Starting phenix.real_space_refine on Tue Mar 3 12:52:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cxo_27062/03_2026/8cxo_27062.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cxo_27062/03_2026/8cxo_27062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cxo_27062/03_2026/8cxo_27062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cxo_27062/03_2026/8cxo_27062.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cxo_27062/03_2026/8cxo_27062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cxo_27062/03_2026/8cxo_27062.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2863 2.51 5 N 724 2.21 5 O 775 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4392 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4364 Classifications: {'peptide': 551} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 535} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.12, per 1000 atoms: 0.26 Number of scatterers: 4392 At special positions: 0 Unit cell: (75.985, 65.13, 123.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 775 8.00 N 724 7.00 C 2863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 299 " distance=2.02 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 494 " - pdb=" SG CYS A 511 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 265.9 milliseconds 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1010 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 3 sheets defined 65.5% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 227 through 259 removed outlier: 3.998A pdb=" N ASP A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 265 through 268 Processing helix chain 'A' and resid 269 through 287 removed outlier: 3.595A pdb=" N TYR A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 292 through 299 Processing helix chain 'A' and resid 316 through 347 removed outlier: 4.079A pdb=" N PHE A 347 " --> pdb=" O TRP A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 360 through 382 Proline residue: A 372 - end of helix removed outlier: 3.526A pdb=" N VAL A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.825A pdb=" N ARG A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 437 Processing helix chain 'A' and resid 1015 through 1027 Processing helix chain 'A' and resid 1047 through 1059 Processing helix chain 'A' and resid 1060 through 1065 removed outlier: 6.464A pdb=" N GLU A1063 " --> pdb=" O SER A1060 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN A1065 " --> pdb=" O LYS A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1090 Processing helix chain 'A' and resid 1101 through 1112 Processing helix chain 'A' and resid 1126 through 1134 removed outlier: 4.036A pdb=" N GLU A1130 " --> pdb=" O LEU A1126 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA A1131 " --> pdb=" O VAL A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1149 removed outlier: 4.029A pdb=" N ARG A1147 " --> pdb=" O GLY A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1178 Processing helix chain 'A' and resid 1181 through 1193 Processing helix chain 'A' and resid 1206 through 452 removed outlier: 3.526A pdb=" N GLU A 451 " --> pdb=" O ALA A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 494 removed outlier: 3.599A pdb=" N PHE A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 518 through 537 removed outlier: 3.690A pdb=" N GLY A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 541 Processing helix chain 'A' and resid 542 through 554 removed outlier: 3.682A pdb=" N LEU A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA2, first strand: chain 'A' and resid 385 through 388 removed outlier: 3.551A pdb=" N ASP A 388 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 393 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1093 through 1096 removed outlier: 5.722A pdb=" N VAL A1033 " --> pdb=" O ARG A1068 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE A1070 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE A1035 " --> pdb=" O ILE A1070 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE A1072 " --> pdb=" O PHE A1035 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE A1037 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR A1034 " --> pdb=" O PHE A1114 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE A1116 " --> pdb=" O THR A1034 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET A1036 " --> pdb=" O ILE A1116 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.70 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1374 1.34 - 1.46: 1147 1.46 - 1.58: 1935 1.58 - 1.70: 0 1.70 - 1.82: 45 Bond restraints: 4501 Sorted by residual: bond pdb=" C13 CLR A1301 " pdb=" C14 CLR A1301 " ideal model delta sigma weight residual 1.537 1.504 0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 CLR A1301 " pdb=" C10 CLR A1301 " ideal model delta sigma weight residual 1.544 1.515 0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C16 CLR A1301 " pdb=" C17 CLR A1301 " ideal model delta sigma weight residual 1.554 1.528 0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" C15 CLR A1301 " pdb=" C16 CLR A1301 " ideal model delta sigma weight residual 1.541 1.517 0.024 2.00e-02 2.50e+03 1.45e+00 bond pdb=" CA VAL A 214 " pdb=" CB VAL A 214 " ideal model delta sigma weight residual 1.527 1.541 -0.014 1.31e-02 5.83e+03 1.19e+00 ... (remaining 4496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 5911 1.39 - 2.77: 145 2.77 - 4.16: 22 4.16 - 5.54: 16 5.54 - 6.93: 2 Bond angle restraints: 6096 Sorted by residual: angle pdb=" N CYS A1004 " pdb=" CA CYS A1004 " pdb=" C CYS A1004 " ideal model delta sigma weight residual 107.20 112.41 -5.21 1.70e+00 3.46e-01 9.41e+00 angle pdb=" C TYR A 211 " pdb=" N GLU A 212 " pdb=" CA GLU A 212 " ideal model delta sigma weight residual 121.19 125.96 -4.77 1.59e+00 3.96e-01 8.98e+00 angle pdb=" N TYR A 266 " pdb=" CA TYR A 266 " pdb=" C TYR A 266 " ideal model delta sigma weight residual 109.81 115.33 -5.52 2.21e+00 2.05e-01 6.24e+00 angle pdb=" N GLY A1001 " pdb=" CA GLY A1001 " pdb=" C GLY A1001 " ideal model delta sigma weight residual 113.99 116.99 -3.00 1.28e+00 6.10e-01 5.50e+00 angle pdb=" C6 CLR A1301 " pdb=" C7 CLR A1301 " pdb=" C8 CLR A1301 " ideal model delta sigma weight residual 113.19 106.26 6.93 3.00e+00 1.11e-01 5.34e+00 ... (remaining 6091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 2541 17.14 - 34.28: 110 34.28 - 51.42: 20 51.42 - 68.56: 3 68.56 - 85.70: 1 Dihedral angle restraints: 2675 sinusoidal: 1098 harmonic: 1577 Sorted by residual: dihedral pdb=" CB CYS A 494 " pdb=" SG CYS A 494 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual 93.00 145.05 -52.05 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CA LEU A 441 " pdb=" C LEU A 441 " pdb=" N GLY A1001 " pdb=" CA GLY A1001 " ideal model delta harmonic sigma weight residual -180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA TYR A 211 " pdb=" C TYR A 211 " pdb=" N GLU A 212 " pdb=" CA GLU A 212 " ideal model delta harmonic sigma weight residual 180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 2672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 553 0.045 - 0.089: 90 0.089 - 0.134: 29 0.134 - 0.178: 4 0.178 - 0.223: 1 Chirality restraints: 677 Sorted by residual: chirality pdb=" C10 CLR A1301 " pdb=" C1 CLR A1301 " pdb=" C5 CLR A1301 " pdb=" C9 CLR A1301 " both_signs ideal model delta sigma weight residual False -2.85 -2.63 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE A1139 " pdb=" N ILE A1139 " pdb=" C ILE A1139 " pdb=" CB ILE A1139 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA ILE A1137 " pdb=" N ILE A1137 " pdb=" C ILE A1137 " pdb=" CB ILE A1137 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 674 not shown) Planarity restraints: 759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1122 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A1123 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A1123 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A1123 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 437 " 0.019 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO A 438 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 438 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 438 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A1201 " -0.005 2.00e-02 2.50e+03 1.05e-02 1.09e+00 pdb=" C MET A1201 " 0.018 2.00e-02 2.50e+03 pdb=" O MET A1201 " -0.007 2.00e-02 2.50e+03 pdb=" N ASP A1202 " -0.006 2.00e-02 2.50e+03 ... (remaining 756 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1443 2.84 - 3.36: 4332 3.36 - 3.87: 7300 3.87 - 4.39: 8453 4.39 - 4.90: 13879 Nonbonded interactions: 35407 Sorted by model distance: nonbonded pdb=" O MET A1201 " pdb=" N ILE A1203 " model vdw 2.329 3.120 nonbonded pdb=" N GLU A1098 " pdb=" OE1 GLU A1098 " model vdw 2.346 3.120 nonbonded pdb=" NZ LYS A 434 " pdb=" C2 CLR A1301 " model vdw 2.353 3.520 nonbonded pdb=" O ARG A1204 " pdb=" ND2 ASN A 450 " model vdw 2.398 3.120 nonbonded pdb=" O GLU A1056 " pdb=" OG SER A1059 " model vdw 2.420 3.040 ... (remaining 35402 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 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.220 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.003 0.033 4505 Z= 0.167 Angle : 0.582 6.930 6104 Z= 0.314 Chirality : 0.040 0.223 677 Planarity : 0.003 0.031 759 Dihedral : 10.103 85.704 1653 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.74 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.36), residues: 547 helix: 1.91 (0.28), residues: 317 sheet: 1.64 (0.82), residues: 29 loop : 0.24 (0.48), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1106 TYR 0.008 0.001 TYR A 398 PHE 0.015 0.001 PHE A1124 TRP 0.010 0.001 TRP A1007 HIS 0.003 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4501) covalent geometry : angle 0.58140 ( 6096) SS BOND : bond 0.00382 ( 4) SS BOND : angle 1.01043 ( 8) hydrogen bonds : bond 0.22656 ( 259) hydrogen bonds : angle 6.12820 ( 753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 TYR cc_start: 0.8547 (t80) cc_final: 0.8130 (t80) REVERT: A 261 ARG cc_start: 0.8833 (mtt90) cc_final: 0.8621 (ttm110) REVERT: A 309 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8525 (mp0) REVERT: A 348 LYS cc_start: 0.8892 (mttt) cc_final: 0.8629 (mtmt) REVERT: A 384 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8310 (mm-40) REVERT: A 390 VAL cc_start: 0.9414 (t) cc_final: 0.9179 (p) REVERT: A 1003 ASP cc_start: 0.6208 (t0) cc_final: 0.5900 (t0) REVERT: A 1090 HIS cc_start: 0.8396 (m-70) cc_final: 0.7929 (m-70) REVERT: A 1122 GLU cc_start: 0.7933 (tp30) cc_final: 0.6644 (tp30) REVERT: A 1123 PRO cc_start: 0.9172 (Cg_exo) cc_final: 0.8716 (Cg_endo) REVERT: A 1130 GLU cc_start: 0.4917 (tt0) cc_final: 0.4673 (tt0) REVERT: A 1132 MET cc_start: 0.9281 (mtp) cc_final: 0.8960 (mtp) REVERT: A 1137 ILE cc_start: 0.8615 (mt) cc_final: 0.8033 (mm) REVERT: A 1154 THR cc_start: 0.9239 (m) cc_final: 0.8875 (p) REVERT: A 1172 LYS cc_start: 0.9369 (tptt) cc_final: 0.8892 (mmtt) REVERT: A 523 LYS cc_start: 0.9276 (mttt) cc_final: 0.9017 (mttt) REVERT: A 530 PHE cc_start: 0.9295 (m-80) cc_final: 0.9062 (m-80) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.0760 time to fit residues: 21.8264 Evaluate side-chains 153 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 0.0670 overall best weight: 2.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 222 GLN ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A1065 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.107184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.086624 restraints weight = 10302.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.089761 restraints weight = 5095.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.091943 restraints weight = 3164.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.093558 restraints weight = 2258.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.094638 restraints weight = 1764.912| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4505 Z= 0.243 Angle : 0.704 9.321 6104 Z= 0.368 Chirality : 0.046 0.153 677 Planarity : 0.005 0.033 759 Dihedral : 5.525 26.612 663 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.74 % Allowed : 15.73 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.35), residues: 547 helix: 2.26 (0.28), residues: 314 sheet: 2.14 (1.05), residues: 19 loop : -0.20 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1102 TYR 0.014 0.002 TYR A 363 PHE 0.016 0.002 PHE A 322 TRP 0.011 0.002 TRP A1007 HIS 0.006 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 4501) covalent geometry : angle 0.70423 ( 6096) SS BOND : bond 0.00235 ( 4) SS BOND : angle 0.73613 ( 8) hydrogen bonds : bond 0.06108 ( 259) hydrogen bonds : angle 4.67635 ( 753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 237 TYR cc_start: 0.8549 (t80) cc_final: 0.8309 (t80) REVERT: A 253 LEU cc_start: 0.9336 (mp) cc_final: 0.9105 (mp) REVERT: A 309 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8564 (mp0) REVERT: A 348 LYS cc_start: 0.9059 (mttt) cc_final: 0.8825 (mtmt) REVERT: A 384 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8465 (mm-40) REVERT: A 441 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6545 (mt) REVERT: A 1003 ASP cc_start: 0.6653 (t0) cc_final: 0.6103 (t0) REVERT: A 1023 LEU cc_start: 0.9692 (mt) cc_final: 0.9488 (mt) REVERT: A 1041 PHE cc_start: 0.7519 (m-10) cc_final: 0.7075 (m-80) REVERT: A 1056 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8713 (tm-30) REVERT: A 1058 LEU cc_start: 0.9543 (tp) cc_final: 0.9271 (tt) REVERT: A 1090 HIS cc_start: 0.8310 (m-70) cc_final: 0.7991 (m-70) REVERT: A 1154 THR cc_start: 0.9161 (m) cc_final: 0.8870 (p) REVERT: A 481 GLN cc_start: 0.9114 (tp40) cc_final: 0.8845 (tt0) REVERT: A 484 TRP cc_start: 0.9204 (m-10) cc_final: 0.8488 (m-90) REVERT: A 487 SER cc_start: 0.9571 (t) cc_final: 0.9245 (p) outliers start: 22 outliers final: 19 residues processed: 156 average time/residue: 0.0618 time to fit residues: 12.4846 Evaluate side-chains 161 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** 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 = 0.3596 r_free = 0.3596 target = 0.113572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.093463 restraints weight = 10403.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.096500 restraints weight = 5132.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.099061 restraints weight = 3256.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.100447 restraints weight = 2271.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.101694 restraints weight = 1782.436| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4505 Z= 0.137 Angle : 0.586 8.779 6104 Z= 0.302 Chirality : 0.043 0.152 677 Planarity : 0.004 0.032 759 Dihedral : 5.069 28.268 663 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.31 % Allowed : 19.18 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.35), residues: 547 helix: 2.32 (0.27), residues: 314 sheet: 1.89 (1.07), residues: 19 loop : -0.33 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1185 TYR 0.015 0.001 TYR A 491 PHE 0.018 0.002 PHE A1035 TRP 0.007 0.001 TRP A 549 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4501) covalent geometry : angle 0.58583 ( 6096) SS BOND : bond 0.00110 ( 4) SS BOND : angle 0.37415 ( 8) hydrogen bonds : bond 0.05307 ( 259) hydrogen bonds : angle 4.27123 ( 753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8672 (pt0) cc_final: 0.7991 (tm-30) REVERT: A 228 GLU cc_start: 0.8449 (tp30) cc_final: 0.8152 (tm-30) REVERT: A 232 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8692 (mm-40) REVERT: A 309 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8520 (mp0) REVERT: A 348 LYS cc_start: 0.9059 (mttt) cc_final: 0.8788 (mtmt) REVERT: A 388 ASP cc_start: 0.9024 (t0) cc_final: 0.8644 (t0) REVERT: A 1041 PHE cc_start: 0.7470 (m-10) cc_final: 0.7208 (m-80) REVERT: A 1090 HIS cc_start: 0.8310 (m-70) cc_final: 0.7981 (m-70) REVERT: A 1113 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7614 (p0) REVERT: A 1188 CYS cc_start: 0.9340 (OUTLIER) cc_final: 0.9067 (t) REVERT: A 1193 MET cc_start: 0.5127 (mmt) cc_final: 0.3240 (mmt) REVERT: A 540 VAL cc_start: 0.9424 (m) cc_final: 0.9212 (t) outliers start: 20 outliers final: 12 residues processed: 158 average time/residue: 0.0598 time to fit residues: 12.5637 Evaluate side-chains 146 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1188 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** 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 = 0.3612 r_free = 0.3612 target = 0.114995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095542 restraints weight = 10343.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098612 restraints weight = 5054.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.101108 restraints weight = 3213.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.102363 restraints weight = 2234.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.103646 restraints weight = 1760.514| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4505 Z= 0.127 Angle : 0.611 12.396 6104 Z= 0.307 Chirality : 0.043 0.167 677 Planarity : 0.004 0.035 759 Dihedral : 4.971 35.680 663 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.74 % Allowed : 20.69 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.35), residues: 547 helix: 2.32 (0.27), residues: 314 sheet: 1.21 (1.23), residues: 18 loop : -0.57 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1178 TYR 0.014 0.001 TYR A1011 PHE 0.014 0.001 PHE A 322 TRP 0.009 0.001 TRP A 484 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4501) covalent geometry : angle 0.61095 ( 6096) SS BOND : bond 0.00098 ( 4) SS BOND : angle 0.35088 ( 8) hydrogen bonds : bond 0.04869 ( 259) hydrogen bonds : angle 4.18314 ( 753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 TYR cc_start: 0.8874 (m-80) cc_final: 0.8490 (m-10) REVERT: A 309 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8535 (mp0) REVERT: A 388 ASP cc_start: 0.8972 (t0) cc_final: 0.8411 (t0) REVERT: A 1056 GLU cc_start: 0.9247 (tt0) cc_final: 0.8942 (pt0) REVERT: A 1090 HIS cc_start: 0.8301 (m-70) cc_final: 0.7966 (m-70) REVERT: A 1113 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7513 (p0) REVERT: A 1132 MET cc_start: 0.9373 (mtp) cc_final: 0.8632 (mmm) REVERT: A 1193 MET cc_start: 0.4966 (mmt) cc_final: 0.3344 (mmt) REVERT: A 484 TRP cc_start: 0.9094 (m-10) cc_final: 0.8865 (m-10) REVERT: A 487 SER cc_start: 0.9511 (t) cc_final: 0.9122 (p) REVERT: A 530 PHE cc_start: 0.9316 (m-80) cc_final: 0.8938 (m-10) outliers start: 22 outliers final: 13 residues processed: 152 average time/residue: 0.0551 time to fit residues: 11.2233 Evaluate side-chains 146 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 538 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.112959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.092076 restraints weight = 10382.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.095306 restraints weight = 5119.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.097596 restraints weight = 3155.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099374 restraints weight = 2223.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.100195 restraints weight = 1700.898| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4505 Z= 0.146 Angle : 0.638 10.352 6104 Z= 0.315 Chirality : 0.043 0.176 677 Planarity : 0.003 0.037 759 Dihedral : 4.982 36.284 663 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.66 % Favored : 96.16 % Rotamer: Outliers : 5.82 % Allowed : 21.34 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.35), residues: 547 helix: 2.42 (0.28), residues: 314 sheet: 1.13 (1.23), residues: 18 loop : -0.65 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1178 TYR 0.011 0.001 TYR A 491 PHE 0.012 0.001 PHE A 322 TRP 0.008 0.001 TRP A 484 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4501) covalent geometry : angle 0.63781 ( 6096) SS BOND : bond 0.00099 ( 4) SS BOND : angle 0.32538 ( 8) hydrogen bonds : bond 0.04891 ( 259) hydrogen bonds : angle 4.20578 ( 753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8727 (pt0) cc_final: 0.8114 (tm-30) REVERT: A 273 TYR cc_start: 0.8825 (m-80) cc_final: 0.8558 (m-10) REVERT: A 309 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8585 (mm-30) REVERT: A 1002 ILE cc_start: 0.8567 (mm) cc_final: 0.7907 (mm) REVERT: A 1040 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6771 (tpt-90) REVERT: A 1056 GLU cc_start: 0.9281 (tt0) cc_final: 0.8968 (pt0) REVERT: A 1058 LEU cc_start: 0.9497 (tp) cc_final: 0.9110 (tt) REVERT: A 1090 HIS cc_start: 0.8368 (m-70) cc_final: 0.8008 (m-70) REVERT: A 1113 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7550 (p0) REVERT: A 1122 GLU cc_start: 0.6303 (tm-30) cc_final: 0.6077 (tm-30) REVERT: A 1130 GLU cc_start: 0.3840 (OUTLIER) cc_final: 0.2334 (mt-10) REVERT: A 1132 MET cc_start: 0.9361 (mtp) cc_final: 0.8606 (mmm) REVERT: A 1193 MET cc_start: 0.4986 (mmt) cc_final: 0.3540 (mmt) REVERT: A 487 SER cc_start: 0.9509 (t) cc_final: 0.9115 (p) REVERT: A 541 TRP cc_start: 0.9107 (m-10) cc_final: 0.8573 (m100) outliers start: 27 outliers final: 21 residues processed: 151 average time/residue: 0.0575 time to fit residues: 11.4984 Evaluate side-chains 154 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1188 CYS Chi-restraints excluded: chain A residue 538 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.115533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095821 restraints weight = 10447.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099250 restraints weight = 5106.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.101659 restraints weight = 3113.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.103336 restraints weight = 2159.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.104369 restraints weight = 1630.860| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4505 Z= 0.123 Angle : 0.622 10.276 6104 Z= 0.306 Chirality : 0.042 0.168 677 Planarity : 0.003 0.034 759 Dihedral : 4.906 39.001 663 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.25 % Allowed : 20.91 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.35), residues: 547 helix: 2.51 (0.28), residues: 314 sheet: 1.12 (1.25), residues: 18 loop : -0.74 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1178 TYR 0.009 0.001 TYR A 237 PHE 0.013 0.001 PHE A 322 TRP 0.010 0.001 TRP A 549 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 4501) covalent geometry : angle 0.62200 ( 6096) SS BOND : bond 0.00098 ( 4) SS BOND : angle 0.31313 ( 8) hydrogen bonds : bond 0.04533 ( 259) hydrogen bonds : angle 4.06201 ( 753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8672 (pt0) cc_final: 0.8086 (tm-30) REVERT: A 309 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8536 (mp0) REVERT: A 1040 ARG cc_start: 0.7064 (OUTLIER) cc_final: 0.6793 (tpt-90) REVERT: A 1056 GLU cc_start: 0.9226 (tt0) cc_final: 0.8958 (pt0) REVERT: A 1058 LEU cc_start: 0.9504 (tp) cc_final: 0.9153 (tt) REVERT: A 1090 HIS cc_start: 0.8317 (m-70) cc_final: 0.7995 (m-70) REVERT: A 1113 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7433 (p0) REVERT: A 1122 GLU cc_start: 0.6088 (tm-30) cc_final: 0.5878 (tm-30) REVERT: A 1130 GLU cc_start: 0.4128 (OUTLIER) cc_final: 0.2601 (mt-10) REVERT: A 1132 MET cc_start: 0.9256 (mtp) cc_final: 0.8639 (mmm) REVERT: A 481 GLN cc_start: 0.9081 (tt0) cc_final: 0.8776 (tt0) REVERT: A 484 TRP cc_start: 0.9151 (m-10) cc_final: 0.8271 (m-10) REVERT: A 487 SER cc_start: 0.9514 (t) cc_final: 0.9168 (p) REVERT: A 530 PHE cc_start: 0.9309 (m-80) cc_final: 0.9104 (m-10) REVERT: A 541 TRP cc_start: 0.9087 (m-10) cc_final: 0.8554 (m100) outliers start: 29 outliers final: 19 residues processed: 159 average time/residue: 0.0640 time to fit residues: 13.4004 Evaluate side-chains 159 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1188 CYS Chi-restraints excluded: chain A residue 538 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** 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 = 0.3593 r_free = 0.3593 target = 0.113627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094117 restraints weight = 10534.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097022 restraints weight = 5298.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.099336 restraints weight = 3421.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.100878 restraints weight = 2421.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.101918 restraints weight = 1868.011| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4505 Z= 0.159 Angle : 0.656 10.466 6104 Z= 0.326 Chirality : 0.044 0.207 677 Planarity : 0.004 0.036 759 Dihedral : 4.966 37.168 663 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.17 % Allowed : 22.84 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.35), residues: 547 helix: 2.42 (0.28), residues: 315 sheet: 1.08 (1.26), residues: 18 loop : -0.79 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1178 TYR 0.012 0.002 TYR A 237 PHE 0.013 0.001 PHE A 226 TRP 0.010 0.001 TRP A 549 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4501) covalent geometry : angle 0.65674 ( 6096) SS BOND : bond 0.00130 ( 4) SS BOND : angle 0.35764 ( 8) hydrogen bonds : bond 0.04669 ( 259) hydrogen bonds : angle 4.23166 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8592 (mm-30) REVERT: A 384 GLN cc_start: 0.8995 (tp40) cc_final: 0.8793 (mm-40) REVERT: A 1040 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6756 (tpt-90) REVERT: A 1056 GLU cc_start: 0.9223 (tt0) cc_final: 0.8970 (pt0) REVERT: A 1058 LEU cc_start: 0.9514 (tp) cc_final: 0.9120 (tt) REVERT: A 1090 HIS cc_start: 0.8277 (m-70) cc_final: 0.7917 (m-70) REVERT: A 1113 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7528 (p0) REVERT: A 1130 GLU cc_start: 0.4084 (OUTLIER) cc_final: 0.2585 (mt-10) REVERT: A 1132 MET cc_start: 0.9271 (mtp) cc_final: 0.8663 (mmm) REVERT: A 1148 ASP cc_start: 0.9048 (m-30) cc_final: 0.8817 (m-30) REVERT: A 1193 MET cc_start: 0.5379 (mmt) cc_final: 0.4300 (mmt) REVERT: A 487 SER cc_start: 0.9522 (t) cc_final: 0.9151 (p) REVERT: A 541 TRP cc_start: 0.9093 (m-10) cc_final: 0.8553 (m100) outliers start: 24 outliers final: 19 residues processed: 146 average time/residue: 0.0654 time to fit residues: 12.5008 Evaluate side-chains 147 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1188 CYS Chi-restraints excluded: chain A residue 538 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** 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 = 0.3593 r_free = 0.3593 target = 0.113859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.094734 restraints weight = 10523.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.097681 restraints weight = 5252.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099986 restraints weight = 3352.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101680 restraints weight = 2352.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102643 restraints weight = 1780.851| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4505 Z= 0.156 Angle : 0.696 12.685 6104 Z= 0.340 Chirality : 0.045 0.230 677 Planarity : 0.004 0.039 759 Dihedral : 5.012 38.850 663 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.60 % Allowed : 23.92 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.35), residues: 547 helix: 2.30 (0.28), residues: 317 sheet: 1.08 (1.28), residues: 18 loop : -0.83 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1178 TYR 0.015 0.002 TYR A 491 PHE 0.013 0.001 PHE A1035 TRP 0.013 0.001 TRP A 549 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4501) covalent geometry : angle 0.69592 ( 6096) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.35999 ( 8) hydrogen bonds : bond 0.04688 ( 259) hydrogen bonds : angle 4.24185 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8744 (pt0) cc_final: 0.8131 (tm-30) REVERT: A 309 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8562 (mm-30) REVERT: A 1040 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6767 (tpt-90) REVERT: A 1056 GLU cc_start: 0.9214 (tt0) cc_final: 0.8936 (pt0) REVERT: A 1058 LEU cc_start: 0.9507 (tp) cc_final: 0.9116 (tt) REVERT: A 1090 HIS cc_start: 0.8309 (m-70) cc_final: 0.7936 (m-70) REVERT: A 1113 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7479 (p0) REVERT: A 1122 GLU cc_start: 0.6326 (tm-30) cc_final: 0.6061 (tm-30) REVERT: A 1130 GLU cc_start: 0.3915 (OUTLIER) cc_final: 0.2450 (mt-10) REVERT: A 1132 MET cc_start: 0.9270 (mtp) cc_final: 0.8656 (mmm) REVERT: A 1193 MET cc_start: 0.5302 (mmt) cc_final: 0.3971 (mmt) REVERT: A 481 GLN cc_start: 0.9065 (tt0) cc_final: 0.8629 (tt0) REVERT: A 484 TRP cc_start: 0.9167 (m-10) cc_final: 0.8216 (m-10) REVERT: A 487 SER cc_start: 0.9516 (t) cc_final: 0.9139 (p) REVERT: A 541 TRP cc_start: 0.9110 (m-10) cc_final: 0.8513 (m100) outliers start: 26 outliers final: 22 residues processed: 144 average time/residue: 0.0633 time to fit residues: 11.9067 Evaluate side-chains 152 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1188 CYS Chi-restraints excluded: chain A residue 538 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.2980 chunk 27 optimal weight: 0.0970 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 0.0060 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.117925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.098056 restraints weight = 10324.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101193 restraints weight = 5129.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.103768 restraints weight = 3265.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.105522 restraints weight = 2282.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106544 restraints weight = 1727.333| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4505 Z= 0.126 Angle : 0.692 12.756 6104 Z= 0.333 Chirality : 0.043 0.186 677 Planarity : 0.003 0.036 759 Dihedral : 4.933 41.347 663 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.09 % Allowed : 25.86 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.35), residues: 547 helix: 2.33 (0.28), residues: 317 sheet: 0.20 (0.84), residues: 36 loop : -0.73 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1178 TYR 0.026 0.002 TYR A 491 PHE 0.010 0.001 PHE A 226 TRP 0.014 0.001 TRP A 549 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4501) covalent geometry : angle 0.69259 ( 6096) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.31077 ( 8) hydrogen bonds : bond 0.04435 ( 259) hydrogen bonds : angle 4.12037 ( 753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8679 (pt0) cc_final: 0.8112 (tm-30) REVERT: A 256 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8407 (t80) REVERT: A 1040 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6719 (tpt-90) REVERT: A 1052 LEU cc_start: 0.8808 (mt) cc_final: 0.8441 (tt) REVERT: A 1056 GLU cc_start: 0.9214 (tt0) cc_final: 0.8891 (pt0) REVERT: A 1058 LEU cc_start: 0.9500 (tp) cc_final: 0.9120 (tt) REVERT: A 1090 HIS cc_start: 0.8316 (m-70) cc_final: 0.7952 (m-70) REVERT: A 1122 GLU cc_start: 0.6376 (tm-30) cc_final: 0.6128 (tm-30) REVERT: A 1130 GLU cc_start: 0.4094 (OUTLIER) cc_final: 0.2697 (mt-10) REVERT: A 1132 MET cc_start: 0.9223 (mtp) cc_final: 0.8637 (mmm) REVERT: A 481 GLN cc_start: 0.9007 (tt0) cc_final: 0.8685 (tt0) REVERT: A 484 TRP cc_start: 0.9133 (m-10) cc_final: 0.8246 (m-90) REVERT: A 487 SER cc_start: 0.9497 (t) cc_final: 0.9111 (p) REVERT: A 541 TRP cc_start: 0.8985 (m-10) cc_final: 0.8740 (m100) outliers start: 19 outliers final: 13 residues processed: 150 average time/residue: 0.0608 time to fit residues: 12.0115 Evaluate side-chains 152 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1188 CYS Chi-restraints excluded: chain A residue 538 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.0570 chunk 36 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** 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 = 0.3611 r_free = 0.3611 target = 0.115528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096474 restraints weight = 10369.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.099475 restraints weight = 5117.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.101918 restraints weight = 3247.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.103428 restraints weight = 2265.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104668 restraints weight = 1737.439| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4505 Z= 0.150 Angle : 0.700 12.526 6104 Z= 0.339 Chirality : 0.044 0.162 677 Planarity : 0.004 0.035 759 Dihedral : 4.915 38.375 663 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.66 % Allowed : 26.29 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.36), residues: 547 helix: 2.35 (0.28), residues: 317 sheet: 0.86 (1.34), residues: 18 loop : -0.70 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1178 TYR 0.013 0.002 TYR A 403 PHE 0.018 0.001 PHE A1035 TRP 0.027 0.002 TRP A 549 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4501) covalent geometry : angle 0.70082 ( 6096) SS BOND : bond 0.00131 ( 4) SS BOND : angle 0.35946 ( 8) hydrogen bonds : bond 0.04560 ( 259) hydrogen bonds : angle 4.23872 ( 753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.174 Fit side-chains REVERT: A 220 GLN cc_start: 0.8745 (pt0) cc_final: 0.8106 (tm-30) REVERT: A 232 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8780 (mm110) REVERT: A 1040 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6686 (tpt-90) REVERT: A 1052 LEU cc_start: 0.8786 (mt) cc_final: 0.8419 (tt) REVERT: A 1056 GLU cc_start: 0.9207 (tt0) cc_final: 0.8900 (pt0) REVERT: A 1058 LEU cc_start: 0.9488 (tp) cc_final: 0.9123 (tt) REVERT: A 1090 HIS cc_start: 0.8301 (m-70) cc_final: 0.7917 (m-70) REVERT: A 1113 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7471 (p0) REVERT: A 1122 GLU cc_start: 0.6540 (tm-30) cc_final: 0.6339 (tm-30) REVERT: A 1130 GLU cc_start: 0.3975 (OUTLIER) cc_final: 0.2837 (mm-30) REVERT: A 1132 MET cc_start: 0.9247 (mtp) cc_final: 0.8957 (mmm) REVERT: A 1193 MET cc_start: 0.5245 (mmt) cc_final: 0.3506 (mmt) REVERT: A 481 GLN cc_start: 0.9013 (tt0) cc_final: 0.8774 (tt0) REVERT: A 484 TRP cc_start: 0.9157 (m-10) cc_final: 0.8749 (m-10) REVERT: A 487 SER cc_start: 0.9495 (t) cc_final: 0.9104 (p) REVERT: A 541 TRP cc_start: 0.8958 (m-10) cc_final: 0.8757 (m100) outliers start: 17 outliers final: 14 residues processed: 149 average time/residue: 0.0622 time to fit residues: 12.2138 Evaluate side-chains 147 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1130 GLU Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1188 CYS Chi-restraints excluded: chain A residue 538 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.116264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.097179 restraints weight = 10460.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100132 restraints weight = 5270.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.102676 restraints weight = 3381.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104263 restraints weight = 2343.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105465 restraints weight = 1799.572| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4505 Z= 0.141 Angle : 0.704 12.505 6104 Z= 0.341 Chirality : 0.044 0.156 677 Planarity : 0.003 0.032 759 Dihedral : 4.949 40.117 663 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.31 % Allowed : 25.86 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.36), residues: 547 helix: 2.34 (0.28), residues: 315 sheet: 0.02 (0.85), residues: 36 loop : -0.64 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1178 TYR 0.012 0.001 TYR A 273 PHE 0.010 0.001 PHE A 322 TRP 0.023 0.002 TRP A 549 HIS 0.003 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4501) covalent geometry : angle 0.70458 ( 6096) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.35264 ( 8) hydrogen bonds : bond 0.04546 ( 259) hydrogen bonds : angle 4.25824 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 980.71 seconds wall clock time: 17 minutes 32.08 seconds (1052.08 seconds total)