Starting phenix.real_space_refine on Wed Feb 12 05:32:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dce_30636/02_2025/7dce_30636.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dce_30636/02_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_30636/02_2025/7dce_30636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dce_30636/02_2025/7dce_30636.map" model { file = "/net/cci-nas-00/data/ceres_data/7dce_30636/02_2025/7dce_30636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dce_30636/02_2025/7dce_30636.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.78, per 1000 atoms: 0.67 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: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.06 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: 2.30 Time building geometry restraints manager: 2.35 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: 0.340 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: 0.220 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.920 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.420 ------------------------------------------------------------------------------- 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 7290 Z= 0.611 Angle : 1.212 14.698 9944 Z= 0.665 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 : 11.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.053 0.004 TRP X 303 HIS 0.010 0.003 HIS X 232 PHE 0.026 0.003 PHE L 102 TYR 0.028 0.003 TYR L 98 ARG 0.086 0.003 ARG X 262 *********************** 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 : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8162 (p0) REVERT: B 123 MET cc_start: 0.9055 (ttp) cc_final: 0.8611 (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: 0.8154 (t80) REVERT: X 43 TYR cc_start: 0.7301 (p90) cc_final: 0.6745 (p90) REVERT: X 66 LEU cc_start: 0.9346 (mm) cc_final: 0.9072 (mp) REVERT: X 103 LEU cc_start: 0.9205 (mt) cc_final: 0.8900 (mt) REVERT: X 132 MET cc_start: 0.9183 (mmm) cc_final: 0.8786 (mmp) 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: 0.8574 (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: 0.6063 (t-100) REVERT: X 299 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8276 (mp) REVERT: X 326 CYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8511 (t) REVERT: H 28 LEU cc_start: 0.9142 (mt) cc_final: 0.8870 (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: 0.6049 (m) REVERT: H 140 LEU cc_start: 0.9212 (tp) cc_final: 0.8795 (tt) REVERT: H 143 ASP cc_start: 0.7615 (m-30) cc_final: 0.7188 (m-30) REVERT: H 144 TYR cc_start: 0.8260 (p90) cc_final: 0.8026 (p90) REVERT: H 153 TRP cc_start: 0.7771 (m100) cc_final: 0.6836 (m100) REVERT: L 5 MET cc_start: 0.8959 (mmm) cc_final: 0.8100 (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: 0.1907 time to fit residues: 65.2335 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 : 0.751 ------------------------------------------------------------------------------- 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 75 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS B 205 HIS X 105 GLN ** 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 = 0.3870 r_free = 0.3870 target = 0.148714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112488 restraints weight = 12353.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111850 restraints weight = 9617.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112477 restraints weight = 9269.473| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7290 Z= 0.221 Angle : 0.726 11.109 9944 Z= 0.359 Chirality : 0.044 0.154 1133 Planarity : 0.006 0.060 1234 Dihedral : 8.673 117.624 1053 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.05 % Allowed : 15.56 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.27), residues: 901 helix: 0.88 (0.28), residues: 315 sheet: 0.34 (0.31), residues: 252 loop : -1.67 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 259 HIS 0.004 0.001 HIS H 163 PHE 0.030 0.002 PHE L 213 TYR 0.029 0.002 TYR L 33 ARG 0.007 0.001 ARG B 184 *********************** 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 220 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8265 (p0) REVERT: B 173 ASN cc_start: 0.8998 (t0) cc_final: 0.8762 (t0) REVERT: B 227 PHE cc_start: 0.8551 (t80) cc_final: 0.8161 (t80) REVERT: X 43 TYR cc_start: 0.6962 (p90) cc_final: 0.6033 (p90) REVERT: X 154 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8435 (mp) REVERT: X 180 ASP cc_start: 0.8758 (m-30) cc_final: 0.8293 (m-30) REVERT: X 181 TYR cc_start: 0.9531 (t80) cc_final: 0.9099 (t80) REVERT: X 233 PHE cc_start: 0.8561 (t80) cc_final: 0.8199 (t80) REVERT: X 259 TRP cc_start: 0.6184 (t60) cc_final: 0.5876 (t-100) REVERT: H 28 LEU cc_start: 0.9015 (mt) cc_final: 0.8796 (mp) REVERT: H 86 ASP cc_start: 0.8532 (m-30) cc_final: 0.8265 (m-30) REVERT: H 141 VAL cc_start: 0.9488 (OUTLIER) cc_final: 0.9280 (p) REVERT: H 143 ASP cc_start: 0.7729 (m-30) cc_final: 0.7202 (t70) REVERT: H 144 TYR cc_start: 0.8418 (p90) cc_final: 0.8093 (p90) REVERT: H 153 TRP cc_start: 0.7812 (m100) cc_final: 0.7482 (m100) outliers start: 31 outliers final: 19 residues processed: 206 average time/residue: 0.1564 time to fit residues: 44.9674 Evaluate side-chains 186 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL 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 170 SER 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 141 VAL 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 30 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.0050 chunk 33 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS B 117 ASN X 247 GLN X 288 HIS H 163 HIS L 23 ASN L 142 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.110502 restraints weight = 12353.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110336 restraints weight = 9507.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111456 restraints weight = 7463.843| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7290 Z= 0.274 Angle : 0.693 8.565 9944 Z= 0.342 Chirality : 0.043 0.208 1133 Planarity : 0.005 0.052 1234 Dihedral : 7.814 114.454 1029 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.23 % Allowed : 19.35 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.28), residues: 901 helix: 1.92 (0.28), residues: 316 sheet: 0.79 (0.31), residues: 257 loop : -1.28 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 110 HIS 0.010 0.001 HIS H 163 PHE 0.019 0.002 PHE L 213 TYR 0.018 0.002 TYR X 122 ARG 0.004 0.000 ARG X 158 *********************** 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 214 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8534 (p0) REVERT: B 140 TYR cc_start: 0.8889 (m-80) cc_final: 0.8484 (m-10) REVERT: B 173 ASN cc_start: 0.9088 (t0) cc_final: 0.8862 (t0) REVERT: B 227 PHE cc_start: 0.8651 (t80) cc_final: 0.8300 (t80) REVERT: X 237 TRP cc_start: 0.8766 (t60) cc_final: 0.8305 (t60) REVERT: X 242 LEU cc_start: 0.8717 (tt) cc_final: 0.8230 (mm) REVERT: X 259 TRP cc_start: 0.6160 (t60) cc_final: 0.5888 (t-100) REVERT: H 28 LEU cc_start: 0.9189 (mt) cc_final: 0.8940 (mp) REVERT: H 86 ASP cc_start: 0.8685 (m-30) cc_final: 0.8326 (m-30) REVERT: H 141 VAL cc_start: 0.9539 (OUTLIER) cc_final: 0.9237 (p) REVERT: H 143 ASP cc_start: 0.7550 (m-30) cc_final: 0.6920 (t70) REVERT: H 153 TRP cc_start: 0.7934 (m100) cc_final: 0.7109 (m100) REVERT: L 7 GLN cc_start: 0.8751 (tt0) cc_final: 0.8455 (tt0) REVERT: L 141 ASN cc_start: 0.9085 (t0) cc_final: 0.8560 (t0) REVERT: L 149 LYS cc_start: 0.8364 (tptt) cc_final: 0.8160 (tptp) outliers start: 40 outliers final: 32 residues processed: 199 average time/residue: 0.1641 time to fit residues: 45.4601 Evaluate side-chains 198 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL 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 B residue 219 VAL Chi-restraints excluded: chain B residue 226 ILE 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 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 338 TYR 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 141 VAL 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 Chi-restraints excluded: chain L residue 180 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN B 170 HIS L 142 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.145859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108247 restraints weight = 12733.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108715 restraints weight = 11662.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109003 restraints weight = 10806.053| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7290 Z= 0.328 Angle : 0.691 7.898 9944 Z= 0.343 Chirality : 0.043 0.143 1133 Planarity : 0.005 0.048 1234 Dihedral : 7.726 111.557 1029 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 6.41 % Allowed : 20.39 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.28), residues: 901 helix: 2.11 (0.27), residues: 317 sheet: 0.92 (0.31), residues: 257 loop : -1.08 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 153 HIS 0.003 0.001 HIS X 182 PHE 0.029 0.002 PHE L 213 TYR 0.018 0.002 TYR X 95 ARG 0.003 0.000 ARG X 158 *********************** 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 222 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 PHE cc_start: 0.8649 (t80) cc_final: 0.8363 (t80) REVERT: X 114 GLU cc_start: 0.8968 (tp30) cc_final: 0.8454 (tp30) REVERT: X 181 TYR cc_start: 0.9464 (t80) cc_final: 0.9018 (t80) REVERT: X 237 TRP cc_start: 0.8923 (t60) cc_final: 0.8701 (t60) REVERT: X 242 LEU cc_start: 0.8689 (tt) cc_final: 0.8229 (mm) REVERT: X 259 TRP cc_start: 0.6273 (t60) cc_final: 0.5928 (t-100) REVERT: H 28 LEU cc_start: 0.9206 (mt) cc_final: 0.8854 (mp) REVERT: H 86 ASP cc_start: 0.8744 (m-30) cc_final: 0.8420 (m-30) REVERT: H 143 ASP cc_start: 0.7586 (m-30) cc_final: 0.6913 (t70) REVERT: H 144 TYR cc_start: 0.8508 (p90) cc_final: 0.8092 (p90) REVERT: L 141 ASN cc_start: 0.9148 (t0) cc_final: 0.8656 (t0) REVERT: L 149 LYS cc_start: 0.8413 (tptt) cc_final: 0.8174 (tptp) outliers start: 49 outliers final: 38 residues processed: 199 average time/residue: 0.1673 time to fit residues: 45.9664 Evaluate side-chains 198 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 143 THR 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 212 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 226 ILE 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 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 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 L residue 4 VAL 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 96 ILE 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 39 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 26 optimal weight: 0.4980 chunk 10 optimal weight: 0.0970 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.147959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.111708 restraints weight = 12333.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114596 restraints weight = 10152.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114293 restraints weight = 8911.572| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7290 Z= 0.177 Angle : 0.640 8.543 9944 Z= 0.311 Chirality : 0.041 0.155 1133 Planarity : 0.004 0.046 1234 Dihedral : 7.309 105.371 1026 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.18 % Allowed : 24.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.28), residues: 901 helix: 2.51 (0.28), residues: 317 sheet: 1.24 (0.32), residues: 245 loop : -0.92 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 110 HIS 0.004 0.001 HIS B 170 PHE 0.018 0.001 PHE L 122 TYR 0.020 0.001 TYR L 33 ARG 0.003 0.000 ARG L 112 *********************** 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 207 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 TYR cc_start: 0.8919 (m-80) cc_final: 0.8523 (m-10) REVERT: B 230 GLU cc_start: 0.7747 (mm-30) cc_final: 0.6895 (tt0) REVERT: X 114 GLU cc_start: 0.8851 (tp30) cc_final: 0.8442 (tp30) REVERT: X 181 TYR cc_start: 0.9297 (t80) cc_final: 0.8837 (t80) REVERT: X 237 TRP cc_start: 0.8838 (t60) cc_final: 0.8311 (t60) REVERT: X 242 LEU cc_start: 0.8605 (tt) cc_final: 0.8145 (mm) REVERT: H 28 LEU cc_start: 0.9059 (mt) cc_final: 0.8720 (mp) REVERT: H 86 ASP cc_start: 0.8738 (m-30) cc_final: 0.8459 (m-30) REVERT: H 143 ASP cc_start: 0.7432 (m-30) cc_final: 0.6958 (t70) REVERT: H 144 TYR cc_start: 0.8245 (p90) cc_final: 0.7868 (p90) REVERT: L 141 ASN cc_start: 0.8946 (t0) cc_final: 0.8557 (t0) outliers start: 32 outliers final: 20 residues processed: 193 average time/residue: 0.1703 time to fit residues: 44.8363 Evaluate side-chains 181 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR 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 294 SER Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR 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 L residue 3 VAL Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 167 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 70 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 0.0020 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 34 ASN L 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.145625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.108929 restraints weight = 12585.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114038 restraints weight = 11511.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113292 restraints weight = 7694.579| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7290 Z= 0.265 Angle : 0.666 10.583 9944 Z= 0.325 Chirality : 0.042 0.303 1133 Planarity : 0.005 0.045 1234 Dihedral : 7.335 104.062 1026 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.75 % Allowed : 23.40 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.28), residues: 901 helix: 2.34 (0.28), residues: 323 sheet: 1.26 (0.32), residues: 254 loop : -0.83 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 347 HIS 0.003 0.001 HIS X 182 PHE 0.016 0.001 PHE L 122 TYR 0.018 0.002 TYR X 122 ARG 0.003 0.000 ARG L 112 *********************** 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 205 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 85 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8580 (pp) REVERT: X 167 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7206 (mt) REVERT: X 181 TYR cc_start: 0.9384 (t80) cc_final: 0.9110 (t80) REVERT: X 237 TRP cc_start: 0.8912 (t60) cc_final: 0.8604 (t60) REVERT: X 242 LEU cc_start: 0.8652 (tt) cc_final: 0.8184 (mm) REVERT: H 28 LEU cc_start: 0.9143 (mt) cc_final: 0.8768 (mp) REVERT: H 86 ASP cc_start: 0.8762 (m-30) cc_final: 0.8362 (m-30) REVERT: H 143 ASP cc_start: 0.7336 (m-30) cc_final: 0.6874 (t70) REVERT: H 144 TYR cc_start: 0.8432 (p90) cc_final: 0.8096 (p90) REVERT: L 141 ASN cc_start: 0.8846 (t0) cc_final: 0.8497 (t0) outliers start: 44 outliers final: 38 residues processed: 187 average time/residue: 0.1710 time to fit residues: 43.9423 Evaluate side-chains 194 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 167 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 X residue 62 LEU Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 133 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 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 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE 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 123 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 5 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** 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 = 0.3843 r_free = 0.3843 target = 0.146202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109254 restraints weight = 12584.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110893 restraints weight = 11212.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110785 restraints weight = 10408.203| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 7290 Z= 0.250 Angle : 0.678 12.840 9944 Z= 0.327 Chirality : 0.042 0.365 1133 Planarity : 0.004 0.044 1234 Dihedral : 7.256 101.961 1026 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.36 % Allowed : 24.31 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.28), residues: 901 helix: 2.59 (0.27), residues: 317 sheet: 1.39 (0.32), residues: 252 loop : -0.89 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 110 HIS 0.003 0.001 HIS X 182 PHE 0.023 0.001 PHE L 122 TYR 0.015 0.001 TYR H 57 ARG 0.003 0.000 ARG L 112 *********************** 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 203 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 181 TYR cc_start: 0.9346 (t80) cc_final: 0.9113 (t80) REVERT: X 237 TRP cc_start: 0.8904 (t60) cc_final: 0.8628 (t60) REVERT: X 242 LEU cc_start: 0.8637 (tt) cc_final: 0.8206 (mm) REVERT: H 28 LEU cc_start: 0.9117 (mt) cc_final: 0.8741 (mp) REVERT: H 86 ASP cc_start: 0.8929 (m-30) cc_final: 0.8551 (m-30) REVERT: H 143 ASP cc_start: 0.7468 (m-30) cc_final: 0.6908 (t70) REVERT: H 144 TYR cc_start: 0.8542 (p90) cc_final: 0.8233 (p90) REVERT: L 5 MET cc_start: 0.8831 (mmt) cc_final: 0.7539 (mmm) REVERT: L 141 ASN cc_start: 0.8803 (t0) cc_final: 0.8480 (t0) outliers start: 41 outliers final: 34 residues processed: 186 average time/residue: 0.1691 time to fit residues: 42.8497 Evaluate side-chains 189 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR 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 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 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 H residue 123 LEU 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 91 SER Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 167 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 0.0170 chunk 24 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.109903 restraints weight = 12541.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111046 restraints weight = 11497.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111279 restraints weight = 10800.273| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7290 Z= 0.261 Angle : 0.688 12.345 9944 Z= 0.332 Chirality : 0.043 0.356 1133 Planarity : 0.005 0.044 1234 Dihedral : 7.245 101.012 1026 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.88 % Allowed : 23.01 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.28), residues: 901 helix: 2.47 (0.28), residues: 323 sheet: 1.47 (0.32), residues: 252 loop : -0.80 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 110 HIS 0.003 0.001 HIS X 182 PHE 0.021 0.001 PHE L 122 TYR 0.026 0.002 TYR L 98 ARG 0.003 0.000 ARG L 112 *********************** 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 204 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7742 (ttm-80) REVERT: X 167 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7562 (mt) REVERT: X 180 ASP cc_start: 0.8535 (m-30) cc_final: 0.8310 (m-30) REVERT: X 181 TYR cc_start: 0.9406 (t80) cc_final: 0.9145 (t80) REVERT: X 237 TRP cc_start: 0.8921 (t60) cc_final: 0.8691 (t60) REVERT: X 242 LEU cc_start: 0.8651 (tt) cc_final: 0.8228 (mm) REVERT: X 278 GLU cc_start: 0.7385 (mp0) cc_final: 0.7164 (mp0) REVERT: H 28 LEU cc_start: 0.9118 (mt) cc_final: 0.8702 (mp) REVERT: H 86 ASP cc_start: 0.8886 (m-30) cc_final: 0.8497 (m-30) REVERT: L 5 MET cc_start: 0.8860 (mmt) cc_final: 0.7626 (mmm) REVERT: L 141 ASN cc_start: 0.8741 (t0) cc_final: 0.8410 (t0) REVERT: L 190 TYR cc_start: 0.7843 (t80) cc_final: 0.7601 (t80) outliers start: 45 outliers final: 39 residues processed: 190 average time/residue: 0.1777 time to fit residues: 45.7227 Evaluate side-chains 196 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 133 LEU 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 272 SER 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 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 H residue 123 LEU Chi-restraints excluded: chain L residue 6 THR 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 96 ILE Chi-restraints excluded: chain L residue 137 VAL 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 49 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.145363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.108544 restraints weight = 12621.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110553 restraints weight = 11642.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110730 restraints weight = 9341.961| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7290 Z= 0.297 Angle : 0.703 11.766 9944 Z= 0.338 Chirality : 0.043 0.342 1133 Planarity : 0.005 0.046 1234 Dihedral : 7.279 101.536 1026 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.75 % Allowed : 23.40 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.28), residues: 901 helix: 2.45 (0.28), residues: 323 sheet: 1.49 (0.32), residues: 252 loop : -0.79 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 110 HIS 0.007 0.001 HIS B 115 PHE 0.021 0.001 PHE L 122 TYR 0.028 0.002 TYR H 144 ARG 0.005 0.000 ARG L 112 *********************** 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 197 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7631 (ttp80) REVERT: B 184 ARG cc_start: 0.7950 (ttm-80) cc_final: 0.7690 (ttm-80) REVERT: X 167 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7612 (mt) REVERT: X 180 ASP cc_start: 0.8492 (m-30) cc_final: 0.8267 (m-30) REVERT: X 237 TRP cc_start: 0.8923 (t60) cc_final: 0.8716 (t60) REVERT: X 242 LEU cc_start: 0.8673 (tt) cc_final: 0.8315 (mm) REVERT: H 28 LEU cc_start: 0.9140 (mt) cc_final: 0.8729 (mp) REVERT: H 86 ASP cc_start: 0.8796 (m-30) cc_final: 0.8457 (m-30) REVERT: L 141 ASN cc_start: 0.8731 (t0) cc_final: 0.8401 (t0) REVERT: L 190 TYR cc_start: 0.7924 (t80) cc_final: 0.7661 (t80) outliers start: 44 outliers final: 42 residues processed: 181 average time/residue: 0.1749 time to fit residues: 44.1254 Evaluate side-chains 193 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 135 THR Chi-restraints excluded: chain B residue 162 SER 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 X residue 17 VAL Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 133 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 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 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 H residue 123 LEU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 6 THR 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 96 ILE Chi-restraints excluded: chain L residue 137 VAL 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 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 60 optimal weight: 0.0070 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.148854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.111403 restraints weight = 12668.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111333 restraints weight = 9517.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112344 restraints weight = 7538.856| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7290 Z= 0.189 Angle : 0.700 11.487 9944 Z= 0.329 Chirality : 0.043 0.336 1133 Planarity : 0.005 0.045 1234 Dihedral : 7.071 97.595 1026 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.66 % Allowed : 25.75 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.29), residues: 901 helix: 2.71 (0.28), residues: 319 sheet: 1.63 (0.33), residues: 244 loop : -0.70 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP X 347 HIS 0.003 0.001 HIS X 182 PHE 0.021 0.001 PHE L 122 TYR 0.022 0.002 TYR H 144 ARG 0.004 0.000 ARG L 112 ********************** 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 191 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ARG cc_start: 0.7819 (ttp80) cc_final: 0.7461 (ttp80) REVERT: B 184 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7619 (ttm-80) REVERT: X 180 ASP cc_start: 0.8515 (m-30) cc_final: 0.8287 (m-30) REVERT: X 181 TYR cc_start: 0.9345 (t80) cc_final: 0.9063 (t80) REVERT: X 242 LEU cc_start: 0.8630 (tt) cc_final: 0.8218 (mm) REVERT: H 28 LEU cc_start: 0.9045 (mt) cc_final: 0.8629 (mp) REVERT: H 45 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7534 (mt-10) REVERT: H 86 ASP cc_start: 0.8914 (m-30) cc_final: 0.8645 (m-30) REVERT: L 5 MET cc_start: 0.8891 (mmt) cc_final: 0.7760 (mmm) REVERT: L 141 ASN cc_start: 0.8680 (t0) cc_final: 0.8366 (t0) REVERT: L 190 TYR cc_start: 0.7920 (t80) cc_final: 0.7563 (t80) outliers start: 28 outliers final: 22 residues processed: 183 average time/residue: 0.1910 time to fit residues: 47.3052 Evaluate side-chains 178 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 162 SER Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR 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 294 SER 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 50 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 5 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 62 optimal weight: 0.0670 chunk 40 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.107690 restraints weight = 12669.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111519 restraints weight = 11782.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111052 restraints weight = 8649.868| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 7290 Z= 0.410 Angle : 0.783 11.366 9944 Z= 0.376 Chirality : 0.045 0.336 1133 Planarity : 0.005 0.045 1234 Dihedral : 7.314 101.179 1026 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.31 % Allowed : 26.54 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.29), residues: 901 helix: 2.42 (0.28), residues: 323 sheet: 1.49 (0.33), residues: 252 loop : -0.75 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP X 110 HIS 0.007 0.001 HIS B 115 PHE 0.018 0.002 PHE H 91 TYR 0.031 0.002 TYR L 98 ARG 0.006 0.001 ARG H 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2156.00 seconds wall clock time: 39 minutes 32.77 seconds (2372.77 seconds total)