Starting phenix.real_space_refine on Tue Feb 13 08:21:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/02_2024/8cxo_27062_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/02_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_27062/02_2024/8cxo_27062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/02_2024/8cxo_27062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/02_2024/8cxo_27062_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxo_27062/02_2024/8cxo_27062_updated.pdb" } 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-5238/modules/chem_data/mon_lib" Total number of atoms: 4392 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4392 Unusual residues: {'CLR': 1} Classifications: {'peptide': 551, 'undetermined': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 535, None: 1} Not linked: pdbres="LEU A 556 " pdbres="CLR A1301 " Chain breaks: 1 Time building chain proxies: 2.88, per 1000 atoms: 0.66 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: 2.26 Conformation dependent library (CDL) restraints added in 796.3 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... running ksdssp... Secondary structure from input PDB file: 21 helices and 4 sheets defined 59.5% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 228 through 263 removed outlier: 3.998A pdb=" N ASP A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ASN A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 270 through 289 removed outlier: 4.691A pdb=" N GLN A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N PHE A 289 " --> pdb=" O TRP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 Processing helix chain 'A' and resid 317 through 348 removed outlier: 4.079A pdb=" N PHE A 347 " --> pdb=" O TRP A 343 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LYS A 348 " --> pdb=" O HIS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 382 removed outlier: 4.205A pdb=" N THR A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER A 362 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 364 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 366 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP A 369 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 370 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 371 " --> pdb=" O THR A 368 " (cutoff:3.500A) Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 401 through 407 Processing helix chain 'A' and resid 409 through 437 Processing helix chain 'A' and resid 1016 through 1026 Processing helix chain 'A' and resid 1048 through 1060 removed outlier: 4.213A pdb=" N SER A1060 " --> pdb=" O GLU A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1066 removed outlier: 3.967A pdb=" N GLN A1065 " --> pdb=" O LYS A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1102 through 1111 Processing helix chain 'A' and resid 1126 through 1133 removed outlier: 4.011A pdb=" N GLU A1130 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A1131 " --> pdb=" O ALA A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1148 removed outlier: 4.029A pdb=" N ARG A1147 " --> pdb=" O GLY A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1177 Processing helix chain 'A' and resid 1182 through 1192 Processing helix chain 'A' and resid 1207 through 452 Processing helix chain 'A' and resid 455 through 496 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) removed outlier: 3.815A pdb=" N GLN A 495 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 540 removed outlier: 3.690A pdb=" N GLY A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TRP A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL A 540 " --> pdb=" O MET A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 Processing sheet with id= A, first strand: chain 'A' and resid 201 through 203 Processing sheet with id= B, 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= C, first strand: chain 'A' and resid 1033 through 1038 Processing sheet with id= D, first strand: chain 'A' and resid 1114 through 1117 removed outlier: 6.217A pdb=" N ILE A1137 " --> pdb=" O VAL A1115 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE A1117 " --> pdb=" O ILE A1137 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A1139 " --> pdb=" O ILE A1117 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A1156 " --> pdb=" O ALA A1140 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 230 hydrogen bonds defined for protein. 636 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: 1.23 Time building geometry restraints manager: 1.99 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: 1447 2.84 - 3.36: 4352 3.36 - 3.87: 7307 3.87 - 4.39: 8527 4.39 - 4.90: 13890 Nonbonded interactions: 35523 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 35518 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: 0.680 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: 3.720 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.580 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.150 ------------------------------------------------------------------------------- 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= 0.234 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 : 0.521 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: 0.1733 time to fit residues: 49.3879 Evaluate side-chains 152 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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: 0.9980 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 A 437 HIS A1065 GLN A1090 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4501 Z= 0.220 Angle : 0.609 9.838 6096 Z= 0.314 Chirality : 0.043 0.136 677 Planarity : 0.004 0.029 759 Dihedral : 5.161 26.851 663 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.09 % Allowed : 17.03 % Favored : 78.88 % 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 (0.35), residues: 547 helix: 2.33 (0.27), residues: 307 sheet: 1.59 (0.77), residues: 30 loop : -0.35 (0.45), residues: 210 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 0.015 0.002 PHE A 322 TYR 0.008 0.001 TYR A1109 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 186 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 TYR cc_start: 0.8289 (t80) cc_final: 0.8009 (t80) REVERT: A 309 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8559 (mp0) REVERT: A 348 LYS cc_start: 0.8971 (mttt) cc_final: 0.8697 (mtmt) REVERT: A 384 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8533 (mm-40) REVERT: A 1003 ASP cc_start: 0.6787 (t0) cc_final: 0.6016 (t0) REVERT: A 1023 LEU cc_start: 0.9632 (mt) cc_final: 0.9431 (mt) REVERT: A 1041 PHE cc_start: 0.7450 (m-10) cc_final: 0.7002 (m-10) REVERT: A 1090 HIS cc_start: 0.8352 (m90) cc_final: 0.8090 (m-70) REVERT: A 484 TRP cc_start: 0.9125 (m-10) cc_final: 0.8529 (m-90) REVERT: A 487 SER cc_start: 0.9531 (t) cc_final: 0.9207 (p) REVERT: A 530 PHE cc_start: 0.9395 (m-80) cc_final: 0.9133 (m-10) REVERT: A 549 TRP cc_start: 0.9176 (m100) cc_final: 0.8654 (m100) outliers start: 19 outliers final: 18 residues processed: 177 average time/residue: 0.1433 time to fit residues: 32.3625 Evaluate side-chains 161 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 454 LEU 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: 7.9990 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 0.0040 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.9798 ------------------------------------------------------------------------------- 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: 0.7971 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4501 Z= 0.313 Angle : 0.639 7.692 6096 Z= 0.329 Chirality : 0.044 0.153 677 Planarity : 0.004 0.054 759 Dihedral : 5.211 26.060 663 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.25 % Allowed : 18.32 % Favored : 75.43 % 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: 1.34 (0.35), residues: 547 helix: 1.96 (0.28), residues: 313 sheet: 0.97 (0.86), residues: 30 loop : -0.83 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1007 HIS 0.001 0.001 HIS A 474 PHE 0.020 0.002 PHE A 373 TYR 0.015 0.002 TYR A 491 ARG 0.008 0.001 ARG A1185 *********************** 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 170 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: A 309 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8538 (mp0) REVERT: A 348 LYS cc_start: 0.9016 (mttt) cc_final: 0.8789 (mtmt) REVERT: A 388 ASP cc_start: 0.8998 (t0) cc_final: 0.8641 (t0) REVERT: A 1041 PHE cc_start: 0.7550 (m-10) cc_final: 0.7237 (m-10) REVERT: A 1057 ILE cc_start: 0.9252 (mm) cc_final: 0.9033 (mm) REVERT: A 1058 LEU cc_start: 0.9559 (tp) cc_final: 0.9340 (tt) REVERT: A 1090 HIS cc_start: 0.8476 (m90) cc_final: 0.8176 (m-70) REVERT: A 1124 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7276 (p90) REVERT: A 1130 GLU cc_start: 0.3796 (tt0) cc_final: 0.3520 (tt0) REVERT: A 1193 MET cc_start: 0.4935 (mmt) cc_final: 0.3269 (mmt) REVERT: A 481 GLN cc_start: 0.9069 (tt0) cc_final: 0.8639 (tt0) REVERT: A 484 TRP cc_start: 0.9210 (m-10) cc_final: 0.8333 (m-90) REVERT: A 487 SER cc_start: 0.9555 (t) cc_final: 0.9215 (p) outliers start: 29 outliers final: 21 residues processed: 154 average time/residue: 0.1263 time to fit residues: 25.6804 Evaluate side-chains 140 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 ASP 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 338 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 354 TYR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 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 1154 THR Chi-restraints excluded: chain A residue 1179 SER 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: 0.9980 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 0.0000 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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: 0.7917 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4501 Z= 0.162 Angle : 0.552 7.890 6096 Z= 0.280 Chirality : 0.042 0.138 677 Planarity : 0.003 0.024 759 Dihedral : 4.922 37.151 663 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.60 % Allowed : 21.34 % Favored : 73.06 % 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: 1.38 (0.35), residues: 547 helix: 2.06 (0.28), residues: 310 sheet: 0.86 (0.90), residues: 30 loop : -0.87 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 541 HIS 0.001 0.000 HIS A 344 PHE 0.021 0.001 PHE A 373 TYR 0.008 0.001 TYR A 403 ARG 0.007 0.001 ARG A1185 *********************** 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 166 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 0.603 Fit side-chains REVERT: A 220 GLN cc_start: 0.8542 (pt0) cc_final: 0.8093 (tm-30) REVERT: A 228 GLU cc_start: 0.8503 (tp30) cc_final: 0.7204 (tp30) REVERT: A 232 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8626 (mm110) REVERT: A 309 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8599 (mm-30) REVERT: A 1002 ILE cc_start: 0.8484 (mm) cc_final: 0.7991 (mm) REVERT: A 1057 ILE cc_start: 0.9173 (mm) cc_final: 0.8673 (mm) REVERT: A 1058 LEU cc_start: 0.9525 (tp) cc_final: 0.9240 (tt) REVERT: A 1090 HIS cc_start: 0.8446 (m90) cc_final: 0.8132 (m-70) REVERT: A 1124 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7041 (p90) REVERT: A 1132 MET cc_start: 0.9217 (mtp) cc_final: 0.8845 (mmm) REVERT: A 1193 MET cc_start: 0.4644 (mmt) cc_final: 0.3088 (mmt) REVERT: A 487 SER cc_start: 0.9478 (t) cc_final: 0.9084 (p) outliers start: 26 outliers final: 15 residues processed: 153 average time/residue: 0.1295 time to fit residues: 26.2729 Evaluate side-chains 146 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 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 236 SER Chi-restraints excluded: chain A residue 313 SER 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 1108 LEU Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1188 CYS Chi-restraints excluded: chain A residue 526 LEU 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: 0.0010 chunk 30 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 A 481 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4501 Z= 0.164 Angle : 0.555 8.527 6096 Z= 0.282 Chirality : 0.041 0.136 677 Planarity : 0.003 0.024 759 Dihedral : 4.856 37.403 663 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.82 % Allowed : 21.55 % Favored : 72.63 % 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: 1.38 (0.35), residues: 547 helix: 2.07 (0.28), residues: 310 sheet: 0.81 (0.90), residues: 30 loop : -0.89 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 484 HIS 0.001 0.000 HIS A 344 PHE 0.024 0.001 PHE A 373 TYR 0.012 0.001 TYR A1011 ARG 0.006 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 165 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8543 (pt0) cc_final: 0.8041 (tm-30) REVERT: A 309 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8591 (mm-30) REVERT: A 1002 ILE cc_start: 0.8573 (mm) cc_final: 0.8163 (mm) REVERT: A 1058 LEU cc_start: 0.9552 (tp) cc_final: 0.9178 (tt) REVERT: A 1090 HIS cc_start: 0.8472 (m90) cc_final: 0.8141 (m-70) REVERT: A 1113 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.8072 (p0) REVERT: A 1124 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6997 (p90) REVERT: A 1193 MET cc_start: 0.4595 (mmt) cc_final: 0.3188 (mmt) REVERT: A 481 GLN cc_start: 0.9055 (tt0) cc_final: 0.8815 (tt0) REVERT: A 487 SER cc_start: 0.9453 (t) cc_final: 0.9063 (p) outliers start: 27 outliers final: 18 residues processed: 150 average time/residue: 0.1249 time to fit residues: 24.8236 Evaluate side-chains 153 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 354 TYR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1067 MET 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 1108 LEU Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1124 PHE Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 529 MET 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: 0.6980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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: 0.7939 moved from start: 0.5274 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= 0.226 Angle : 0.608 9.606 6096 Z= 0.303 Chirality : 0.042 0.145 677 Planarity : 0.004 0.035 759 Dihedral : 4.914 35.789 663 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 7.54 % Allowed : 21.12 % Favored : 71.34 % 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: 1.18 (0.35), residues: 547 helix: 2.05 (0.28), residues: 311 sheet: -0.59 (0.79), residues: 40 loop : -1.04 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 484 HIS 0.002 0.000 HIS A 474 PHE 0.022 0.001 PHE A 373 TYR 0.008 0.001 TYR A1011 ARG 0.007 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 153 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: A 228 GLU cc_start: 0.8479 (tp30) cc_final: 0.7129 (tp30) REVERT: A 232 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8689 (mm110) REVERT: A 309 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8544 (mp0) REVERT: A 1040 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6742 (tpt-90) REVERT: A 1058 LEU cc_start: 0.9541 (tp) cc_final: 0.9168 (tt) REVERT: A 1090 HIS cc_start: 0.8523 (m90) cc_final: 0.8212 (m-70) REVERT: A 1113 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7997 (p0) REVERT: A 1122 GLU cc_start: 0.6352 (tm-30) cc_final: 0.6040 (tm-30) REVERT: A 1124 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.6826 (p90) REVERT: A 1193 MET cc_start: 0.4333 (mmt) cc_final: 0.2994 (mmt) REVERT: A 487 SER cc_start: 0.9463 (t) cc_final: 0.9063 (p) outliers start: 35 outliers final: 28 residues processed: 134 average time/residue: 0.1335 time to fit residues: 23.3662 Evaluate side-chains 141 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 236 SER 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 298 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 354 TYR 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 1067 MET 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 1085 SER Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 ILE 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 1179 SER Chi-restraints excluded: chain A residue 1188 CYS Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 526 LEU 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: 0.7980 chunk 30 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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: 0.7954 moved from start: 0.5443 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= 0.242 Angle : 0.631 10.139 6096 Z= 0.309 Chirality : 0.043 0.171 677 Planarity : 0.004 0.039 759 Dihedral : 4.956 36.175 663 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 7.11 % Allowed : 23.28 % 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: 1.06 (0.36), residues: 547 helix: 2.02 (0.29), residues: 310 sheet: -0.94 (0.78), residues: 40 loop : -1.10 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 484 HIS 0.002 0.000 HIS A 474 PHE 0.022 0.001 PHE A 373 TYR 0.009 0.001 TYR A 476 ARG 0.005 0.000 ARG A1185 *********************** 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 146 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: A 309 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8566 (mm-30) REVERT: A 1040 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6791 (tpt-90) REVERT: A 1052 LEU cc_start: 0.9027 (mt) cc_final: 0.8501 (tt) REVERT: A 1053 LYS cc_start: 0.9280 (tppt) cc_final: 0.9065 (mmmt) REVERT: A 1058 LEU cc_start: 0.9535 (tp) cc_final: 0.9188 (tt) REVERT: A 1090 HIS cc_start: 0.8550 (m90) cc_final: 0.8198 (m-70) REVERT: A 1124 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7184 (p90) REVERT: A 1193 MET cc_start: 0.4200 (mmt) cc_final: 0.2857 (mmt) REVERT: A 481 GLN cc_start: 0.9065 (tt0) cc_final: 0.8658 (tt0) REVERT: A 487 SER cc_start: 0.9474 (t) cc_final: 0.9071 (p) outliers start: 33 outliers final: 26 residues processed: 128 average time/residue: 0.1335 time to fit residues: 22.3721 Evaluate side-chains 138 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 298 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 390 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1067 MET 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 1108 LEU Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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: 0.7972 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4501 Z= 0.293 Angle : 0.662 10.375 6096 Z= 0.329 Chirality : 0.043 0.183 677 Planarity : 0.004 0.041 759 Dihedral : 5.085 35.898 663 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 7.76 % Allowed : 23.06 % Favored : 69.18 % 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: 0.89 (0.35), residues: 547 helix: 1.90 (0.29), residues: 310 sheet: -1.16 (0.78), residues: 40 loop : -1.19 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.003 TRP A 484 HIS 0.002 0.001 HIS A 474 PHE 0.019 0.001 PHE A 373 TYR 0.010 0.001 TYR A 476 ARG 0.005 0.001 ARG A1185 *********************** 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 144 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 0.411 Fit side-chains REVERT: A 220 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: A 228 GLU cc_start: 0.8506 (tp30) cc_final: 0.7269 (tp30) REVERT: A 232 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8705 (mm110) REVERT: A 309 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8560 (mm-30) REVERT: A 1052 LEU cc_start: 0.8982 (mt) cc_final: 0.8448 (tt) REVERT: A 1053 LYS cc_start: 0.9267 (tppt) cc_final: 0.9035 (mmmt) REVERT: A 1058 LEU cc_start: 0.9540 (tp) cc_final: 0.9181 (tt) REVERT: A 1090 HIS cc_start: 0.8549 (m90) cc_final: 0.8177 (m-70) REVERT: A 1114 PHE cc_start: 0.8976 (m-80) cc_final: 0.8761 (m-10) REVERT: A 1124 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7172 (p90) REVERT: A 1130 GLU cc_start: 0.3431 (tt0) cc_final: 0.3070 (tt0) REVERT: A 1201 MET cc_start: 0.8053 (mpp) cc_final: 0.7816 (mpp) REVERT: A 481 GLN cc_start: 0.9055 (tt0) cc_final: 0.8817 (tt0) REVERT: A 487 SER cc_start: 0.9500 (t) cc_final: 0.9090 (p) outliers start: 36 outliers final: 29 residues processed: 126 average time/residue: 0.1384 time to fit residues: 22.7374 Evaluate side-chains 135 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 236 SER 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 298 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 390 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1067 MET 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 1108 LEU Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 ILE 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 1179 SER Chi-restraints excluded: chain A residue 1188 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.7957 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4501 Z= 0.254 Angle : 0.634 10.412 6096 Z= 0.318 Chirality : 0.043 0.197 677 Planarity : 0.004 0.047 759 Dihedral : 5.057 37.664 663 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 6.90 % Allowed : 23.06 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.36), residues: 547 helix: 1.84 (0.29), residues: 311 sheet: -1.19 (0.79), residues: 40 loop : -1.15 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.120 0.004 TRP A 484 HIS 0.003 0.001 HIS A 365 PHE 0.019 0.001 PHE A 373 TYR 0.020 0.001 TYR A 273 ARG 0.005 0.000 ARG A1185 *********************** 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 139 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 107 time to evaluate : 0.441 Fit side-chains REVERT: A 228 GLU cc_start: 0.8495 (tp30) cc_final: 0.7198 (tp30) REVERT: A 232 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8621 (mm110) REVERT: A 1052 LEU cc_start: 0.8966 (mt) cc_final: 0.8466 (tt) REVERT: A 1053 LYS cc_start: 0.9271 (tppt) cc_final: 0.9041 (mmmt) REVERT: A 1058 LEU cc_start: 0.9533 (tp) cc_final: 0.9174 (tt) REVERT: A 1090 HIS cc_start: 0.8523 (m90) cc_final: 0.8137 (m-70) REVERT: A 1124 PHE cc_start: 0.7763 (OUTLIER) cc_final: 0.7134 (p90) REVERT: A 1130 GLU cc_start: 0.3347 (tt0) cc_final: 0.2964 (tt0) REVERT: A 1201 MET cc_start: 0.8084 (mpp) cc_final: 0.7681 (mpp) REVERT: A 481 GLN cc_start: 0.9073 (tt0) cc_final: 0.8843 (tt0) REVERT: A 487 SER cc_start: 0.9497 (t) cc_final: 0.9102 (p) outliers start: 32 outliers final: 29 residues processed: 123 average time/residue: 0.1283 time to fit residues: 20.9919 Evaluate side-chains 133 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 103 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 247 LEU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 298 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 390 VAL 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 1022 SER Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 ILE 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 1179 SER Chi-restraints excluded: chain A residue 1188 CYS 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 24 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 43 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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: 0.7974 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4501 Z= 0.288 Angle : 0.671 12.318 6096 Z= 0.332 Chirality : 0.043 0.177 677 Planarity : 0.004 0.047 759 Dihedral : 5.179 36.830 663 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 6.68 % Allowed : 24.14 % Favored : 69.18 % 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: 0.94 (0.36), residues: 547 helix: 1.91 (0.29), residues: 306 sheet: -1.35 (0.77), residues: 40 loop : -0.98 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.003 TRP A 484 HIS 0.002 0.001 HIS A 474 PHE 0.018 0.002 PHE A 373 TYR 0.023 0.002 TYR A 273 ARG 0.005 0.001 ARG A1185 ********************** 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 136 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 228 GLU cc_start: 0.8490 (tp30) cc_final: 0.7193 (tp30) REVERT: A 232 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8619 (mm110) REVERT: A 1058 LEU cc_start: 0.9531 (tp) cc_final: 0.9169 (tt) REVERT: A 1090 HIS cc_start: 0.8570 (m90) cc_final: 0.8187 (m-70) REVERT: A 1122 GLU cc_start: 0.6527 (tm-30) cc_final: 0.6294 (tm-30) REVERT: A 1124 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7195 (p90) REVERT: A 1130 GLU cc_start: 0.3434 (tt0) cc_final: 0.3091 (tt0) REVERT: A 1201 MET cc_start: 0.8119 (mpp) cc_final: 0.7660 (mpp) REVERT: A 487 SER cc_start: 0.9516 (t) cc_final: 0.9065 (p) outliers start: 31 outliers final: 27 residues processed: 120 average time/residue: 0.1305 time to fit residues: 20.6632 Evaluate side-chains 130 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 298 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 390 VAL 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 1022 SER Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain A residue 1070 ILE Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 ILE 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: 6.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 0.0370 chunk 44 optimal weight: 0.0470 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.113302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092873 restraints weight = 10131.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.096176 restraints weight = 5043.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098350 restraints weight = 3134.948| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 4501 Z= 0.180 Angle : 0.648 12.616 6096 Z= 0.313 Chirality : 0.042 0.204 677 Planarity : 0.004 0.043 759 Dihedral : 4.965 41.638 663 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.74 % Allowed : 25.86 % 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: 1.13 (0.36), residues: 547 helix: 1.92 (0.29), residues: 306 sheet: -0.16 (0.91), residues: 30 loop : -0.88 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP A 484 HIS 0.002 0.000 HIS A 365 PHE 0.021 0.001 PHE A 373 TYR 0.012 0.001 TYR A 237 ARG 0.004 0.001 ARG A1185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1291.82 seconds wall clock time: 23 minutes 55.26 seconds (1435.26 seconds total)