Starting phenix.real_space_refine on Fri Dec 27 12:01:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cxo_27062/12_2024/8cxo_27062.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cxo_27062/12_2024/8cxo_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cxo_27062/12_2024/8cxo_27062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cxo_27062/12_2024/8cxo_27062.map" model { file = "/net/cci-nas-00/data/ceres_data/8cxo_27062/12_2024/8cxo_27062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cxo_27062/12_2024/8cxo_27062.cif" } resolution = 3.7 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: 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 3.42, per 1000 atoms: 0.78 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: 1.21 Conformation dependent library (CDL) restraints added in 594.8 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: 0.46 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: 1.24 Time building geometry restraints manager: 1.35 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: 0.720 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.870 ------------------------------------------------------------------------------- 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 4501 Z= 0.227 Angle : 0.581 6.930 6096 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 (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: 1.90 (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 TRP 0.010 0.001 TRP A1007 HIS 0.003 0.001 HIS A 231 PHE 0.015 0.001 PHE A1124 TYR 0.008 0.001 TYR A 398 ARG 0.003 0.000 ARG A1106 *********************** 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 : 0.484 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: 0.8309 (mm-40) REVERT: A 390 VAL cc_start: 0.9414 (t) cc_final: 0.9178 (p) REVERT: A 1003 ASP cc_start: 0.6208 (t0) cc_final: 0.5898 (t0) REVERT: A 1090 HIS cc_start: 0.8396 (m-70) cc_final: 0.7930 (m-70) REVERT: A 1122 GLU cc_start: 0.7933 (tp30) cc_final: 0.6643 (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: 0.8876 (p) 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: 0.1808 time to fit residues: 51.4252 Evaluate side-chains 152 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN A 344 HIS A1065 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4501 Z= 0.206 Angle : 0.619 8.680 6096 Z= 0.324 Chirality : 0.043 0.147 677 Planarity : 0.004 0.026 759 Dihedral : 5.195 29.233 663 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.66 % Allowed : 15.95 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 2.13 (0.35), residues: 547 helix: 2.33 (0.27), residues: 314 sheet: 2.03 (1.03), residues: 19 loop : -0.01 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 343 HIS 0.006 0.001 HIS A 344 PHE 0.019 0.002 PHE A 322 TYR 0.012 0.001 TYR A 363 ARG 0.005 0.001 ARG A1102 *********************** 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 184 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 237 TYR cc_start: 0.8506 (t80) cc_final: 0.8289 (t80) REVERT: A 253 LEU cc_start: 0.9236 (mp) cc_final: 0.9027 (mp) REVERT: A 309 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8574 (mp0) REVERT: A 348 LYS cc_start: 0.8986 (mttt) cc_final: 0.8717 (mtmt) REVERT: A 1003 ASP cc_start: 0.6692 (t0) cc_final: 0.5919 (t0) REVERT: A 1041 PHE cc_start: 0.7483 (m-10) cc_final: 0.7057 (m-10) REVERT: A 1056 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8717 (tm-30) REVERT: A 1090 HIS cc_start: 0.8334 (m-70) cc_final: 0.8013 (m-70) REVERT: A 1123 PRO cc_start: 0.8945 (Cg_exo) cc_final: 0.8729 (Cg_endo) REVERT: A 1154 THR cc_start: 0.9156 (m) cc_final: 0.8800 (p) REVERT: A 484 TRP cc_start: 0.9096 (m-10) cc_final: 0.8557 (m-90) REVERT: A 530 PHE cc_start: 0.9407 (m-80) cc_final: 0.9156 (m-10) outliers start: 17 outliers final: 15 residues processed: 174 average time/residue: 0.1564 time to fit residues: 34.4139 Evaluate side-chains 159 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 280 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 427 VAL 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 472 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN A 481 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4501 Z= 0.263 Angle : 0.620 7.208 6096 Z= 0.326 Chirality : 0.044 0.152 677 Planarity : 0.004 0.039 759 Dihedral : 5.144 26.748 663 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.82 % Allowed : 18.53 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 2.00 (0.35), residues: 547 helix: 2.35 (0.27), residues: 314 sheet: 1.95 (1.06), residues: 19 loop : -0.29 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1007 HIS 0.001 0.001 HIS A 365 PHE 0.015 0.002 PHE A 322 TYR 0.015 0.002 TYR A 491 ARG 0.009 0.001 ARG A1178 *********************** 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 172 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8488 (tp30) cc_final: 0.8137 (tm-30) REVERT: A 232 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8683 (mm-40) REVERT: A 253 LEU cc_start: 0.9309 (mp) cc_final: 0.9076 (mp) REVERT: A 309 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8541 (mp0) REVERT: A 348 LYS cc_start: 0.9026 (mttt) cc_final: 0.8821 (mtpt) REVERT: A 384 GLN cc_start: 0.8999 (tp40) cc_final: 0.8199 (mt0) REVERT: A 388 ASP cc_start: 0.9046 (t0) cc_final: 0.8774 (t0) REVERT: A 1041 PHE cc_start: 0.7563 (m-10) cc_final: 0.7314 (m-10) REVERT: A 1057 ILE cc_start: 0.9187 (mm) cc_final: 0.8971 (mm) REVERT: A 1090 HIS cc_start: 0.8436 (m-70) cc_final: 0.8108 (m-70) REVERT: A 1193 MET cc_start: 0.5181 (mmt) cc_final: 0.3965 (mmt) REVERT: A 481 GLN cc_start: 0.9143 (tt0) cc_final: 0.8849 (tt0) REVERT: A 484 TRP cc_start: 0.9164 (m-10) cc_final: 0.8414 (m-90) REVERT: A 487 SER cc_start: 0.9541 (t) cc_final: 0.9205 (p) outliers start: 27 outliers final: 18 residues processed: 157 average time/residue: 0.1352 time to fit residues: 27.5475 Evaluate side-chains 155 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 280 VAL Chi-restraints excluded: chain A residue 337 VAL 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 417 ILE Chi-restraints excluded: chain A residue 441 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 50 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 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 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4501 Z= 0.179 Angle : 0.593 12.292 6096 Z= 0.302 Chirality : 0.042 0.145 677 Planarity : 0.004 0.039 759 Dihedral : 4.951 36.202 663 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.74 % Allowed : 19.61 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.90 (0.35), residues: 547 helix: 2.37 (0.28), residues: 314 sheet: 1.24 (1.26), residues: 18 loop : -0.42 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 539 HIS 0.001 0.000 HIS A 365 PHE 0.016 0.001 PHE A 373 TYR 0.010 0.001 TYR A 363 ARG 0.010 0.001 ARG A1178 *********************** 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 : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.9297 (mp) cc_final: 0.9095 (mp) REVERT: A 309 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8500 (mp0) REVERT: A 388 ASP cc_start: 0.9031 (t0) cc_final: 0.8523 (t0) REVERT: A 1058 LEU cc_start: 0.9546 (tp) cc_final: 0.9320 (tt) REVERT: A 1067 MET cc_start: 0.8621 (mpp) cc_final: 0.8416 (pmm) REVERT: A 1090 HIS cc_start: 0.8415 (m-70) cc_final: 0.8071 (m-70) REVERT: A 1113 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7484 (p0) REVERT: A 1124 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7094 (p90) REVERT: A 1132 MET cc_start: 0.9254 (mtp) cc_final: 0.8808 (mmm) REVERT: A 1154 THR cc_start: 0.9272 (m) cc_final: 0.8908 (p) REVERT: A 481 GLN cc_start: 0.9071 (tt0) cc_final: 0.8797 (tt0) REVERT: A 484 TRP cc_start: 0.9141 (m-10) cc_final: 0.8372 (m-10) REVERT: A 487 SER cc_start: 0.9511 (t) cc_final: 0.9120 (p) REVERT: A 549 TRP cc_start: 0.9017 (m100) cc_final: 0.8768 (m100) outliers start: 22 outliers final: 13 residues processed: 155 average time/residue: 0.1290 time to fit residues: 26.0923 Evaluate side-chains 148 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 280 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 TYR 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 1124 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 44 optimal weight: 0.0980 chunk 30 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4501 Z= 0.236 Angle : 0.628 10.050 6096 Z= 0.316 Chirality : 0.044 0.184 677 Planarity : 0.004 0.039 759 Dihedral : 4.957 35.395 663 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.82 % Allowed : 19.83 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.90 (0.35), residues: 547 helix: 2.47 (0.28), residues: 314 sheet: 0.92 (1.24), residues: 18 loop : -0.57 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 541 HIS 0.002 0.001 HIS A 365 PHE 0.020 0.001 PHE A 373 TYR 0.009 0.001 TYR A 363 ARG 0.011 0.001 ARG A1178 *********************** 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 158 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 253 LEU cc_start: 0.9318 (mp) cc_final: 0.9112 (mp) REVERT: A 273 TYR cc_start: 0.8926 (m-80) cc_final: 0.8682 (m-10) REVERT: A 309 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8511 (mp0) REVERT: A 1058 LEU cc_start: 0.9541 (tp) cc_final: 0.9303 (tt) REVERT: A 1090 HIS cc_start: 0.8439 (m-70) cc_final: 0.8080 (m-70) REVERT: A 1113 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7519 (p0) REVERT: A 1124 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.6890 (p90) REVERT: A 1154 THR cc_start: 0.9258 (m) cc_final: 0.8967 (p) REVERT: A 1193 MET cc_start: 0.4778 (mmt) cc_final: 0.3135 (mmt) REVERT: A 481 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8717 (tt0) REVERT: A 484 TRP cc_start: 0.9178 (m-10) cc_final: 0.8345 (m-10) REVERT: A 487 SER cc_start: 0.9513 (t) cc_final: 0.9119 (p) outliers start: 27 outliers final: 21 residues processed: 147 average time/residue: 0.1269 time to fit residues: 24.7911 Evaluate side-chains 147 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 337 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1033 VAL 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 1124 PHE Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 526 LEU 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 47 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4501 Z= 0.164 Angle : 0.614 10.275 6096 Z= 0.307 Chirality : 0.042 0.170 677 Planarity : 0.004 0.040 759 Dihedral : 4.859 38.868 663 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.66 % Favored : 96.16 % Rotamer: Outliers : 6.03 % Allowed : 20.69 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.97 (0.35), residues: 547 helix: 2.58 (0.28), residues: 314 sheet: 0.17 (0.81), residues: 36 loop : -0.63 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 539 HIS 0.001 0.000 HIS A 365 PHE 0.016 0.001 PHE A 373 TYR 0.013 0.001 TYR A 237 ARG 0.012 0.001 ARG A1178 *********************** 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 168 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.9283 (mp) cc_final: 0.9080 (mp) REVERT: A 309 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8491 (mp0) REVERT: A 1002 ILE cc_start: 0.8535 (mm) cc_final: 0.8139 (mm) REVERT: A 1040 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6726 (tpt-90) REVERT: A 1058 LEU cc_start: 0.9537 (tp) cc_final: 0.9185 (tt) REVERT: A 1090 HIS cc_start: 0.8413 (m-70) cc_final: 0.8042 (m-70) REVERT: A 1113 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7350 (p0) REVERT: A 1124 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.7049 (p90) REVERT: A 1154 THR cc_start: 0.9259 (m) cc_final: 0.8984 (p) REVERT: A 1193 MET cc_start: 0.4328 (mmt) cc_final: 0.3542 (mmt) REVERT: A 481 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8728 (tt0) REVERT: A 484 TRP cc_start: 0.9163 (m-10) cc_final: 0.8462 (m-90) REVERT: A 487 SER cc_start: 0.9470 (t) cc_final: 0.9074 (p) REVERT: A 541 TRP cc_start: 0.9167 (m-10) cc_final: 0.8578 (m100) outliers start: 28 outliers final: 18 residues processed: 154 average time/residue: 0.1324 time to fit residues: 26.6615 Evaluate side-chains 155 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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 415 VAL Chi-restraints excluded: chain A residue 441 LEU 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 1179 SER Chi-restraints excluded: chain A residue 481 GLN 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 5 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 33 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4501 Z= 0.228 Angle : 0.639 10.554 6096 Z= 0.323 Chirality : 0.044 0.204 677 Planarity : 0.004 0.037 759 Dihedral : 4.957 36.490 663 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.60 % Allowed : 23.49 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.94 (0.36), residues: 547 helix: 2.57 (0.28), residues: 315 sheet: 0.37 (1.25), residues: 18 loop : -0.66 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 539 HIS 0.002 0.001 HIS A 365 PHE 0.025 0.001 PHE A 373 TYR 0.017 0.002 TYR A 403 ARG 0.014 0.001 ARG A1178 *********************** 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 157 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8548 (mm-30) REVERT: A 1002 ILE cc_start: 0.8574 (mm) cc_final: 0.8128 (mm) REVERT: A 1040 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6717 (tpt-90) REVERT: A 1058 LEU cc_start: 0.9503 (tp) cc_final: 0.9128 (tt) REVERT: A 1090 HIS cc_start: 0.8441 (m-70) cc_final: 0.8106 (m-70) REVERT: A 1113 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7431 (p0) REVERT: A 1124 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7153 (p90) REVERT: A 1154 THR cc_start: 0.9215 (m) cc_final: 0.8939 (p) REVERT: A 1193 MET cc_start: 0.4798 (mmt) cc_final: 0.3396 (mmt) REVERT: A 481 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8697 (tt0) REVERT: A 484 TRP cc_start: 0.9208 (m-10) cc_final: 0.8386 (m-10) REVERT: A 487 SER cc_start: 0.9488 (t) cc_final: 0.9081 (p) REVERT: A 541 TRP cc_start: 0.9198 (m-10) cc_final: 0.8573 (m100) outliers start: 26 outliers final: 22 residues processed: 146 average time/residue: 0.1451 time to fit residues: 27.6859 Evaluate side-chains 157 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 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 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 441 LEU 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 1124 PHE Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 481 GLN 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 15 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4501 Z= 0.317 Angle : 0.720 12.207 6096 Z= 0.362 Chirality : 0.046 0.213 677 Planarity : 0.004 0.039 759 Dihedral : 5.176 35.317 663 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 6.25 % Allowed : 23.06 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.48 (0.36), residues: 547 helix: 2.31 (0.28), residues: 315 sheet: -1.53 (0.96), residues: 28 loop : -0.80 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 539 HIS 0.002 0.001 HIS A 474 PHE 0.022 0.002 PHE A 373 TYR 0.023 0.002 TYR A 273 ARG 0.014 0.001 ARG A1178 *********************** 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 155 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1040 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6735 (tpt-90) REVERT: A 1058 LEU cc_start: 0.9507 (tp) cc_final: 0.9133 (tt) REVERT: A 1090 HIS cc_start: 0.8435 (m-70) cc_final: 0.8053 (m-70) REVERT: A 1113 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7502 (p0) REVERT: A 1122 GLU cc_start: 0.6476 (tm-30) cc_final: 0.6146 (tm-30) REVERT: A 1124 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7241 (p90) REVERT: A 1130 GLU cc_start: 0.3705 (tt0) cc_final: 0.3199 (tt0) REVERT: A 1154 THR cc_start: 0.9217 (m) cc_final: 0.8941 (p) REVERT: A 1193 MET cc_start: 0.4798 (mmt) cc_final: 0.3620 (mmt) REVERT: A 487 SER cc_start: 0.9528 (t) cc_final: 0.9148 (p) REVERT: A 541 TRP cc_start: 0.9134 (m-10) cc_final: 0.8595 (m100) outliers start: 29 outliers final: 22 residues processed: 141 average time/residue: 0.1381 time to fit residues: 25.3662 Evaluate side-chains 134 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 256 PHE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 VAL 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 415 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 423 LEU 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 1124 PHE Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 451 GLU 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 50 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4501 Z= 0.219 Angle : 0.720 14.937 6096 Z= 0.347 Chirality : 0.045 0.242 677 Planarity : 0.004 0.040 759 Dihedral : 5.041 38.967 663 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.31 % Allowed : 26.29 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.64 (0.36), residues: 547 helix: 2.34 (0.28), residues: 317 sheet: -0.14 (1.31), residues: 18 loop : -0.79 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 549 HIS 0.002 0.001 HIS A 365 PHE 0.018 0.001 PHE A 373 TYR 0.017 0.002 TYR A 273 ARG 0.016 0.001 ARG A1178 *********************** 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 152 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 232 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8787 (mm110) REVERT: A 1002 ILE cc_start: 0.8602 (mm) cc_final: 0.8213 (mm) REVERT: A 1040 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6787 (tpt-90) REVERT: A 1058 LEU cc_start: 0.9493 (tp) cc_final: 0.9102 (tt) REVERT: A 1090 HIS cc_start: 0.8406 (m-70) cc_final: 0.8023 (m-70) REVERT: A 1113 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7419 (p0) REVERT: A 1122 GLU cc_start: 0.6412 (tm-30) cc_final: 0.6141 (tm-30) REVERT: A 1124 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7175 (p90) REVERT: A 1130 GLU cc_start: 0.3508 (tt0) cc_final: 0.2977 (tt0) REVERT: A 1154 THR cc_start: 0.9219 (m) cc_final: 0.8948 (p) REVERT: A 1193 MET cc_start: 0.4616 (mmt) cc_final: 0.3196 (mmt) REVERT: A 481 GLN cc_start: 0.9122 (tt0) cc_final: 0.8781 (tt0) REVERT: A 487 SER cc_start: 0.9503 (t) cc_final: 0.9123 (p) REVERT: A 541 TRP cc_start: 0.9115 (m-10) cc_final: 0.8579 (m100) outliers start: 20 outliers final: 15 residues processed: 144 average time/residue: 0.1389 time to fit residues: 26.0898 Evaluate side-chains 148 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 366 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 423 LEU 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 1124 PHE Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 451 GLU 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 24 optimal weight: 0.0980 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4501 Z= 0.203 Angle : 0.716 15.249 6096 Z= 0.345 Chirality : 0.044 0.182 677 Planarity : 0.003 0.033 759 Dihedral : 4.915 39.405 663 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.09 % Allowed : 26.94 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.69 (0.36), residues: 547 helix: 2.34 (0.28), residues: 317 sheet: -0.27 (1.29), residues: 18 loop : -0.67 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 549 HIS 0.002 0.000 HIS A 365 PHE 0.019 0.001 PHE A 373 TYR 0.014 0.001 TYR A 273 ARG 0.016 0.001 ARG A1178 ********************** 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 160 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 1002 ILE cc_start: 0.8590 (mm) cc_final: 0.8246 (mm) REVERT: A 1040 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6766 (tpt-90) REVERT: A 1052 LEU cc_start: 0.8922 (mt) cc_final: 0.8582 (tt) REVERT: A 1058 LEU cc_start: 0.9507 (tp) cc_final: 0.9124 (tt) REVERT: A 1090 HIS cc_start: 0.8391 (m-70) cc_final: 0.8007 (m-70) REVERT: A 1113 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7243 (p0) REVERT: A 1124 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7287 (p90) REVERT: A 1154 THR cc_start: 0.9201 (m) cc_final: 0.8928 (p) REVERT: A 1193 MET cc_start: 0.4522 (mmt) cc_final: 0.3162 (mmt) REVERT: A 484 TRP cc_start: 0.9169 (m-10) cc_final: 0.8908 (m-10) REVERT: A 487 SER cc_start: 0.9501 (t) cc_final: 0.9127 (p) REVERT: A 541 TRP cc_start: 0.9094 (m-10) cc_final: 0.8555 (m100) outliers start: 19 outliers final: 15 residues processed: 153 average time/residue: 0.1425 time to fit residues: 28.3293 Evaluate side-chains 152 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 1071 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 1179 SER Chi-restraints excluded: chain A residue 451 GLU 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 40 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.0470 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 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 = 0.3612 r_free = 0.3612 target = 0.115402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095183 restraints weight = 9964.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.098381 restraints weight = 4905.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.100719 restraints weight = 3000.251| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4501 Z= 0.204 Angle : 0.732 15.211 6096 Z= 0.355 Chirality : 0.044 0.180 677 Planarity : 0.003 0.034 759 Dihedral : 4.890 39.221 663 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.88 % Allowed : 27.37 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.65 (0.36), residues: 547 helix: 2.27 (0.28), residues: 317 sheet: -0.24 (1.30), residues: 18 loop : -0.62 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 549 HIS 0.002 0.000 HIS A 365 PHE 0.021 0.001 PHE A 373 TYR 0.015 0.001 TYR A1011 ARG 0.013 0.000 ARG A1178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1271.33 seconds wall clock time: 23 minutes 54.09 seconds (1434.09 seconds total)