Starting phenix.real_space_refine on Mon May 12 15:32:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jum_61830/05_2025/9jum_61830.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jum_61830/05_2025/9jum_61830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jum_61830/05_2025/9jum_61830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jum_61830/05_2025/9jum_61830.map" model { file = "/net/cci-nas-00/data/ceres_data/9jum_61830/05_2025/9jum_61830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jum_61830/05_2025/9jum_61830.cif" } resolution = 3.1 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= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 41 5.16 5 C 5784 2.51 5 N 1555 2.21 5 O 1681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9069 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 8971 Classifications: {'peptide': 1165} Link IDs: {'PTRANS': 30, 'TRANS': 1134} Chain breaks: 1 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 98 Unusual residues: {' MG': 2, 'ANP': 2, 'BLD': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.91, per 1000 atoms: 0.65 Number of scatterers: 9069 At special positions: 0 Unit cell: (106.02, 98.58, 129.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 6 15.00 Mg 2 11.99 O 1681 8.00 N 1555 7.00 C 5784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.2 seconds 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 3 sheets defined 70.0% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 37 through 75 Proline residue: A 59 - end of helix removed outlier: 4.048A pdb=" N LEU A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 132 removed outlier: 3.701A pdb=" N LYS A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 143 through 187 removed outlier: 4.440A pdb=" N ALA A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 236 Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 245 through 299 Processing helix chain 'A' and resid 303 through 347 Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 408 through 418 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 472 through 480 Processing helix chain 'A' and resid 499 through 504 removed outlier: 4.153A pdb=" N ARG A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 564 through 571 removed outlier: 4.030A pdb=" N ILE A 568 " --> pdb=" O ARG A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 696 through 729 removed outlier: 3.649A pdb=" N TYR A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 787 removed outlier: 4.140A pdb=" N SER A 752 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 798 through 869 removed outlier: 4.303A pdb=" N ARG A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 828 " --> pdb=" O ILE A 824 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N ARG A 844 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Proline residue: A 854 - end of helix Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 878 through 891 Processing helix chain 'A' and resid 891 through 898 Processing helix chain 'A' and resid 900 through 954 Proline residue: A 914 - end of helix Processing helix chain 'A' and resid 958 through 978 Processing helix chain 'A' and resid 979 through 982 Processing helix chain 'A' and resid 985 through 1002 removed outlier: 4.276A pdb=" N GLN A 991 " --> pdb=" O ILE A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1073 Processing helix chain 'A' and resid 1094 through 1101 Processing helix chain 'A' and resid 1115 through 1122 Processing helix chain 'A' and resid 1129 through 1139 Processing helix chain 'A' and resid 1141 through 1148 Processing helix chain 'A' and resid 1150 through 1154 removed outlier: 3.507A pdb=" N LYS A1153 " --> pdb=" O GLU A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1180 removed outlier: 3.575A pdb=" N LYS A1180 " --> pdb=" O ALA A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1191 Processing helix chain 'A' and resid 1194 through 1211 Processing helix chain 'A' and resid 1234 through 1237 Processing helix chain 'A' and resid 1243 through 1250 Processing helix chain 'A' and resid 1254 through 1264 Processing sheet with id=AA1, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.862A pdb=" N ALA A 575 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1025 through 1027 Processing sheet with id=AA3, first strand: chain 'A' and resid 1102 through 1105 removed outlier: 7.072A pdb=" N ALA A1103 " --> pdb=" O LEU A1185 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N MET A1184 " --> pdb=" O ILE A1215 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL A1217 " --> pdb=" O MET A1184 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A1186 " --> pdb=" O VAL A1217 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A1229 " --> pdb=" O THR A1054 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A1058 " --> pdb=" O ALA A1231 " (cutoff:3.500A) 639 hydrogen bonds defined for protein. 1884 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: 2.94 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1647 1.33 - 1.45: 2256 1.45 - 1.57: 5259 1.57 - 1.69: 10 1.69 - 1.81: 68 Bond restraints: 9240 Sorted by residual: bond pdb=" N3B ANP A1304 " pdb=" PG ANP A1304 " ideal model delta sigma weight residual 1.795 1.632 0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" N3B ANP A1303 " pdb=" PG ANP A1303 " ideal model delta sigma weight residual 1.795 1.635 0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" O3A ANP A1303 " pdb=" PB ANP A1303 " ideal model delta sigma weight residual 1.700 1.602 0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O3A ANP A1304 " pdb=" PB ANP A1304 " ideal model delta sigma weight residual 1.700 1.604 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" N HIS A1251 " pdb=" CA HIS A1251 " ideal model delta sigma weight residual 1.458 1.489 -0.031 7.40e-03 1.83e+04 1.81e+01 ... (remaining 9235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 12192 2.08 - 4.16: 284 4.16 - 6.25: 40 6.25 - 8.33: 8 8.33 - 10.41: 5 Bond angle restraints: 12529 Sorted by residual: angle pdb=" CA GLY A1254 " pdb=" C GLY A1254 " pdb=" O GLY A1254 " ideal model delta sigma weight residual 122.22 118.24 3.98 6.50e-01 2.37e+00 3.74e+01 angle pdb=" N3B ANP A1303 " pdb=" PG ANP A1303 " pdb=" O2G ANP A1303 " ideal model delta sigma weight residual 101.05 111.46 -10.41 3.00e+00 1.11e-01 1.20e+01 angle pdb=" N LYS A 262 " pdb=" CA LYS A 262 " pdb=" C LYS A 262 " ideal model delta sigma weight residual 111.28 107.54 3.74 1.09e+00 8.42e-01 1.18e+01 angle pdb=" CG ARG A1019 " pdb=" CD ARG A1019 " pdb=" NE ARG A1019 " ideal model delta sigma weight residual 112.00 119.37 -7.37 2.20e+00 2.07e-01 1.12e+01 angle pdb=" C ASP A1253 " pdb=" CA ASP A1253 " pdb=" CB ASP A1253 " ideal model delta sigma weight residual 116.63 112.94 3.69 1.16e+00 7.43e-01 1.01e+01 ... (remaining 12524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.05: 5422 31.05 - 62.11: 149 62.11 - 93.16: 39 93.16 - 124.21: 0 124.21 - 155.27: 2 Dihedral angle restraints: 5612 sinusoidal: 2258 harmonic: 3354 Sorted by residual: dihedral pdb=" O1B ANP A1304 " pdb=" N3B ANP A1304 " pdb=" PB ANP A1304 " pdb=" PG ANP A1304 " ideal model delta sinusoidal sigma weight residual 35.15 -169.58 -155.27 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" O1A ANP A1303 " pdb=" O3A ANP A1303 " pdb=" PA ANP A1303 " pdb=" PB ANP A1303 " ideal model delta sinusoidal sigma weight residual 83.11 -55.72 138.83 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" CA ASP A1194 " pdb=" C ASP A1194 " pdb=" N ALA A1195 " pdb=" CA ALA A1195 " ideal model delta harmonic sigma weight residual -180.00 -162.75 -17.25 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 5609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1287 0.067 - 0.135: 136 0.135 - 0.202: 19 0.202 - 0.269: 4 0.269 - 0.336: 3 Chirality restraints: 1449 Sorted by residual: chirality pdb=" C3' ANP A1304 " pdb=" C2' ANP A1304 " pdb=" C4' ANP A1304 " pdb=" O3' ANP A1304 " both_signs ideal model delta sigma weight residual False -2.36 -2.69 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C3' ANP A1303 " pdb=" C2' ANP A1303 " pdb=" C4' ANP A1303 " pdb=" O3' ANP A1303 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C10 BLD A1305 " pdb=" C01 BLD A1305 " pdb=" C05 BLD A1305 " pdb=" C09 BLD A1305 " both_signs ideal model delta sigma weight residual False -3.02 -2.70 -0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 1446 not shown) Planarity restraints: 1575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 58 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO A 59 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 59 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 59 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1021 " -0.184 9.50e-02 1.11e+02 8.26e-02 4.46e+00 pdb=" NE ARG A1021 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A1021 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A1021 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A1021 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 706 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C GLY A 706 " -0.034 2.00e-02 2.50e+03 pdb=" O GLY A 706 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 707 " 0.011 2.00e-02 2.50e+03 ... (remaining 1572 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 53 2.52 - 3.11: 7758 3.11 - 3.71: 15462 3.71 - 4.30: 20744 4.30 - 4.90: 33499 Nonbonded interactions: 77516 Sorted by model distance: nonbonded pdb="MG MG A1302 " pdb=" O1A ANP A1304 " model vdw 1.922 2.170 nonbonded pdb=" OG SER A 410 " pdb="MG MG A1301 " model vdw 1.992 2.170 nonbonded pdb=" N SER A1066 " pdb="MG MG A1302 " model vdw 2.138 2.250 nonbonded pdb=" NZ LYS A 409 " pdb="MG MG A1301 " model vdw 2.186 2.250 nonbonded pdb=" O TRP A 791 " pdb=" ND2 ASN A 797 " model vdw 2.226 3.120 ... (remaining 77511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 24.990 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.005 0.163 9240 Z= 0.296 Angle : 0.759 10.409 12529 Z= 0.434 Chirality : 0.048 0.336 1449 Planarity : 0.006 0.083 1575 Dihedral : 15.660 155.266 3454 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.25), residues: 1161 helix: 1.53 (0.19), residues: 771 sheet: -1.76 (1.01), residues: 31 loop : -1.40 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 441 HIS 0.006 0.001 HIS A 54 PHE 0.019 0.001 PHE A1144 TYR 0.021 0.002 TYR A 286 ARG 0.010 0.001 ARG A1050 Details of bonding type rmsd hydrogen bonds : bond 0.12780 ( 639) hydrogen bonds : angle 5.75747 ( 1884) covalent geometry : bond 0.00530 ( 9240) covalent geometry : angle 0.75915 (12529) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.8911 (mtp) cc_final: 0.8562 (mtp) REVERT: A 421 ASP cc_start: 0.8559 (t70) cc_final: 0.8317 (t0) REVERT: A 437 LEU cc_start: 0.9491 (pt) cc_final: 0.9162 (pp) REVERT: A 488 PHE cc_start: 0.8442 (t80) cc_final: 0.8140 (t80) REVERT: A 796 GLU cc_start: 0.8090 (tp30) cc_final: 0.7890 (tp30) REVERT: A 994 ARG cc_start: 0.8555 (ppt170) cc_final: 0.8272 (tmm-80) REVERT: A 1007 GLU cc_start: 0.8412 (mp0) cc_final: 0.8195 (mp0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2277 time to fit residues: 48.0736 Evaluate side-chains 123 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN A 878 HIS A1073 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.110575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.073734 restraints weight = 21480.511| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.07 r_work: 0.3036 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9240 Z= 0.146 Angle : 0.608 8.033 12529 Z= 0.315 Chirality : 0.041 0.162 1449 Planarity : 0.004 0.053 1575 Dihedral : 10.271 152.422 1403 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.26 % Allowed : 8.64 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.40 (0.25), residues: 1161 helix: 2.04 (0.18), residues: 783 sheet: -1.73 (1.01), residues: 31 loop : -1.49 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 950 HIS 0.005 0.001 HIS A 54 PHE 0.015 0.001 PHE A 72 TYR 0.023 0.001 TYR A1122 ARG 0.005 0.001 ARG A 556 Details of bonding type rmsd hydrogen bonds : bond 0.05712 ( 639) hydrogen bonds : angle 4.59614 ( 1884) covalent geometry : bond 0.00293 ( 9240) covalent geometry : angle 0.60830 (12529) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8192 (mp) REVERT: A 241 MET cc_start: 0.9008 (mtp) cc_final: 0.8521 (mtp) REVERT: A 421 ASP cc_start: 0.8753 (t70) cc_final: 0.8508 (t0) REVERT: A 488 PHE cc_start: 0.8452 (t80) cc_final: 0.8167 (t80) REVERT: A 507 LEU cc_start: 0.8356 (mm) cc_final: 0.8094 (mm) REVERT: A 531 ASP cc_start: 0.7309 (t0) cc_final: 0.6960 (t70) REVERT: A 796 GLU cc_start: 0.8283 (tp30) cc_final: 0.7984 (tp30) REVERT: A 994 ARG cc_start: 0.8744 (ppt170) cc_final: 0.8477 (tmm-80) REVERT: A 1007 GLU cc_start: 0.8580 (mp0) cc_final: 0.8344 (mp0) REVERT: A 1048 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8267 (mmm-85) REVERT: A 1075 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8298 (m-80) REVERT: A 1117 TYR cc_start: 0.8557 (t80) cc_final: 0.8356 (t80) REVERT: A 1129 GLU cc_start: 0.8854 (tp30) cc_final: 0.8641 (tp30) REVERT: A 1134 GLN cc_start: 0.9072 (mp10) cc_final: 0.8728 (mp10) REVERT: A 1169 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8787 (tm-30) outliers start: 12 outliers final: 8 residues processed: 143 average time/residue: 0.2219 time to fit residues: 44.3668 Evaluate side-chains 135 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1259 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 56 optimal weight: 0.0070 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.110883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.075131 restraints weight = 21906.410| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.05 r_work: 0.3055 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9240 Z= 0.131 Angle : 0.578 6.932 12529 Z= 0.298 Chirality : 0.040 0.155 1449 Planarity : 0.004 0.052 1575 Dihedral : 8.810 157.457 1403 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.90 % Allowed : 12.12 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.57 (0.25), residues: 1161 helix: 2.15 (0.18), residues: 782 sheet: -0.57 (1.19), residues: 24 loop : -1.46 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 950 HIS 0.004 0.001 HIS A 54 PHE 0.013 0.001 PHE A 72 TYR 0.031 0.001 TYR A1122 ARG 0.007 0.001 ARG A1050 Details of bonding type rmsd hydrogen bonds : bond 0.05218 ( 639) hydrogen bonds : angle 4.38521 ( 1884) covalent geometry : bond 0.00260 ( 9240) covalent geometry : angle 0.57822 (12529) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.8933 (mtp) cc_final: 0.8425 (mtp) REVERT: A 421 ASP cc_start: 0.8736 (t70) cc_final: 0.8447 (t0) REVERT: A 488 PHE cc_start: 0.8502 (t80) cc_final: 0.8235 (t80) REVERT: A 507 LEU cc_start: 0.8370 (mm) cc_final: 0.8044 (mm) REVERT: A 521 MET cc_start: 0.8816 (mpp) cc_final: 0.8275 (mtt) REVERT: A 531 ASP cc_start: 0.7252 (t0) cc_final: 0.6906 (t70) REVERT: A 546 GLN cc_start: 0.8872 (mp10) cc_final: 0.8648 (mp10) REVERT: A 796 GLU cc_start: 0.8157 (tp30) cc_final: 0.7897 (tp30) REVERT: A 994 ARG cc_start: 0.8709 (ppt170) cc_final: 0.8418 (tmm-80) REVERT: A 1006 ILE cc_start: 0.9427 (mt) cc_final: 0.9211 (tp) REVERT: A 1007 GLU cc_start: 0.8515 (mp0) cc_final: 0.8305 (mp0) REVERT: A 1048 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8212 (mmm-85) REVERT: A 1075 PHE cc_start: 0.8710 (t80) cc_final: 0.8433 (m-80) REVERT: A 1122 TYR cc_start: 0.8809 (t80) cc_final: 0.8589 (t80) REVERT: A 1129 GLU cc_start: 0.8818 (tp30) cc_final: 0.8608 (tp30) REVERT: A 1184 MET cc_start: 0.7369 (mpp) cc_final: 0.7163 (mpp) outliers start: 18 outliers final: 10 residues processed: 142 average time/residue: 0.2012 time to fit residues: 40.4494 Evaluate side-chains 138 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1259 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 101 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN ** A1028 HIS ** 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 = 0.3844 r_free = 0.3844 target = 0.109016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.072198 restraints weight = 21650.191| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.04 r_work: 0.3008 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9240 Z= 0.162 Angle : 0.579 8.472 12529 Z= 0.302 Chirality : 0.040 0.159 1449 Planarity : 0.004 0.057 1575 Dihedral : 8.320 153.563 1403 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.79 % Allowed : 16.12 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.25), residues: 1161 helix: 2.19 (0.18), residues: 782 sheet: -0.54 (1.18), residues: 24 loop : -1.48 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 950 HIS 0.003 0.001 HIS A 588 PHE 0.016 0.001 PHE A 72 TYR 0.022 0.002 TYR A1122 ARG 0.003 0.000 ARG A 519 Details of bonding type rmsd hydrogen bonds : bond 0.05450 ( 639) hydrogen bonds : angle 4.40848 ( 1884) covalent geometry : bond 0.00351 ( 9240) covalent geometry : angle 0.57894 (12529) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 GLN cc_start: 0.8670 (mm110) cc_final: 0.8446 (mm110) REVERT: A 421 ASP cc_start: 0.8756 (t70) cc_final: 0.8495 (t0) REVERT: A 488 PHE cc_start: 0.8493 (t80) cc_final: 0.8240 (t80) REVERT: A 531 ASP cc_start: 0.7188 (t0) cc_final: 0.6847 (t70) REVERT: A 796 GLU cc_start: 0.8177 (tp30) cc_final: 0.7884 (tp30) REVERT: A 994 ARG cc_start: 0.8740 (ppt170) cc_final: 0.8409 (tmm-80) REVERT: A 1006 ILE cc_start: 0.9445 (mt) cc_final: 0.9215 (tp) REVERT: A 1122 TYR cc_start: 0.8996 (t80) cc_final: 0.8758 (t80) outliers start: 17 outliers final: 13 residues processed: 136 average time/residue: 0.2032 time to fit residues: 39.3193 Evaluate side-chains 133 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain A residue 1259 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.106139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068816 restraints weight = 21909.405| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.02 r_work: 0.2942 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9240 Z= 0.254 Angle : 0.655 9.347 12529 Z= 0.343 Chirality : 0.043 0.198 1449 Planarity : 0.005 0.064 1575 Dihedral : 8.316 146.524 1403 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.32 % Allowed : 16.65 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.34 (0.25), residues: 1161 helix: 1.95 (0.18), residues: 777 sheet: -0.87 (0.98), residues: 32 loop : -1.42 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 950 HIS 0.004 0.001 HIS A 762 PHE 0.022 0.002 PHE A 72 TYR 0.021 0.002 TYR A1122 ARG 0.009 0.001 ARG A1050 Details of bonding type rmsd hydrogen bonds : bond 0.06102 ( 639) hydrogen bonds : angle 4.63410 ( 1884) covalent geometry : bond 0.00567 ( 9240) covalent geometry : angle 0.65478 (12529) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.9327 (mtm) cc_final: 0.8920 (mtp) REVERT: A 488 PHE cc_start: 0.8496 (t80) cc_final: 0.8250 (t80) REVERT: A 531 ASP cc_start: 0.7214 (t0) cc_final: 0.6892 (t70) REVERT: A 796 GLU cc_start: 0.8253 (tp30) cc_final: 0.7964 (tp30) REVERT: A 994 ARG cc_start: 0.8748 (ppt170) cc_final: 0.8480 (tmm-80) REVERT: A 1184 MET cc_start: 0.7603 (mpp) cc_final: 0.7388 (mpp) outliers start: 22 outliers final: 16 residues processed: 136 average time/residue: 0.2026 time to fit residues: 38.8067 Evaluate side-chains 141 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1088 LYS Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1259 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN ** A1028 HIS ** 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 = 0.3828 r_free = 0.3828 target = 0.108064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.071294 restraints weight = 21565.467| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 3.03 r_work: 0.2982 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9240 Z= 0.158 Angle : 0.613 7.802 12529 Z= 0.316 Chirality : 0.041 0.189 1449 Planarity : 0.004 0.056 1575 Dihedral : 8.073 140.160 1403 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.32 % Allowed : 18.12 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.50 (0.25), residues: 1161 helix: 2.12 (0.18), residues: 776 sheet: -0.87 (0.97), residues: 32 loop : -1.47 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 950 HIS 0.003 0.001 HIS A 588 PHE 0.013 0.001 PHE A 72 TYR 0.025 0.001 TYR A1122 ARG 0.009 0.000 ARG A1050 Details of bonding type rmsd hydrogen bonds : bond 0.05587 ( 639) hydrogen bonds : angle 4.51233 ( 1884) covalent geometry : bond 0.00339 ( 9240) covalent geometry : angle 0.61329 (12529) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.9238 (mtm) cc_final: 0.8925 (mtp) REVERT: A 488 PHE cc_start: 0.8469 (t80) cc_final: 0.8238 (t80) REVERT: A 521 MET cc_start: 0.8767 (mtm) cc_final: 0.8407 (mtm) REVERT: A 531 ASP cc_start: 0.7286 (t0) cc_final: 0.6958 (t70) REVERT: A 796 GLU cc_start: 0.8190 (tp30) cc_final: 0.7836 (tp30) REVERT: A 994 ARG cc_start: 0.8731 (ppt170) cc_final: 0.8389 (tmm-80) outliers start: 22 outliers final: 14 residues processed: 136 average time/residue: 0.2016 time to fit residues: 38.7940 Evaluate side-chains 135 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 1028 HIS Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain A residue 1259 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 53 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 11 optimal weight: 0.0170 chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN ** A1028 HIS ** 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 = 0.3840 r_free = 0.3840 target = 0.107206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.072099 restraints weight = 21904.367| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.87 r_work: 0.3067 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9240 Z= 0.165 Angle : 0.625 8.472 12529 Z= 0.323 Chirality : 0.041 0.202 1449 Planarity : 0.004 0.057 1575 Dihedral : 7.980 135.757 1403 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.63 % Allowed : 18.86 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.50 (0.25), residues: 1161 helix: 2.13 (0.18), residues: 776 sheet: -0.90 (0.97), residues: 32 loop : -1.49 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 950 HIS 0.003 0.001 HIS A 588 PHE 0.014 0.001 PHE A 72 TYR 0.019 0.001 TYR A1093 ARG 0.004 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05559 ( 639) hydrogen bonds : angle 4.50538 ( 1884) covalent geometry : bond 0.00358 ( 9240) covalent geometry : angle 0.62532 (12529) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.9105 (mtm) cc_final: 0.8883 (mtp) REVERT: A 488 PHE cc_start: 0.8512 (t80) cc_final: 0.8288 (t80) REVERT: A 521 MET cc_start: 0.8798 (mtm) cc_final: 0.8480 (mtm) REVERT: A 531 ASP cc_start: 0.7259 (t0) cc_final: 0.6975 (t70) REVERT: A 582 VAL cc_start: 0.7387 (OUTLIER) cc_final: 0.7174 (p) REVERT: A 796 GLU cc_start: 0.8069 (tp30) cc_final: 0.7739 (tp30) REVERT: A 994 ARG cc_start: 0.8622 (ppt170) cc_final: 0.8371 (tmm-80) REVERT: A 1050 ARG cc_start: 0.8966 (mmt90) cc_final: 0.8750 (mmm160) REVERT: A 1118 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8540 (pt0) outliers start: 25 outliers final: 17 residues processed: 141 average time/residue: 0.1978 time to fit residues: 39.6152 Evaluate side-chains 140 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 1028 HIS Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1206 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 19 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN A1207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.108034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.072658 restraints weight = 22015.773| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.90 r_work: 0.3080 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9240 Z= 0.150 Angle : 0.631 9.150 12529 Z= 0.322 Chirality : 0.042 0.213 1449 Planarity : 0.004 0.055 1575 Dihedral : 7.874 131.502 1403 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.74 % Allowed : 19.39 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.25), residues: 1161 helix: 2.16 (0.18), residues: 776 sheet: -0.94 (0.96), residues: 32 loop : -1.46 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 950 HIS 0.003 0.001 HIS A 588 PHE 0.024 0.001 PHE A1112 TYR 0.012 0.001 TYR A1122 ARG 0.007 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05420 ( 639) hydrogen bonds : angle 4.49274 ( 1884) covalent geometry : bond 0.00321 ( 9240) covalent geometry : angle 0.63084 (12529) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ILE cc_start: 0.8566 (mp) cc_final: 0.8316 (mp) REVERT: A 241 MET cc_start: 0.9102 (mtm) cc_final: 0.8740 (mtp) REVERT: A 488 PHE cc_start: 0.8501 (t80) cc_final: 0.8272 (t80) REVERT: A 521 MET cc_start: 0.8768 (mtm) cc_final: 0.8466 (mtm) REVERT: A 531 ASP cc_start: 0.7273 (t0) cc_final: 0.7019 (t70) REVERT: A 582 VAL cc_start: 0.7448 (OUTLIER) cc_final: 0.7212 (p) REVERT: A 796 GLU cc_start: 0.8061 (tp30) cc_final: 0.7735 (tp30) REVERT: A 994 ARG cc_start: 0.8617 (ppt170) cc_final: 0.8308 (tmm-80) REVERT: A 1043 ARG cc_start: 0.8031 (mmt180) cc_final: 0.7799 (mmp80) REVERT: A 1118 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8532 (pt0) outliers start: 26 outliers final: 20 residues processed: 143 average time/residue: 0.2004 time to fit residues: 40.5676 Evaluate side-chains 150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1028 HIS Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain A residue 1213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 96 optimal weight: 0.0170 chunk 90 optimal weight: 9.9990 chunk 32 optimal weight: 0.0010 chunk 67 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 overall best weight: 0.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 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 = 0.3887 r_free = 0.3887 target = 0.110427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075616 restraints weight = 21702.697| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.89 r_work: 0.3096 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9240 Z= 0.131 Angle : 0.622 9.409 12529 Z= 0.315 Chirality : 0.041 0.225 1449 Planarity : 0.004 0.051 1575 Dihedral : 7.668 127.467 1403 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.32 % Allowed : 19.60 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.60 (0.25), residues: 1161 helix: 2.22 (0.18), residues: 774 sheet: -1.73 (0.82), residues: 44 loop : -1.33 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 950 HIS 0.003 0.001 HIS A 208 PHE 0.028 0.001 PHE A1112 TYR 0.011 0.001 TYR A1122 ARG 0.007 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.04929 ( 639) hydrogen bonds : angle 4.41834 ( 1884) covalent geometry : bond 0.00251 ( 9240) covalent geometry : angle 0.62231 (12529) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ILE cc_start: 0.8422 (mp) cc_final: 0.8194 (mp) REVERT: A 241 MET cc_start: 0.9012 (mtm) cc_final: 0.8574 (mtm) REVERT: A 488 PHE cc_start: 0.8512 (t80) cc_final: 0.8294 (t80) REVERT: A 521 MET cc_start: 0.8688 (mtm) cc_final: 0.8474 (mtm) REVERT: A 531 ASP cc_start: 0.7282 (t0) cc_final: 0.7027 (t70) REVERT: A 582 VAL cc_start: 0.7459 (OUTLIER) cc_final: 0.7210 (p) REVERT: A 796 GLU cc_start: 0.8091 (tp30) cc_final: 0.7755 (tp30) REVERT: A 994 ARG cc_start: 0.8642 (ppt170) cc_final: 0.8359 (tmm-80) REVERT: A 1043 ARG cc_start: 0.8072 (mmt180) cc_final: 0.7839 (mmp80) outliers start: 22 outliers final: 15 residues processed: 151 average time/residue: 0.2065 time to fit residues: 43.5048 Evaluate side-chains 145 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1028 HIS Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1193 LEU Chi-restraints excluded: chain A residue 1213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 57 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.109637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.074315 restraints weight = 21822.001| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.93 r_work: 0.3078 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9240 Z= 0.136 Angle : 0.629 8.308 12529 Z= 0.318 Chirality : 0.042 0.265 1449 Planarity : 0.004 0.052 1575 Dihedral : 7.640 125.534 1403 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.90 % Allowed : 20.44 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.25), residues: 1161 helix: 2.25 (0.18), residues: 775 sheet: -1.74 (0.83), residues: 44 loop : -1.35 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 950 HIS 0.003 0.001 HIS A 208 PHE 0.036 0.001 PHE A1112 TYR 0.010 0.001 TYR A1093 ARG 0.006 0.000 ARG A1050 Details of bonding type rmsd hydrogen bonds : bond 0.05024 ( 639) hydrogen bonds : angle 4.39859 ( 1884) covalent geometry : bond 0.00281 ( 9240) covalent geometry : angle 0.62863 (12529) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ILE cc_start: 0.8424 (mp) cc_final: 0.8192 (mp) REVERT: A 241 MET cc_start: 0.9291 (mtm) cc_final: 0.8900 (mtm) REVERT: A 488 PHE cc_start: 0.8514 (t80) cc_final: 0.8291 (t80) REVERT: A 531 ASP cc_start: 0.7305 (t0) cc_final: 0.7041 (t70) REVERT: A 582 VAL cc_start: 0.7520 (OUTLIER) cc_final: 0.7270 (p) REVERT: A 796 GLU cc_start: 0.8096 (tp30) cc_final: 0.7778 (tp30) REVERT: A 994 ARG cc_start: 0.8657 (ppt170) cc_final: 0.8368 (tmm-80) REVERT: A 1043 ARG cc_start: 0.8091 (mmt180) cc_final: 0.7820 (mmp80) outliers start: 18 outliers final: 14 residues processed: 141 average time/residue: 0.2149 time to fit residues: 42.9028 Evaluate side-chains 141 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 527 ILE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1088 LYS Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 83 optimal weight: 0.8980 chunk 39 optimal weight: 0.0670 chunk 92 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 98 optimal weight: 0.0170 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.110251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.074967 restraints weight = 21746.441| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.92 r_work: 0.3093 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9240 Z= 0.133 Angle : 0.638 9.016 12529 Z= 0.322 Chirality : 0.042 0.300 1449 Planarity : 0.004 0.052 1575 Dihedral : 7.600 123.051 1403 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.90 % Allowed : 20.76 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.25), residues: 1161 helix: 2.26 (0.18), residues: 774 sheet: -1.75 (0.83), residues: 44 loop : -1.35 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 950 HIS 0.003 0.001 HIS A 208 PHE 0.024 0.001 PHE A1112 TYR 0.011 0.001 TYR A 172 ARG 0.006 0.000 ARG A1050 Details of bonding type rmsd hydrogen bonds : bond 0.04951 ( 639) hydrogen bonds : angle 4.39616 ( 1884) covalent geometry : bond 0.00271 ( 9240) covalent geometry : angle 0.63831 (12529) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4862.48 seconds wall clock time: 85 minutes 1.61 seconds (5101.61 seconds total)