Starting phenix.real_space_refine on Thu Jul 18 23:25:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/07_2024/8cxo_27062.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/07_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/07_2024/8cxo_27062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/07_2024/8cxo_27062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/07_2024/8cxo_27062.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/07_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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 3.27, per 1000 atoms: 0.74 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 - 3.50 Amino acid : False - 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: 1.69 Conformation dependent library (CDL) restraints added in 778.0 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: 0.51 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: 1.22 Time building geometry restraints manager: 1.88 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: 100.25 - 107.01: 103 107.01 - 113.77: 2461 113.77 - 120.53: 1873 120.53 - 127.29: 1609 127.29 - 134.04: 50 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 2.520 nonbonded pdb=" N GLU A1098 " pdb=" OE1 GLU A1098 " model vdw 2.346 2.520 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 2.520 nonbonded pdb=" O GLU A1056 " pdb=" OG SER A1059 " model vdw 2.420 2.440 ... (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: 1.160 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.860 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.150 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 0.506 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: 0.1716 time to fit residues: 48.9946 Evaluate side-chains 152 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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: 1.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.7868 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4501 Z= 0.212 Angle : 0.609 9.024 6096 Z= 0.317 Chirality : 0.043 0.144 677 Planarity : 0.004 0.030 759 Dihedral : 5.177 28.520 663 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.47 % Favored : 96.34 % Rotamer: Outliers : 4.31 % Allowed : 15.95 % Favored : 79.74 % 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: 2.14 (0.35), residues: 547 helix: 2.37 (0.27), residues: 315 sheet: 2.10 (1.08), residues: 19 loop : -0.08 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 343 HIS 0.006 0.001 HIS A 344 PHE 0.018 0.002 PHE A 289 TYR 0.013 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 fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 TYR cc_start: 0.8409 (t80) cc_final: 0.8183 (t80) REVERT: A 309 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8567 (mp0) REVERT: A 348 LYS cc_start: 0.8965 (mttt) cc_final: 0.8684 (mtmt) REVERT: A 1003 ASP cc_start: 0.6675 (t0) cc_final: 0.5882 (t0) REVERT: A 1023 LEU cc_start: 0.9618 (mt) cc_final: 0.9415 (mt) REVERT: A 1041 PHE cc_start: 0.7498 (m-10) cc_final: 0.7177 (m-10) REVERT: A 1056 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8870 (tm-30) REVERT: A 1090 HIS cc_start: 0.8363 (m-70) cc_final: 0.8031 (m-70) REVERT: A 1123 PRO cc_start: 0.8956 (Cg_exo) cc_final: 0.8754 (Cg_endo) REVERT: A 1132 MET cc_start: 0.9268 (mtp) cc_final: 0.8829 (mtp) REVERT: A 1154 THR cc_start: 0.9102 (m) cc_final: 0.8709 (p) REVERT: A 484 TRP cc_start: 0.9078 (m-10) cc_final: 0.8512 (m-90) REVERT: A 487 SER cc_start: 0.9525 (t) cc_final: 0.9198 (p) REVERT: A 530 PHE cc_start: 0.9400 (m-80) cc_final: 0.9147 (m-80) outliers start: 20 outliers final: 18 residues processed: 175 average time/residue: 0.1424 time to fit residues: 31.9635 Evaluate side-chains 164 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 236 SER 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 427 VAL Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1085 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 49 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 overall best weight: 2.3564 ------------------------------------------------------------------------------- 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: 0.7978 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4501 Z= 0.348 Angle : 0.681 8.603 6096 Z= 0.353 Chirality : 0.045 0.157 677 Planarity : 0.005 0.042 759 Dihedral : 5.348 26.245 663 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 7.76 % Allowed : 15.52 % Favored : 76.72 % 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: 1.70 (0.35), residues: 547 helix: 2.18 (0.27), residues: 313 sheet: 1.73 (1.09), residues: 19 loop : -0.53 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 541 HIS 0.002 0.001 HIS A 437 PHE 0.017 0.002 PHE A 527 TYR 0.011 0.002 TYR A 363 ARG 0.004 0.001 ARG A1106 *********************** 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 174 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8603 (pt0) cc_final: 0.7922 (tm-30) REVERT: A 273 TYR cc_start: 0.8942 (m-80) cc_final: 0.8536 (m-10) REVERT: A 309 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8496 (mp0) REVERT: A 348 LYS cc_start: 0.8967 (mttt) cc_final: 0.8726 (mtmt) REVERT: A 388 ASP cc_start: 0.9020 (t0) cc_final: 0.8637 (t0) REVERT: A 441 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6714 (mp) REVERT: A 1057 ILE cc_start: 0.9237 (mm) cc_final: 0.9018 (mm) REVERT: A 1067 MET cc_start: 0.8657 (mpp) cc_final: 0.8423 (pmm) REVERT: A 1090 HIS cc_start: 0.8529 (m-70) cc_final: 0.8194 (m-70) REVERT: A 1113 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7669 (p0) REVERT: A 1124 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7073 (p90) REVERT: A 1130 GLU cc_start: 0.3849 (tt0) cc_final: 0.3516 (tt0) REVERT: A 1132 MET cc_start: 0.9478 (mtp) cc_final: 0.9199 (mtp) REVERT: A 481 GLN cc_start: 0.9065 (tt0) cc_final: 0.8609 (tt0) REVERT: A 484 TRP cc_start: 0.9205 (m-10) cc_final: 0.8320 (m-90) REVERT: A 487 SER cc_start: 0.9571 (t) cc_final: 0.9237 (p) outliers start: 36 outliers final: 25 residues processed: 155 average time/residue: 0.1344 time to fit residues: 27.1699 Evaluate side-chains 150 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 236 SER 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 298 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 345 THR 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 1013 THR Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1085 SER 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 1129 LEU Chi-restraints excluded: chain A residue 1148 ASP Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1188 CYS Chi-restraints excluded: chain A residue 472 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: 0.8980 chunk 25 optimal weight: 0.0040 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4501 Z= 0.166 Angle : 0.586 12.256 6096 Z= 0.294 Chirality : 0.042 0.139 677 Planarity : 0.004 0.035 759 Dihedral : 4.977 37.643 663 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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 (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: 1.91 (0.35), residues: 547 helix: 2.52 (0.27), residues: 313 sheet: 1.26 (1.28), residues: 18 loop : -0.66 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 549 HIS 0.001 0.000 HIS A1090 PHE 0.015 0.001 PHE A 373 TYR 0.009 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 163 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8508 (pt0) cc_final: 0.7890 (tm-30) REVERT: A 228 GLU cc_start: 0.8421 (tp30) cc_final: 0.7902 (tm-30) REVERT: A 232 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8746 (mm-40) REVERT: A 273 TYR cc_start: 0.8914 (m-80) cc_final: 0.8689 (m-10) REVERT: A 309 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8483 (mp0) REVERT: A 388 ASP cc_start: 0.8919 (t0) cc_final: 0.8333 (t0) REVERT: A 1058 LEU cc_start: 0.9563 (tp) cc_final: 0.9318 (tt) REVERT: A 1090 HIS cc_start: 0.8455 (m-70) cc_final: 0.8089 (m-70) REVERT: A 1124 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.7223 (p90) REVERT: A 481 GLN cc_start: 0.9065 (tt0) cc_final: 0.8779 (tt0) REVERT: A 484 TRP cc_start: 0.9151 (m-10) cc_final: 0.8436 (m-90) REVERT: A 487 SER cc_start: 0.9498 (t) cc_final: 0.9105 (p) outliers start: 27 outliers final: 16 residues processed: 149 average time/residue: 0.1374 time to fit residues: 26.5633 Evaluate side-chains 146 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 236 SER Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 433 ILE 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 1115 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1188 CYS Chi-restraints excluded: chain A residue 529 MET 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: 5.9990 chunk 30 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** A1065 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4501 Z= 0.192 Angle : 0.602 9.344 6096 Z= 0.300 Chirality : 0.041 0.144 677 Planarity : 0.003 0.036 759 Dihedral : 4.913 35.995 663 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.39 % Allowed : 23.06 % Favored : 71.55 % 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: 2.63 (0.27), residues: 313 sheet: 1.05 (1.27), residues: 18 loop : -0.72 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 343 HIS 0.001 0.000 HIS A 474 PHE 0.014 0.001 PHE A 322 TYR 0.012 0.001 TYR A 237 ARG 0.011 0.000 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 157 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8492 (pt0) cc_final: 0.7823 (tm-30) REVERT: A 309 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8496 (mp0) REVERT: A 1058 LEU cc_start: 0.9520 (tp) cc_final: 0.9174 (tt) REVERT: A 1090 HIS cc_start: 0.8470 (m-70) cc_final: 0.8125 (m-70) REVERT: A 1124 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7065 (p90) REVERT: A 1130 GLU cc_start: 0.3448 (tt0) cc_final: 0.3124 (tt0) REVERT: A 1132 MET cc_start: 0.9408 (mtp) cc_final: 0.8602 (mmm) REVERT: A 1193 MET cc_start: 0.4709 (mmt) cc_final: 0.2999 (mmt) REVERT: A 481 GLN cc_start: 0.9063 (tt0) cc_final: 0.8770 (tt0) REVERT: A 484 TRP cc_start: 0.9166 (m-10) cc_final: 0.8324 (m-10) REVERT: A 487 SER cc_start: 0.9511 (t) cc_final: 0.9123 (p) outliers start: 25 outliers final: 18 residues processed: 141 average time/residue: 0.1365 time to fit residues: 24.9786 Evaluate side-chains 147 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 313 SER 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 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 1115 VAL Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1188 CYS Chi-restraints excluded: chain A residue 523 LYS 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: 3.9990 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4501 Z= 0.196 Angle : 0.624 9.729 6096 Z= 0.308 Chirality : 0.041 0.145 677 Planarity : 0.004 0.037 759 Dihedral : 4.890 36.785 663 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 6.47 % Allowed : 21.98 % Favored : 71.55 % 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: 2.01 (0.35), residues: 547 helix: 2.70 (0.28), residues: 314 sheet: 1.13 (1.28), residues: 18 loop : -0.81 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 539 HIS 0.001 0.000 HIS A 474 PHE 0.015 0.001 PHE A 373 TYR 0.013 0.001 TYR A1011 ARG 0.013 0.000 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 fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8496 (pt0) cc_final: 0.7840 (tm-30) REVERT: A 309 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8510 (mp0) REVERT: A 1007 TRP cc_start: 0.6351 (OUTLIER) cc_final: 0.6124 (t-100) REVERT: A 1052 LEU cc_start: 0.9005 (mt) cc_final: 0.8544 (tt) REVERT: A 1056 GLU cc_start: 0.9346 (pt0) cc_final: 0.9072 (pt0) REVERT: A 1058 LEU cc_start: 0.9511 (tp) cc_final: 0.9151 (tt) REVERT: A 1090 HIS cc_start: 0.8449 (m-70) cc_final: 0.8072 (m-70) REVERT: A 1122 GLU cc_start: 0.6655 (tm-30) cc_final: 0.6310 (tm-30) REVERT: A 1124 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.7161 (p90) REVERT: A 1130 GLU cc_start: 0.3474 (tt0) cc_final: 0.3100 (tt0) REVERT: A 1132 MET cc_start: 0.9367 (mtp) cc_final: 0.8649 (mmm) REVERT: A 481 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8758 (tt0) REVERT: A 484 TRP cc_start: 0.9184 (m-10) cc_final: 0.8389 (m-10) REVERT: A 487 SER cc_start: 0.9482 (t) cc_final: 0.9079 (p) REVERT: A 541 TRP cc_start: 0.9154 (m-10) cc_final: 0.8667 (m100) outliers start: 30 outliers final: 22 residues processed: 152 average time/residue: 0.1400 time to fit residues: 27.6046 Evaluate side-chains 154 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 277 CYS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 313 SER 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 390 VAL Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 1007 TRP 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 1115 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1188 CYS Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 529 MET 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: 0.9990 chunk 30 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 44 optimal weight: 0.0970 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5421 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= 0.187 Angle : 0.621 10.006 6096 Z= 0.308 Chirality : 0.042 0.172 677 Planarity : 0.003 0.036 759 Dihedral : 4.843 38.108 663 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 6.03 % Allowed : 23.71 % Favored : 70.26 % 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: 2.02 (0.35), residues: 547 helix: 2.70 (0.28), residues: 314 sheet: 1.18 (1.29), residues: 18 loop : -0.80 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 539 HIS 0.001 0.000 HIS A 474 PHE 0.018 0.001 PHE A 373 TYR 0.012 0.001 TYR A 403 ARG 0.013 0.000 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 164 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8479 (pt0) cc_final: 0.7822 (tm-30) REVERT: A 309 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8545 (mm-30) REVERT: A 1058 LEU cc_start: 0.9491 (tp) cc_final: 0.9114 (tt) REVERT: A 1090 HIS cc_start: 0.8449 (m-70) cc_final: 0.8070 (m-70) REVERT: A 1132 MET cc_start: 0.9309 (mtp) cc_final: 0.8454 (mmm) REVERT: A 484 TRP cc_start: 0.9183 (m-10) cc_final: 0.8951 (m-10) REVERT: A 487 SER cc_start: 0.9466 (t) cc_final: 0.9061 (p) REVERT: A 541 TRP cc_start: 0.9175 (m-10) cc_final: 0.8673 (m100) outliers start: 28 outliers final: 20 residues processed: 149 average time/residue: 0.1385 time to fit residues: 26.9540 Evaluate side-chains 153 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 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 277 CYS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 313 SER 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 390 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1188 CYS Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 523 LYS 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: 0.9980 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1065 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4501 Z= 0.261 Angle : 0.676 10.989 6096 Z= 0.338 Chirality : 0.044 0.166 677 Planarity : 0.004 0.039 759 Dihedral : 4.968 35.665 663 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.68 % Allowed : 23.06 % Favored : 70.26 % 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: 1.91 (0.36), residues: 547 helix: 2.65 (0.28), residues: 314 sheet: 1.39 (1.32), residues: 18 loop : -0.93 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1007 HIS 0.002 0.000 HIS A 474 PHE 0.020 0.001 PHE A 373 TYR 0.015 0.002 TYR A 403 ARG 0.015 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 156 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8771 (mm110) REVERT: A 384 GLN cc_start: 0.8945 (tp40) cc_final: 0.8415 (mt0) REVERT: A 1058 LEU cc_start: 0.9480 (tp) cc_final: 0.9100 (tt) REVERT: A 1090 HIS cc_start: 0.8508 (m-70) cc_final: 0.8108 (m-70) REVERT: A 1124 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.7135 (p90) REVERT: A 1130 GLU cc_start: 0.3422 (tt0) cc_final: 0.2947 (tt0) REVERT: A 1132 MET cc_start: 0.9433 (mtp) cc_final: 0.8743 (mmm) REVERT: A 1193 MET cc_start: 0.4704 (mmt) cc_final: 0.2657 (mmt) REVERT: A 1201 MET cc_start: 0.8023 (mpp) cc_final: 0.7691 (mpp) REVERT: A 481 GLN cc_start: 0.9118 (tt0) cc_final: 0.8823 (tt0) REVERT: A 487 SER cc_start: 0.9504 (t) cc_final: 0.9101 (p) REVERT: A 541 TRP cc_start: 0.9090 (m-10) cc_final: 0.8679 (m100) outliers start: 31 outliers final: 23 residues processed: 140 average time/residue: 0.1384 time to fit residues: 25.2005 Evaluate side-chains 148 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 313 SER 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 390 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 520 LEU 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: 6.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4501 Z= 0.215 Angle : 0.667 12.582 6096 Z= 0.330 Chirality : 0.043 0.193 677 Planarity : 0.004 0.042 759 Dihedral : 4.864 37.763 663 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.82 % Allowed : 24.57 % Favored : 69.61 % 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: 1.92 (0.36), residues: 547 helix: 2.63 (0.28), residues: 315 sheet: 1.48 (1.34), residues: 18 loop : -0.91 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 539 HIS 0.001 0.000 HIS A 474 PHE 0.018 0.001 PHE A 373 TYR 0.011 0.001 TYR A 403 ARG 0.016 0.000 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 160 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 232 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8766 (mm110) REVERT: A 1052 LEU cc_start: 0.8647 (mt) cc_final: 0.8309 (tt) REVERT: A 1058 LEU cc_start: 0.9473 (tp) cc_final: 0.9081 (tt) REVERT: A 1090 HIS cc_start: 0.8455 (m-70) cc_final: 0.8071 (m-70) REVERT: A 1124 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7149 (p90) REVERT: A 1132 MET cc_start: 0.9378 (mtp) cc_final: 0.8502 (mmm) REVERT: A 1193 MET cc_start: 0.4591 (mmt) cc_final: 0.2637 (mmt) REVERT: A 1201 MET cc_start: 0.8046 (mpp) cc_final: 0.7614 (mpp) REVERT: A 481 GLN cc_start: 0.9095 (tt0) cc_final: 0.8661 (tt0) REVERT: A 484 TRP cc_start: 0.9206 (m-10) cc_final: 0.8334 (m-10) REVERT: A 487 SER cc_start: 0.9483 (t) cc_final: 0.9117 (p) REVERT: A 541 TRP cc_start: 0.9053 (m-10) cc_final: 0.8638 (m100) outliers start: 27 outliers final: 22 residues processed: 147 average time/residue: 0.1350 time to fit residues: 25.9141 Evaluate side-chains 151 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 313 SER 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 423 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 529 MET 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: 3.9990 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4501 Z= 0.228 Angle : 0.694 12.402 6096 Z= 0.338 Chirality : 0.044 0.201 677 Planarity : 0.004 0.035 759 Dihedral : 4.868 36.953 663 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.96 % Allowed : 25.43 % Favored : 69.61 % 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: 1.82 (0.36), residues: 547 helix: 2.53 (0.28), residues: 315 sheet: 1.54 (1.35), residues: 18 loop : -0.92 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 539 HIS 0.001 0.000 HIS A 474 PHE 0.019 0.001 PHE A 373 TYR 0.013 0.001 TYR A 237 ARG 0.016 0.000 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 153 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8800 (mm110) REVERT: A 1052 LEU cc_start: 0.8619 (mt) cc_final: 0.8277 (tt) REVERT: A 1058 LEU cc_start: 0.9476 (tp) cc_final: 0.9097 (tt) REVERT: A 1090 HIS cc_start: 0.8518 (m-70) cc_final: 0.7999 (m-70) REVERT: A 1124 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7182 (p90) REVERT: A 1130 GLU cc_start: 0.3289 (tt0) cc_final: 0.2828 (tt0) REVERT: A 1132 MET cc_start: 0.9372 (mtp) cc_final: 0.8471 (mmm) REVERT: A 1178 ARG cc_start: 0.8807 (mtm110) cc_final: 0.8480 (mtm110) REVERT: A 481 GLN cc_start: 0.9043 (tt0) cc_final: 0.8829 (tt0) REVERT: A 484 TRP cc_start: 0.9200 (m-10) cc_final: 0.8910 (m-10) REVERT: A 487 SER cc_start: 0.9496 (t) cc_final: 0.9114 (p) REVERT: A 541 TRP cc_start: 0.9068 (m-10) cc_final: 0.8639 (m100) outliers start: 23 outliers final: 21 residues processed: 142 average time/residue: 0.1371 time to fit residues: 25.3764 Evaluate side-chains 150 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 313 SER 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 423 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 529 MET 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: 0.0770 chunk 6 optimal weight: 0.0060 chunk 12 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.120422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.101651 restraints weight = 10044.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.104984 restraints weight = 4955.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.107270 restraints weight = 3021.585| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4501 Z= 0.179 Angle : 0.679 12.509 6096 Z= 0.327 Chirality : 0.043 0.238 677 Planarity : 0.003 0.030 759 Dihedral : 4.722 39.149 663 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % 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: 1.88 (0.36), residues: 547 helix: 2.57 (0.28), residues: 315 sheet: 1.57 (1.41), residues: 18 loop : -0.88 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 549 HIS 0.000 0.000 HIS A1090 PHE 0.019 0.001 PHE A 373 TYR 0.010 0.001 TYR A 237 ARG 0.015 0.001 ARG A1178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1295.48 seconds wall clock time: 23 minutes 38.67 seconds (1418.67 seconds total)