Starting phenix.real_space_refine on Wed Mar 12 05:28:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dce_30636/03_2025/7dce_30636.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dce_30636/03_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_30636/03_2025/7dce_30636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dce_30636/03_2025/7dce_30636.map" model { file = "/net/cci-nas-00/data/ceres_data/7dce_30636/03_2025/7dce_30636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dce_30636/03_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-5624/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: 4.41, per 1000 atoms: 0.62 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: 1.63 Conformation dependent library (CDL) restraints added in 954.9 milliseconds 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1690 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 40.4% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 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: 2.21 Time building geometry restraints manager: 1.96 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.500 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.260 ------------------------------------------------------------------------------- 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 : 0.726 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: 0.1802 time to fit residues: 61.8230 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 : 0.757 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.111850 restraints weight = 9617.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112477 restraints weight = 9269.466| |-----------------------------------------------------------------------------| 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 : 2.491 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: 0.8914 (OUTLIER) cc_final: 0.8266 (p0) REVERT: B 173 ASN cc_start: 0.8998 (t0) cc_final: 0.8762 (t0) REVERT: B 227 PHE cc_start: 0.8550 (t80) cc_final: 0.8160 (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: 0.6185 (t60) cc_final: 0.5877 (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: 0.7730 (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: 0.2496 time to fit residues: 74.9743 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 : 0.794 ------------------------------------------------------------------------------- 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: 0.8980 chunk 65 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 0.0070 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: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.7802 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.147069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.110531 restraints weight = 12338.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110070 restraints weight = 9605.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111341 restraints weight = 7519.504| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2828 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= 0.272 Angle : 0.689 8.592 9944 Z= 0.340 Chirality : 0.043 0.181 1133 Planarity : 0.005 0.052 1234 Dihedral : 7.797 114.049 1029 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.10 % Allowed : 19.61 % Favored : 75.29 % 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: 0.73 (0.28), residues: 901 helix: 1.94 (0.28), residues: 316 sheet: 0.80 (0.31), residues: 257 loop : -1.27 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 110 HIS 0.014 0.002 HIS H 163 PHE 0.017 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 217 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8536 (p0) REVERT: B 140 TYR cc_start: 0.8885 (m-80) cc_final: 0.8490 (m-10) REVERT: B 173 ASN cc_start: 0.9075 (t0) cc_final: 0.8855 (t0) REVERT: B 227 PHE cc_start: 0.8639 (t80) cc_final: 0.8291 (t80) REVERT: X 181 TYR cc_start: 0.9459 (t80) cc_final: 0.9108 (t80) REVERT: X 237 TRP cc_start: 0.8770 (t60) cc_final: 0.8320 (t60) REVERT: X 242 LEU cc_start: 0.8723 (tt) cc_final: 0.8235 (mm) REVERT: X 259 TRP cc_start: 0.6142 (t60) cc_final: 0.5885 (t-100) REVERT: H 28 LEU cc_start: 0.9184 (mt) cc_final: 0.8941 (mp) REVERT: H 86 ASP cc_start: 0.8683 (m-30) cc_final: 0.8330 (m-30) REVERT: H 141 VAL cc_start: 0.9534 (OUTLIER) cc_final: 0.9231 (p) REVERT: H 143 ASP cc_start: 0.7535 (m-30) cc_final: 0.6980 (t70) REVERT: H 153 TRP cc_start: 0.7896 (m100) cc_final: 0.7093 (m100) REVERT: L 7 GLN cc_start: 0.8745 (tt0) cc_final: 0.8475 (tt0) REVERT: L 141 ASN cc_start: 0.9075 (t0) cc_final: 0.8560 (t0) REVERT: L 149 LYS cc_start: 0.8358 (tptt) cc_final: 0.8158 (tptp) outliers start: 39 outliers final: 31 residues processed: 203 average time/residue: 0.2248 time to fit residues: 64.7395 Evaluate side-chains 198 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 18 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.144655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.107565 restraints weight = 12631.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110226 restraints weight = 11309.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110580 restraints weight = 9097.758| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3167 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= 0.327 Angle : 0.703 10.600 9944 Z= 0.345 Chirality : 0.044 0.346 1133 Planarity : 0.005 0.048 1234 Dihedral : 7.717 111.465 1029 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.27 % Allowed : 20.78 % Favored : 72.94 % 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: 2.10 (0.27), residues: 317 sheet: 0.94 (0.31), residues: 257 loop : -1.08 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 210 HIS 0.003 0.001 HIS X 182 PHE 0.027 0.002 PHE L 213 TYR 0.017 0.002 TYR H 144 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 219 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 PHE cc_start: 0.8622 (t80) cc_final: 0.8338 (t80) REVERT: X 114 GLU cc_start: 0.8896 (tp30) cc_final: 0.8408 (tp30) REVERT: X 181 TYR cc_start: 0.9473 (t80) cc_final: 0.9027 (t80) REVERT: X 237 TRP cc_start: 0.8907 (t60) cc_final: 0.8689 (t60) REVERT: X 242 LEU cc_start: 0.8699 (tt) cc_final: 0.8242 (mm) REVERT: X 259 TRP cc_start: 0.6211 (t60) cc_final: 0.5911 (t-100) REVERT: H 28 LEU cc_start: 0.9203 (mt) cc_final: 0.8867 (mp) REVERT: H 86 ASP cc_start: 0.8714 (m-30) cc_final: 0.8435 (m-30) REVERT: H 143 ASP cc_start: 0.7366 (m-30) cc_final: 0.6839 (t70) REVERT: L 7 GLN cc_start: 0.8810 (tt0) cc_final: 0.8596 (tt0) REVERT: L 141 ASN cc_start: 0.9114 (t0) cc_final: 0.8625 (t0) REVERT: L 149 LYS cc_start: 0.8408 (tptt) cc_final: 0.8196 (tptp) outliers start: 48 outliers final: 39 residues processed: 196 average time/residue: 0.2115 time to fit residues: 58.4122 Evaluate side-chains 198 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 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: 0.0870 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.147617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111364 restraints weight = 12346.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113915 restraints weight = 10312.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113675 restraints weight = 9216.063| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3459 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= 0.180 Angle : 0.645 9.795 9944 Z= 0.313 Chirality : 0.042 0.241 1133 Planarity : 0.005 0.052 1234 Dihedral : 7.355 106.298 1026 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.58 % Allowed : 23.40 % Favored : 72.03 % 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: 1.34 (0.28), residues: 901 helix: 2.35 (0.28), residues: 322 sheet: 1.26 (0.32), residues: 245 loop : -0.91 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 110 HIS 0.003 0.001 HIS B 170 PHE 0.018 0.001 PHE L 122 TYR 0.019 0.001 TYR L 33 ARG 0.003 0.000 ARG X 158 *********************** 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 208 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 TYR cc_start: 0.8923 (m-80) cc_final: 0.8532 (m-10) REVERT: B 230 GLU cc_start: 0.7750 (mm-30) cc_final: 0.6920 (tt0) REVERT: X 114 GLU cc_start: 0.8864 (tp30) cc_final: 0.8432 (tp30) REVERT: X 181 TYR cc_start: 0.9330 (t80) cc_final: 0.8839 (t80) REVERT: X 237 TRP cc_start: 0.8843 (t60) cc_final: 0.8487 (t60) REVERT: X 242 LEU cc_start: 0.8623 (tt) cc_final: 0.8139 (mm) REVERT: H 28 LEU cc_start: 0.9101 (mt) cc_final: 0.8766 (mp) REVERT: H 86 ASP cc_start: 0.8792 (m-30) cc_final: 0.8433 (m-30) REVERT: H 143 ASP cc_start: 0.7475 (m-30) cc_final: 0.6970 (t70) REVERT: H 144 TYR cc_start: 0.8264 (p90) cc_final: 0.7875 (p90) REVERT: L 141 ASN cc_start: 0.8981 (t0) cc_final: 0.8570 (t0) outliers start: 35 outliers final: 22 residues processed: 193 average time/residue: 0.2203 time to fit residues: 58.9752 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 : 1.163 ------------------------------------------------------------------------------- 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 163 SER Chi-restraints excluded: chain B residue 195 GLN 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 236 LEU 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: 2.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 34 ASN ** 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 = 0.3803 r_free = 0.3803 target = 0.142994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106075 restraints weight = 12683.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109827 restraints weight = 12144.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108996 restraints weight = 9309.993| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7290 Z= 0.409 Angle : 0.733 9.948 9944 Z= 0.360 Chirality : 0.044 0.278 1133 Planarity : 0.005 0.047 1234 Dihedral : 7.610 108.150 1026 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 7.19 % Allowed : 21.18 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (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: 1.25 (0.28), residues: 901 helix: 2.15 (0.28), residues: 323 sheet: 1.23 (0.32), residues: 252 loop : -0.89 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 347 HIS 0.004 0.001 HIS B 170 PHE 0.018 0.002 PHE H 91 TYR 0.018 0.002 TYR X 95 ARG 0.003 0.001 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 213 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 85 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8622 (pp) REVERT: X 114 GLU cc_start: 0.8860 (tp30) cc_final: 0.8495 (tp30) REVERT: X 237 TRP cc_start: 0.8956 (t60) cc_final: 0.8731 (t60) REVERT: X 242 LEU cc_start: 0.8685 (tt) cc_final: 0.8257 (mm) REVERT: H 28 LEU cc_start: 0.9232 (mt) cc_final: 0.8851 (mp) REVERT: H 86 ASP cc_start: 0.8737 (m-30) cc_final: 0.8450 (m-30) REVERT: H 143 ASP cc_start: 0.7414 (m-30) cc_final: 0.6884 (t70) REVERT: H 144 TYR cc_start: 0.8535 (p90) cc_final: 0.8206 (p90) REVERT: L 5 MET cc_start: 0.9057 (mmt) cc_final: 0.7694 (mmm) REVERT: L 141 ASN cc_start: 0.8905 (t0) cc_final: 0.8500 (t0) outliers start: 55 outliers final: 49 residues processed: 192 average time/residue: 0.1627 time to fit residues: 43.5720 Evaluate side-chains 198 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 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 135 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 174 LEU 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 219 VAL Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 85 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 260 LEU Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 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 3 VAL 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 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: 9.9990 chunk 8 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.146534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109479 restraints weight = 12606.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109383 restraints weight = 10785.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109580 restraints weight = 11603.911| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7290 Z= 0.225 Angle : 0.688 12.047 9944 Z= 0.330 Chirality : 0.043 0.335 1133 Planarity : 0.005 0.045 1234 Dihedral : 7.380 104.871 1026 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.71 % Allowed : 24.84 % Favored : 70.46 % 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: 1.48 (0.28), residues: 901 helix: 2.40 (0.28), residues: 322 sheet: 1.47 (0.32), residues: 246 loop : -0.88 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 110 HIS 0.005 0.001 HIS B 115 PHE 0.022 0.001 PHE L 122 TYR 0.019 0.002 TYR X 181 ARG 0.004 0.000 ARG B 201 *********************** 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 191 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 GLU cc_start: 0.8745 (mp0) cc_final: 0.8474 (mp0) REVERT: X 114 GLU cc_start: 0.8886 (tp30) cc_final: 0.8515 (tp30) REVERT: X 237 TRP cc_start: 0.8926 (t60) cc_final: 0.8686 (t60) REVERT: X 242 LEU cc_start: 0.8652 (tt) cc_final: 0.8209 (mm) REVERT: H 28 LEU cc_start: 0.9103 (mt) cc_final: 0.8731 (mp) REVERT: H 86 ASP cc_start: 0.8846 (m-30) cc_final: 0.8484 (m-30) REVERT: H 143 ASP cc_start: 0.7612 (m-30) cc_final: 0.6965 (t70) REVERT: H 144 TYR cc_start: 0.8606 (p90) cc_final: 0.8309 (p90) REVERT: L 141 ASN cc_start: 0.8819 (t0) cc_final: 0.8476 (t0) outliers start: 36 outliers final: 31 residues processed: 179 average time/residue: 0.1560 time to fit residues: 38.8763 Evaluate side-chains 181 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 195 GLN 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 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 236 LEU Chi-restraints excluded: chain X residue 287 ILE 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 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 91 SER 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: 0.8980 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 92 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.108003 restraints weight = 12584.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111960 restraints weight = 11828.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111288 restraints weight = 9499.778| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7290 Z= 0.290 Angle : 0.712 12.609 9944 Z= 0.341 Chirality : 0.044 0.355 1133 Planarity : 0.005 0.045 1234 Dihedral : 7.402 104.679 1026 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.62 % Allowed : 23.92 % Favored : 70.46 % 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: 1.48 (0.28), residues: 901 helix: 2.40 (0.28), residues: 321 sheet: 1.48 (0.32), residues: 240 loop : -0.83 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 110 HIS 0.005 0.001 HIS B 115 PHE 0.021 0.002 PHE L 122 TYR 0.016 0.002 TYR L 98 ARG 0.002 0.000 ARG B 106 *********************** 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 195 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 132 MET cc_start: 0.8603 (tpp) cc_final: 0.8213 (mpp) REVERT: X 167 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7546 (mt) REVERT: X 237 TRP cc_start: 0.8955 (t60) cc_final: 0.8711 (t60) REVERT: X 242 LEU cc_start: 0.8643 (tt) cc_final: 0.8293 (mm) REVERT: H 28 LEU cc_start: 0.9154 (mt) cc_final: 0.8730 (mp) REVERT: H 86 ASP cc_start: 0.8872 (m-30) cc_final: 0.8542 (m-30) REVERT: L 141 ASN cc_start: 0.8749 (t0) cc_final: 0.8408 (t0) REVERT: L 190 TYR cc_start: 0.7815 (t80) cc_final: 0.7560 (t80) outliers start: 43 outliers final: 37 residues processed: 177 average time/residue: 0.1669 time to fit residues: 40.6919 Evaluate side-chains 188 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain X residue 17 VAL 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 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: 7.9990 chunk 6 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.146545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.109638 restraints weight = 12688.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109396 restraints weight = 11082.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111152 restraints weight = 7946.872| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7290 Z= 0.241 Angle : 0.714 12.129 9944 Z= 0.336 Chirality : 0.044 0.339 1133 Planarity : 0.005 0.045 1234 Dihedral : 7.309 102.717 1026 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.58 % Allowed : 25.10 % 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: 1.61 (0.28), residues: 901 helix: 2.48 (0.28), residues: 321 sheet: 1.54 (0.33), residues: 237 loop : -0.71 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 110 HIS 0.004 0.001 HIS B 115 PHE 0.022 0.001 PHE L 122 TYR 0.024 0.002 TYR L 98 ARG 0.004 0.000 ARG B 201 *********************** 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 187 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7755 (ttm-80) REVERT: B 230 GLU cc_start: 0.7781 (mm-30) cc_final: 0.6840 (tt0) REVERT: X 205 LEU cc_start: 0.9206 (tp) cc_final: 0.8872 (tp) REVERT: X 242 LEU cc_start: 0.8626 (tt) cc_final: 0.8221 (mm) REVERT: H 28 LEU cc_start: 0.9110 (mt) cc_final: 0.8696 (mp) REVERT: H 86 ASP cc_start: 0.8928 (m-30) cc_final: 0.8609 (m-30) REVERT: L 141 ASN cc_start: 0.8719 (t0) cc_final: 0.8380 (t0) REVERT: L 190 TYR cc_start: 0.7910 (t80) cc_final: 0.7583 (t80) outliers start: 35 outliers final: 29 residues processed: 176 average time/residue: 0.1737 time to fit residues: 41.6455 Evaluate side-chains 185 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain X residue 17 VAL 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 171 PHE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 287 ILE 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 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 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 91 SER 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: 0.0020 chunk 8 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.1392 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.144866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097156 restraints weight = 12800.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100661 restraints weight = 7464.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102999 restraints weight = 5453.958| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7290 Z= 0.314 Angle : 0.733 11.708 9944 Z= 0.348 Chirality : 0.044 0.336 1133 Planarity : 0.005 0.045 1234 Dihedral : 7.355 103.566 1026 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.71 % Allowed : 24.84 % Favored : 70.46 % 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: 2.42 (0.28), residues: 321 sheet: 1.56 (0.32), residues: 239 loop : -0.78 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 110 HIS 0.003 0.001 HIS X 182 PHE 0.013 0.001 PHE L 213 TYR 0.029 0.002 TYR L 98 ARG 0.005 0.001 ARG X 214 ********************** 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 188 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7490 (ttp80) REVERT: B 184 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7689 (ttm-80) REVERT: X 242 LEU cc_start: 0.8604 (tt) cc_final: 0.8245 (mm) REVERT: X 286 ILE cc_start: 0.8480 (pt) cc_final: 0.8078 (mm) REVERT: H 28 LEU cc_start: 0.9162 (mt) cc_final: 0.8731 (mp) REVERT: H 86 ASP cc_start: 0.8919 (m-30) cc_final: 0.8646 (m-30) REVERT: L 141 ASN cc_start: 0.8758 (t0) cc_final: 0.8414 (t0) REVERT: L 190 TYR cc_start: 0.8009 (t80) cc_final: 0.7750 (t80) outliers start: 36 outliers final: 34 residues processed: 176 average time/residue: 0.1570 time to fit residues: 38.2772 Evaluate side-chains 181 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 167 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 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 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 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 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 91 SER 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 5 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 0.0010 chunk 46 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3828 r_free = 0.3828 target = 0.145036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.107860 restraints weight = 12608.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111403 restraints weight = 11306.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110934 restraints weight = 9562.458| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.004 0.048 7290 Z= 0.298 Angle : 0.742 11.514 9944 Z= 0.349 Chirality : 0.044 0.327 1133 Planarity : 0.005 0.046 1234 Dihedral : 7.361 103.849 1026 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.84 % Allowed : 25.23 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (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: 2.44 (0.28), residues: 321 sheet: 1.65 (0.33), residues: 233 loop : -0.74 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP X 110 HIS 0.003 0.001 HIS X 182 PHE 0.014 0.001 PHE L 213 TYR 0.027 0.002 TYR H 144 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: 2454.65 seconds wall clock time: 45 minutes 53.72 seconds (2753.72 seconds total)