REVERT: X 299 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8275 (mp) REVERT: X 326 CYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8510 (t) REVERT: H 28 LEU cc_start: 0.9142 (mt) cc_final: 0.8869 (mp) REVERT: H 33 MET cc_start: 0.8744 (mmm) cc_final: 0.8376 (mmt) REVERT: H 86 ASP cc_start: 0.8595 (m-30) cc_final: 0.8263 (m-30) REVERT: H 139 CYS cc_start: 0.6328 (m) cc_final: 0.6067 (m) REVERT: H 140 LEU cc_start: 0.9212 (tp) cc_final: 0.8793 (tt) REVERT: H 141 VAL cc_start: 0.9563 (t) cc_final: 0.9312 (p) REVERT: H 143 ASP cc_start: 0.7615 (m-30) cc_final: 0.7190 (m-30) REVERT: H 144 TYR cc_start: 0.8260 (p90) cc_final: 0.8020 (p90) REVERT: H 153 TRP cc_start: 0.7771 (m100) cc_final: 0.6835 (m100) REVERT: L 5 MET cc_start: 0.8959 (mmm) cc_final: 0.8101 (mmm) REVERT: L 91 SER cc_start: 0.9447 (t) cc_final: 0.9016 (m) REVERT: L 129 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7478 (mm) REVERT: L 180 SER cc_start: 0.7513 (p) cc_final: 0.7016 (p) REVERT: L 191 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8760 (mm-30) outliers start: 25 outliers final: 11 residues processed: 258 average time/residue: 0.0668 time to fit residues: 23.2254 Evaluate side-chains 183 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 220 LEU Chi-restraints excluded: chain X residue 263 VAL Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 326 CYS Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 24 CYS Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 129 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS B 205 HIS ** X 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 306 HIS X 339 HIS H 163 HIS L 128 GLN L 142 ASN L 164 GLN L 214 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.110770 restraints weight = 12558.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110296 restraints weight = 9363.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110839 restraints weight = 10032.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111837 restraints weight = 6181.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112614 restraints weight = 5271.680| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7296 Z= 0.179 Angle : 0.738 10.884 9956 Z= 0.366 Chirality : 0.044 0.156 1133 Planarity : 0.006 0.061 1234 Dihedral : 8.688 118.603 1053 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.92 % Allowed : 15.95 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.43 (0.27), residues: 901 helix: 0.71 (0.28), residues: 315 sheet: 0.27 (0.31), residues: 252 loop : -1.67 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 184 TYR 0.029 0.002 TYR L 33 PHE 0.028 0.002 PHE L 213 TRP 0.016 0.002 TRP X 259 HIS 0.004 0.001 HIS H 163 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 7290) covalent geometry : angle 0.73702 ( 9944) SS BOND : bond 0.00282 ( 6) SS BOND : angle 1.12490 ( 12) hydrogen bonds : bond 0.04740 ( 412) hydrogen bonds : angle 5.58574 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8502 (p0) REVERT: B 173 ASN cc_start: 0.9016 (t0) cc_final: 0.8777 (t0) REVERT: B 227 PHE cc_start: 0.8561 (t80) cc_final: 0.8193 (t80) REVERT: X 154 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8493 (mp) REVERT: X 180 ASP cc_start: 0.8806 (m-30) cc_final: 0.8587 (m-30) REVERT: X 181 TYR cc_start: 0.9470 (t80) cc_final: 0.9135 (t80) REVERT: X 182 HIS cc_start: 0.9201 (t-90) cc_final: 0.8515 (t-90) REVERT: X 259 TRP cc_start: 0.6239 (t60) cc_final: 0.5894 (t-100) REVERT: X 347 TRP cc_start: 0.6962 (t-100) cc_final: 0.6744 (t-100) REVERT: H 28 LEU cc_start: 0.9067 (mt) cc_final: 0.8841 (mp) REVERT: H 86 ASP cc_start: 0.8543 (m-30) cc_final: 0.8231 (m-30) REVERT: H 141 VAL cc_start: 0.9482 (t) cc_final: 0.9209 (p) REVERT: H 143 ASP cc_start: 0.7737 (m-30) cc_final: 0.7160 (t70) REVERT: H 144 TYR cc_start: 0.8419 (p90) cc_final: 0.8039 (p90) REVERT: H 153 TRP cc_start: 0.7889 (m100) cc_final: 0.7530 (m100) outliers start: 30 outliers final: 21 residues processed: 203 average time/residue: 0.0522 time to fit residues: 15.2881 Evaluate side-chains 182 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 170 SER Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 163 HIS Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS X 247 GLN X 288 HIS H 163 HIS L 23 ASN L 142 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.146124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.109799 restraints weight = 12407.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108560 restraints weight = 9429.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110016 restraints weight = 7440.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111543 restraints weight = 5823.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112027 restraints weight = 5503.544| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7296 Z= 0.193 Angle : 0.695 8.618 9956 Z= 0.345 Chirality : 0.043 0.176 1133 Planarity : 0.005 0.052 1234 Dihedral : 8.010 115.132 1031 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.10 % Allowed : 19.08 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.61 (0.28), residues: 901 helix: 1.85 (0.28), residues: 316 sheet: 0.69 (0.31), residues: 257 loop : -1.30 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 158 TYR 0.018 0.002 TYR X 122 PHE 0.019 0.002 PHE L 213 TRP 0.015 0.001 TRP X 110 HIS 0.007 0.001 HIS H 163 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 7290) covalent geometry : angle 0.69326 ( 9944) SS BOND : bond 0.00440 ( 6) SS BOND : angle 1.49756 ( 12) hydrogen bonds : bond 0.04030 ( 412) hydrogen bonds : angle 5.07559 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 TYR cc_start: 0.8879 (m-80) cc_final: 0.8503 (m-10) REVERT: B 173 ASN cc_start: 0.9093 (t0) cc_final: 0.8865 (t0) REVERT: B 227 PHE cc_start: 0.8628 (t80) cc_final: 0.8251 (t80) REVERT: X 145 GLN cc_start: 0.8836 (tp40) cc_final: 0.8633 (tp-100) REVERT: X 181 TYR cc_start: 0.9459 (t80) cc_final: 0.9196 (t80) REVERT: X 237 TRP cc_start: 0.8785 (t60) cc_final: 0.8336 (t60) REVERT: X 242 LEU cc_start: 0.8808 (tt) cc_final: 0.8325 (mm) REVERT: X 259 TRP cc_start: 0.6173 (t60) cc_final: 0.5886 (t-100) REVERT: H 28 LEU cc_start: 0.9191 (mt) cc_final: 0.8951 (mp) REVERT: H 86 ASP cc_start: 0.8617 (m-30) cc_final: 0.8287 (m-30) REVERT: H 141 VAL cc_start: 0.9489 (t) cc_final: 0.9204 (p) REVERT: H 143 ASP cc_start: 0.7539 (m-30) cc_final: 0.6908 (t70) REVERT: H 144 TYR cc_start: 0.8564 (p90) cc_final: 0.8276 (p90) REVERT: H 153 TRP cc_start: 0.8021 (m100) cc_final: 0.7068 (m100) REVERT: L 7 GLN cc_start: 0.8704 (tt0) cc_final: 0.8411 (tt0) REVERT: L 141 ASN cc_start: 0.9104 (t0) cc_final: 0.8533 (t0) REVERT: L 149 LYS cc_start: 0.8415 (tptt) cc_final: 0.8204 (tptp) outliers start: 39 outliers final: 30 residues processed: 200 average time/residue: 0.0520 time to fit residues: 14.8268 Evaluate side-chains 192 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 252 MET Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN L 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.092376 restraints weight = 12844.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.095493 restraints weight = 7767.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097278 restraints weight = 5816.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098694 restraints weight = 4956.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099346 restraints weight = 4490.620| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 7296 Z= 0.363 Angle : 0.795 7.445 9956 Z= 0.398 Chirality : 0.045 0.189 1133 Planarity : 0.005 0.051 1234 Dihedral : 8.291 117.103 1029 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 7.19 % Allowed : 20.13 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.53 (0.27), residues: 901 helix: 1.56 (0.27), residues: 322 sheet: 0.77 (0.31), residues: 251 loop : -1.22 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 214 TYR 0.030 0.003 TYR L 33 PHE 0.020 0.002 PHE H 91 TRP 0.017 0.002 TRP H 153 HIS 0.004 0.001 HIS L 202 Details of bonding type rmsd covalent geometry : bond 0.00823 ( 7290) covalent geometry : angle 0.79385 ( 9944) SS BOND : bond 0.00623 ( 6) SS BOND : angle 1.59764 ( 12) hydrogen bonds : bond 0.04293 ( 412) hydrogen bonds : angle 5.23222 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 PHE cc_start: 0.8760 (t80) cc_final: 0.8440 (t80) REVERT: X 181 TYR cc_start: 0.9495 (t80) cc_final: 0.9244 (t80) REVERT: X 237 TRP cc_start: 0.8979 (t60) cc_final: 0.8763 (t60) REVERT: X 252 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8086 (ptm) REVERT: X 259 TRP cc_start: 0.6436 (t60) cc_final: 0.6210 (t-100) REVERT: H 28 LEU cc_start: 0.9278 (mt) cc_final: 0.8826 (mp) REVERT: H 57 TYR cc_start: 0.9026 (m-80) cc_final: 0.8810 (m-80) REVERT: H 141 VAL cc_start: 0.9632 (t) cc_final: 0.9275 (p) REVERT: H 143 ASP cc_start: 0.7668 (m-30) cc_final: 0.6930 (t70) REVERT: H 179 SER cc_start: 0.9328 (t) cc_final: 0.9118 (t) REVERT: L 141 ASN cc_start: 0.9258 (t0) cc_final: 0.8738 (t0) REVERT: L 149 LYS cc_start: 0.8653 (tptt) cc_final: 0.8397 (tptp) outliers start: 55 outliers final: 42 residues processed: 199 average time/residue: 0.0554 time to fit residues: 15.6777 Evaluate side-chains 195 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 252 MET Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 81 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.107205 restraints weight = 12778.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107966 restraints weight = 12364.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108136 restraints weight = 11045.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.108865 restraints weight = 6285.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109875 restraints weight = 5408.841| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7296 Z= 0.219 Angle : 0.713 10.757 9956 Z= 0.350 Chirality : 0.043 0.341 1133 Planarity : 0.005 0.048 1234 Dihedral : 8.146 115.103 1029 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 6.93 % Allowed : 21.31 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.91 (0.28), residues: 901 helix: 1.96 (0.28), residues: 322 sheet: 1.01 (0.32), residues: 252 loop : -1.14 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 112 TYR 0.021 0.002 TYR H 144 PHE 0.016 0.002 PHE L 122 TRP 0.014 0.001 TRP B 210 HIS 0.002 0.001 HIS X 182 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 7290) covalent geometry : angle 0.71217 ( 9944) SS BOND : bond 0.00426 ( 6) SS BOND : angle 1.12240 ( 12) hydrogen bonds : bond 0.03860 ( 412) hydrogen bonds : angle 4.91886 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 167 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 PHE cc_start: 0.8667 (t80) cc_final: 0.8445 (t80) REVERT: X 237 TRP cc_start: 0.8949 (t60) cc_final: 0.8723 (t60) REVERT: X 242 LEU cc_start: 0.8789 (tt) cc_final: 0.8309 (mm) REVERT: X 252 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.8075 (ptm) REVERT: H 28 LEU cc_start: 0.9187 (mt) cc_final: 0.8783 (mp) REVERT: H 141 VAL cc_start: 0.9637 (t) cc_final: 0.9391 (m) REVERT: H 143 ASP cc_start: 0.7458 (m-30) cc_final: 0.6823 (t70) REVERT: L 141 ASN cc_start: 0.9007 (t0) cc_final: 0.8600 (t0) REVERT: L 149 LYS cc_start: 0.8619 (tptt) cc_final: 0.8368 (tptp) outliers start: 53 outliers final: 43 residues processed: 200 average time/residue: 0.0570 time to fit residues: 15.9696 Evaluate side-chains 201 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 252 MET Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 63 optimal weight: 0.0030 chunk 76 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN L 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.108702 restraints weight = 12586.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111237 restraints weight = 10140.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111393 restraints weight = 8456.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113653 restraints weight = 5694.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.113650 restraints weight = 4325.443| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7296 Z= 0.136 Angle : 0.681 12.194 9956 Z= 0.328 Chirality : 0.043 0.336 1133 Planarity : 0.005 0.047 1234 Dihedral : 7.899 111.158 1029 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.44 % Allowed : 23.92 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.26 (0.28), residues: 901 helix: 2.40 (0.27), residues: 317 sheet: 1.31 (0.33), residues: 234 loop : -1.05 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 203 TYR 0.023 0.002 TYR H 144 PHE 0.019 0.001 PHE L 122 TRP 0.014 0.001 TRP X 110 HIS 0.003 0.001 HIS X 182 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7290) covalent geometry : angle 0.68053 ( 9944) SS BOND : bond 0.00348 ( 6) SS BOND : angle 1.18482 ( 12) hydrogen bonds : bond 0.03561 ( 412) hydrogen bonds : angle 4.68314 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 230 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6841 (tt0) REVERT: X 114 GLU cc_start: 0.8849 (tp30) cc_final: 0.8429 (tp30) REVERT: X 180 ASP cc_start: 0.8834 (m-30) cc_final: 0.8469 (m-30) REVERT: X 181 TYR cc_start: 0.9493 (t80) cc_final: 0.9137 (t80) REVERT: X 205 LEU cc_start: 0.9179 (tp) cc_final: 0.8890 (tp) REVERT: X 237 TRP cc_start: 0.8897 (t60) cc_final: 0.8651 (t60) REVERT: X 242 LEU cc_start: 0.8699 (tt) cc_final: 0.8226 (mm) REVERT: H 28 LEU cc_start: 0.9100 (mt) cc_final: 0.8743 (mp) REVERT: H 143 ASP cc_start: 0.7269 (m-30) cc_final: 0.6793 (t70) REVERT: L 141 ASN cc_start: 0.8871 (t0) cc_final: 0.8650 (t0) REVERT: L 149 LYS cc_start: 0.8495 (tptt) cc_final: 0.8254 (tptp) outliers start: 34 outliers final: 28 residues processed: 189 average time/residue: 0.0590 time to fit residues: 15.5175 Evaluate side-chains 188 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 172 LEU Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 167 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.141139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.093728 restraints weight = 12747.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097028 restraints weight = 7501.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099225 restraints weight = 5539.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.100593 restraints weight = 4629.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101125 restraints weight = 4160.450| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 7296 Z= 0.294 Angle : 0.763 12.322 9956 Z= 0.373 Chirality : 0.045 0.356 1133 Planarity : 0.005 0.047 1234 Dihedral : 8.027 113.853 1028 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 6.93 % Allowed : 22.35 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.08 (0.28), residues: 901 helix: 2.08 (0.27), residues: 322 sheet: 1.33 (0.33), residues: 234 loop : -1.11 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 112 TYR 0.020 0.002 TYR X 95 PHE 0.018 0.002 PHE L 122 TRP 0.015 0.002 TRP X 110 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00677 ( 7290) covalent geometry : angle 0.76180 ( 9944) SS BOND : bond 0.00453 ( 6) SS BOND : angle 1.32463 ( 12) hydrogen bonds : bond 0.03897 ( 412) hydrogen bonds : angle 4.91051 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 155 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ARG cc_start: 0.8373 (mtm110) cc_final: 0.7956 (mtm110) REVERT: X 114 GLU cc_start: 0.8916 (tp30) cc_final: 0.8502 (tp30) REVERT: X 181 TYR cc_start: 0.9522 (t80) cc_final: 0.9239 (t80) REVERT: X 237 TRP cc_start: 0.8955 (t60) cc_final: 0.8677 (t60) REVERT: X 286 ILE cc_start: 0.8496 (pt) cc_final: 0.8137 (mm) REVERT: H 28 LEU cc_start: 0.9234 (mt) cc_final: 0.8801 (mp) REVERT: H 141 VAL cc_start: 0.9616 (t) cc_final: 0.9370 (m) REVERT: H 143 ASP cc_start: 0.7743 (m-30) cc_final: 0.6897 (t70) REVERT: L 141 ASN cc_start: 0.8884 (t0) cc_final: 0.8581 (t0) REVERT: L 146 ARG cc_start: 0.8245 (tmm-80) cc_final: 0.7873 (tmm-80) REVERT: L 149 LYS cc_start: 0.8547 (tptt) cc_final: 0.8247 (tptp) outliers start: 53 outliers final: 45 residues processed: 190 average time/residue: 0.0575 time to fit residues: 15.1960 Evaluate side-chains 194 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 260 LEU Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 86 optimal weight: 30.0000 chunk 49 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN L 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.107229 restraints weight = 12785.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106870 restraints weight = 11742.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108581 restraints weight = 8353.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111441 restraints weight = 6306.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111770 restraints weight = 5276.324| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7296 Z= 0.171 Angle : 0.723 12.958 9956 Z= 0.346 Chirality : 0.044 0.353 1133 Planarity : 0.005 0.049 1234 Dihedral : 7.893 111.374 1028 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.62 % Allowed : 24.31 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.22 (0.28), residues: 901 helix: 2.27 (0.27), residues: 321 sheet: 1.35 (0.33), residues: 234 loop : -1.04 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 112 TYR 0.030 0.002 TYR H 144 PHE 0.020 0.001 PHE L 122 TRP 0.028 0.002 TRP X 259 HIS 0.003 0.001 HIS X 182 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 7290) covalent geometry : angle 0.72240 ( 9944) SS BOND : bond 0.00364 ( 6) SS BOND : angle 0.99688 ( 12) hydrogen bonds : bond 0.03606 ( 412) hydrogen bonds : angle 4.74915 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ARG cc_start: 0.8305 (mtm110) cc_final: 0.7934 (mtm110) REVERT: B 230 GLU cc_start: 0.7695 (mm-30) cc_final: 0.6871 (tt0) REVERT: X 30 ASP cc_start: 0.8335 (t0) cc_final: 0.8107 (m-30) REVERT: X 114 GLU cc_start: 0.8845 (tp30) cc_final: 0.8512 (tp30) REVERT: X 180 ASP cc_start: 0.8861 (m-30) cc_final: 0.8473 (m-30) REVERT: X 181 TYR cc_start: 0.9520 (t80) cc_final: 0.9223 (t80) REVERT: X 205 LEU cc_start: 0.9174 (tp) cc_final: 0.8885 (tp) REVERT: X 237 TRP cc_start: 0.8939 (t60) cc_final: 0.8642 (t60) REVERT: X 242 LEU cc_start: 0.8754 (tt) cc_final: 0.8327 (mm) REVERT: X 286 ILE cc_start: 0.8526 (pt) cc_final: 0.8151 (mm) REVERT: H 28 LEU cc_start: 0.9134 (mt) cc_final: 0.8725 (mp) REVERT: H 143 ASP cc_start: 0.7317 (m-30) cc_final: 0.6825 (t70) REVERT: L 141 ASN cc_start: 0.8761 (t0) cc_final: 0.8434 (t0) REVERT: L 146 ARG cc_start: 0.8138 (tmm-80) cc_final: 0.7806 (tmm-80) REVERT: L 190 TYR cc_start: 0.7890 (t80) cc_final: 0.7577 (t80) outliers start: 43 outliers final: 39 residues processed: 193 average time/residue: 0.0516 time to fit residues: 14.0234 Evaluate side-chains 199 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 335 LEU Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 167 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 74 optimal weight: 8.9990 chunk 23 optimal weight: 40.0000 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 72 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.143903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.106613 restraints weight = 12663.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106872 restraints weight = 10619.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107267 restraints weight = 10564.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108202 restraints weight = 6548.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110555 restraints weight = 5610.261| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7296 Z= 0.185 Angle : 0.728 12.625 9956 Z= 0.349 Chirality : 0.044 0.355 1133 Planarity : 0.005 0.047 1234 Dihedral : 7.823 110.213 1028 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 6.41 % Allowed : 23.66 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.31 (0.28), residues: 901 helix: 2.30 (0.27), residues: 321 sheet: 1.44 (0.33), residues: 234 loop : -0.98 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 203 TYR 0.025 0.002 TYR H 144 PHE 0.021 0.001 PHE L 122 TRP 0.018 0.001 TRP X 110 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 7290) covalent geometry : angle 0.72742 ( 9944) SS BOND : bond 0.00380 ( 6) SS BOND : angle 1.01555 ( 12) hydrogen bonds : bond 0.03593 ( 412) hydrogen bonds : angle 4.71062 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 163 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7493 (ttp80) REVERT: B 203 ARG cc_start: 0.8373 (mtm110) cc_final: 0.8002 (mtm110) REVERT: B 230 GLU cc_start: 0.7680 (mm-30) cc_final: 0.6885 (tt0) REVERT: X 30 ASP cc_start: 0.8306 (t0) cc_final: 0.8090 (m-30) REVERT: X 114 GLU cc_start: 0.8884 (tp30) cc_final: 0.8577 (tp30) REVERT: X 167 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7519 (mt) REVERT: X 180 ASP cc_start: 0.8874 (m-30) cc_final: 0.8484 (m-30) REVERT: X 181 TYR cc_start: 0.9479 (t80) cc_final: 0.9239 (t80) REVERT: X 205 LEU cc_start: 0.9165 (tp) cc_final: 0.8878 (tp) REVERT: X 237 TRP cc_start: 0.8918 (t60) cc_final: 0.8623 (t60) REVERT: X 242 LEU cc_start: 0.8737 (tt) cc_final: 0.8294 (mm) REVERT: X 286 ILE cc_start: 0.8523 (pt) cc_final: 0.8152 (mm) REVERT: H 28 LEU cc_start: 0.9149 (mt) cc_final: 0.8731 (mp) REVERT: H 143 ASP cc_start: 0.7460 (m-30) cc_final: 0.6894 (t70) REVERT: L 141 ASN cc_start: 0.8747 (t0) cc_final: 0.8429 (t0) REVERT: L 146 ARG cc_start: 0.8197 (tmm-80) cc_final: 0.7889 (tmm-80) REVERT: L 190 TYR cc_start: 0.8030 (t80) cc_final: 0.7722 (t80) outliers start: 49 outliers final: 48 residues processed: 194 average time/residue: 0.0716 time to fit residues: 19.6382 Evaluate side-chains 206 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 172 LEU Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 335 LEU Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 17 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.146505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109963 restraints weight = 12670.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110806 restraints weight = 10910.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111362 restraints weight = 10237.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112093 restraints weight = 6288.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114326 restraints weight = 5493.407| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7296 Z= 0.141 Angle : 0.709 12.620 9956 Z= 0.337 Chirality : 0.043 0.350 1133 Planarity : 0.005 0.048 1234 Dihedral : 7.642 105.920 1028 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.97 % Allowed : 25.23 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.29), residues: 901 helix: 2.48 (0.28), residues: 322 sheet: 1.52 (0.34), residues: 233 loop : -0.90 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 112 TYR 0.025 0.002 TYR H 144 PHE 0.018 0.001 PHE L 122 TRP 0.021 0.001 TRP X 110 HIS 0.004 0.001 HIS X 182 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7290) covalent geometry : angle 0.70900 ( 9944) SS BOND : bond 0.00309 ( 6) SS BOND : angle 0.87077 ( 12) hydrogen bonds : bond 0.03332 ( 412) hydrogen bonds : angle 4.54913 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 ARG cc_start: 0.8307 (mtm110) cc_final: 0.7967 (mtm110) REVERT: B 230 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6792 (tt0) REVERT: X 114 GLU cc_start: 0.8816 (tp30) cc_final: 0.8520 (tp30) REVERT: X 180 ASP cc_start: 0.8803 (m-30) cc_final: 0.8467 (m-30) REVERT: X 181 TYR cc_start: 0.9361 (t80) cc_final: 0.9080 (t80) REVERT: X 205 LEU cc_start: 0.9149 (tp) cc_final: 0.8868 (tp) REVERT: X 242 LEU cc_start: 0.8691 (tt) cc_final: 0.8191 (mm) REVERT: X 286 ILE cc_start: 0.8436 (pt) cc_final: 0.8027 (mm) REVERT: H 28 LEU cc_start: 0.9059 (mt) cc_final: 0.8662 (mp) REVERT: H 45 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7590 (mt-10) REVERT: H 143 ASP cc_start: 0.7262 (m-30) cc_final: 0.6847 (t70) REVERT: L 141 ASN cc_start: 0.8628 (t0) cc_final: 0.8362 (t0) REVERT: L 146 ARG cc_start: 0.8174 (tmm-80) cc_final: 0.7878 (tmm-80) REVERT: L 190 TYR cc_start: 0.7941 (t80) cc_final: 0.7563 (t80) outliers start: 38 outliers final: 36 residues processed: 199 average time/residue: 0.0714 time to fit residues: 19.7330 Evaluate side-chains 199 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 335 LEU Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.098028 restraints weight = 12811.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101521 restraints weight = 7544.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103793 restraints weight = 5529.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104911 restraints weight = 4606.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105933 restraints weight = 4164.830| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7296 Z= 0.177 Angle : 0.739 12.316 9956 Z= 0.354 Chirality : 0.044 0.348 1133 Planarity : 0.005 0.047 1234 Dihedral : 7.630 105.171 1028 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.71 % Allowed : 26.01 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.45 (0.29), residues: 901 helix: 2.39 (0.28), residues: 322 sheet: 1.47 (0.33), residues: 240 loop : -0.89 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 184 TYR 0.025 0.002 TYR H 144 PHE 0.019 0.001 PHE L 122 TRP 0.021 0.002 TRP X 259 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 7290) covalent geometry : angle 0.73904 ( 9944) SS BOND : bond 0.00352 ( 6) SS BOND : angle 1.03216 ( 12) hydrogen bonds : bond 0.03555 ( 412) hydrogen bonds : angle 4.61692 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 999.05 seconds wall clock time: 17 minutes 57.48 seconds (1077.48 seconds total)