Starting phenix.real_space_refine on Tue Feb 11 20:23:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qsq_18639/02_2025/8qsq_18639.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qsq_18639/02_2025/8qsq_18639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qsq_18639/02_2025/8qsq_18639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qsq_18639/02_2025/8qsq_18639.map" model { file = "/net/cci-nas-00/data/ceres_data/8qsq_18639/02_2025/8qsq_18639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qsq_18639/02_2025/8qsq_18639.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= 0.024 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 37 5.16 5 C 4174 2.51 5 N 1073 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6512 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "B" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.98, per 1000 atoms: 0.61 Number of scatterers: 6512 At special positions: 0 Unit cell: (74.46, 99.28, 116.8, 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 37 16.00 O 1228 8.00 N 1073 7.00 C 4174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 801 " - " ASN B 322 " " NAG B 802 " - " ASN B 546 " " NAG B 803 " - " ASN B 432 " " NAG B 804 " - " ASN B 53 " " NAG B 805 " - " ASN B 90 " " NAG B 806 " - " ASN B 103 " Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 934.7 milliseconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 7 sheets defined 58.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 334 through 339 removed outlier: 4.330A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.896A pdb=" N ALA A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 removed outlier: 4.951A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 387 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 3.854A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'B' and resid 20 through 52 removed outlier: 3.751A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 81 removed outlier: 3.505A pdb=" N VAL B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 83 No H-bonds generated for 'chain 'B' and resid 82 through 83' Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.539A pdb=" N GLN B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.620A pdb=" N SER B 106 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 130 Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 157 through 172 removed outlier: 3.651A pdb=" N ARG B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 194 Proline residue: B 178 - end of helix removed outlier: 3.543A pdb=" N GLU B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 205 through 208 Processing helix chain 'B' and resid 218 through 252 removed outlier: 3.757A pdb=" N LEU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 303 through 318 removed outlier: 3.615A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 removed outlier: 3.568A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.526A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.803A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 Processing helix chain 'B' and resid 431 through 446 removed outlier: 3.651A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 465 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.702A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 547 through 559 removed outlier: 4.104A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 575 removed outlier: 3.841A pdb=" N VAL B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 359 removed outlier: 7.322A pdb=" N CYS A 358 " --> pdb=" O CYS A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA4, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 263 removed outlier: 5.865A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 352 removed outlier: 6.138A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) 315 hydrogen bonds defined for protein. 879 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: 1.87 Time building geometry restraints manager: 1.94 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: 2073 1.34 - 1.46: 1700 1.46 - 1.58: 2870 1.58 - 1.70: 0 1.70 - 1.81: 58 Bond restraints: 6701 Sorted by residual: bond pdb=" C1 NAG B 806 " pdb=" O5 NAG B 806 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C1 NAG B 801 " pdb=" O5 NAG B 801 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C1 NAG B 805 " pdb=" O5 NAG B 805 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" C1 NAG B 803 " pdb=" O5 NAG B 803 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C1 NAG B 802 " pdb=" O5 NAG B 802 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 ... (remaining 6696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 8845 1.12 - 2.24: 193 2.24 - 3.36: 56 3.36 - 4.48: 10 4.48 - 5.60: 5 Bond angle restraints: 9109 Sorted by residual: angle pdb=" CA LYS A 478 " pdb=" CB LYS A 478 " pdb=" CG LYS A 478 " ideal model delta sigma weight residual 114.10 118.03 -3.93 2.00e+00 2.50e-01 3.85e+00 angle pdb=" C CYS A 477 " pdb=" N LYS A 478 " pdb=" CA LYS A 478 " ideal model delta sigma weight residual 121.54 125.22 -3.68 1.91e+00 2.74e-01 3.72e+00 angle pdb=" N VAL B 573 " pdb=" CA VAL B 573 " pdb=" C VAL B 573 " ideal model delta sigma weight residual 111.67 109.98 1.69 9.50e-01 1.11e+00 3.17e+00 angle pdb=" CA TYR B 385 " pdb=" CB TYR B 385 " pdb=" CG TYR B 385 " ideal model delta sigma weight residual 113.90 117.08 -3.18 1.80e+00 3.09e-01 3.12e+00 angle pdb=" CA HIS A 515 " pdb=" C HIS A 515 " pdb=" N ALA A 516 " ideal model delta sigma weight residual 118.22 116.47 1.75 1.03e+00 9.43e-01 2.89e+00 ... (remaining 9104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 3811 17.29 - 34.57: 166 34.57 - 51.86: 37 51.86 - 69.14: 10 69.14 - 86.43: 4 Dihedral angle restraints: 4028 sinusoidal: 1704 harmonic: 2324 Sorted by residual: dihedral pdb=" N LYS B 476 " pdb=" CA LYS B 476 " pdb=" CB LYS B 476 " pdb=" CG LYS B 476 " ideal model delta sinusoidal sigma weight residual -60.00 -119.49 59.49 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N HIS B 401 " pdb=" CA HIS B 401 " pdb=" CB HIS B 401 " pdb=" CG HIS B 401 " ideal model delta sinusoidal sigma weight residual -180.00 -128.43 -51.57 3 1.50e+01 4.44e-03 9.03e+00 dihedral pdb=" N GLU B 56 " pdb=" CA GLU B 56 " pdb=" CB GLU B 56 " pdb=" CG GLU B 56 " ideal model delta sinusoidal sigma weight residual 180.00 -131.28 -48.72 3 1.50e+01 4.44e-03 8.68e+00 ... (remaining 4025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 879 0.071 - 0.142: 83 0.142 - 0.214: 1 0.214 - 0.285: 1 0.285 - 0.356: 1 Chirality restraints: 965 Sorted by residual: chirality pdb=" C1 NAG B 806 " pdb=" ND2 ASN B 103 " pdb=" C2 NAG B 806 " pdb=" O5 NAG B 806 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C1 NAG B 801 " pdb=" ND2 ASN B 322 " pdb=" C2 NAG B 801 " pdb=" O5 NAG B 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C1 NAG B 805 " pdb=" ND2 ASN B 90 " pdb=" C2 NAG B 805 " pdb=" O5 NAG B 805 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 962 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 103 " -0.037 2.00e-02 2.50e+03 4.04e-02 2.05e+01 pdb=" CG ASN B 103 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN B 103 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 103 " 0.065 2.00e-02 2.50e+03 pdb=" C1 NAG B 806 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 432 " -0.026 2.00e-02 2.50e+03 2.75e-02 9.44e+00 pdb=" CG ASN B 432 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN B 432 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 432 " 0.043 2.00e-02 2.50e+03 pdb=" C1 NAG B 803 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 322 " 0.016 2.00e-02 2.50e+03 1.77e-02 3.91e+00 pdb=" CG ASN B 322 " -0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN B 322 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 322 " -0.029 2.00e-02 2.50e+03 pdb=" C1 NAG B 801 " 0.021 2.00e-02 2.50e+03 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1662 2.79 - 3.32: 6121 3.32 - 3.85: 11106 3.85 - 4.37: 13721 4.37 - 4.90: 22537 Nonbonded interactions: 55147 Sorted by model distance: nonbonded pdb=" OG SER B 607 " pdb=" OD1 ASP B 609 " model vdw 2.268 3.040 nonbonded pdb=" NZ LYS B 288 " pdb=" OD2 ASP B 431 " model vdw 2.276 3.120 nonbonded pdb=" O ASP B 499 " pdb=" OG SER B 502 " model vdw 2.293 3.040 nonbonded pdb=" OG1 THR B 276 " pdb=" OG1 THR B 445 " model vdw 2.318 3.040 nonbonded pdb=" NZ LYS B 31 " pdb=" OE2 GLU B 35 " model vdw 2.330 3.120 ... (remaining 55142 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.050 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.740 Find NCS groups from input model: 0.050 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 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 : 0.002 0.035 6701 Z= 0.149 Angle : 0.462 5.602 9109 Z= 0.232 Chirality : 0.043 0.356 965 Planarity : 0.003 0.031 1171 Dihedral : 10.949 86.426 2515 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.15 % Allowed : 4.17 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.43 (0.28), residues: 787 helix: -1.37 (0.21), residues: 390 sheet: 0.15 (0.74), residues: 49 loop : -0.35 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 478 HIS 0.003 0.001 HIS B 241 PHE 0.006 0.001 PHE B 523 TYR 0.015 0.001 TYR B 385 ARG 0.002 0.000 ARG B 245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 ASN cc_start: 0.8572 (m-40) cc_final: 0.8165 (t0) REVERT: A 415 ILE cc_start: 0.8974 (mm) cc_final: 0.8569 (pt) REVERT: B 56 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8579 (pm20) REVERT: B 213 ASP cc_start: 0.9163 (m-30) cc_final: 0.8412 (p0) REVERT: B 322 ASN cc_start: 0.4723 (OUTLIER) cc_final: 0.4312 (p0) REVERT: B 323 MET cc_start: 0.6861 (mmp) cc_final: 0.6469 (mmp) REVERT: B 455 MET cc_start: 0.5113 (tmt) cc_final: 0.3262 (ttp) REVERT: B 474 MET cc_start: -0.0441 (mmm) cc_final: -0.2701 (mmp) REVERT: B 572 ASN cc_start: 0.7642 (m-40) cc_final: 0.7303 (t0) outliers start: 8 outliers final: 1 residues processed: 91 average time/residue: 0.2390 time to fit residues: 27.9129 Evaluate side-chains 42 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 401 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 45 optimal weight: 8.9990 chunk 70 optimal weight: 0.0270 overall best weight: 6.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 210 ASN B 340 GLN B 552 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.048322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.039682 restraints weight = 95996.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.040568 restraints weight = 57784.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.041196 restraints weight = 39808.078| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6701 Z= 0.310 Angle : 0.709 7.502 9109 Z= 0.379 Chirality : 0.045 0.198 965 Planarity : 0.006 0.057 1171 Dihedral : 5.935 58.211 991 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.87 % Allowed : 10.36 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.00 (0.29), residues: 787 helix: 0.38 (0.24), residues: 390 sheet: 0.11 (0.74), residues: 49 loop : -0.30 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 328 HIS 0.008 0.002 HIS A 501 PHE 0.018 0.002 PHE A 368 TYR 0.029 0.002 TYR B 385 ARG 0.006 0.001 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.4795 (mtp) cc_final: 0.4594 (ptm) REVERT: B 455 MET cc_start: 0.4488 (tmt) cc_final: 0.3255 (ttp) REVERT: B 572 ASN cc_start: 0.8589 (m-40) cc_final: 0.8087 (t0) outliers start: 13 outliers final: 8 residues processed: 50 average time/residue: 0.2046 time to fit residues: 14.4399 Evaluate side-chains 38 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 522 GLN Chi-restraints excluded: chain B residue 534 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 6.9990 chunk 49 optimal weight: 50.0000 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.049090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.041038 restraints weight = 86611.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.041927 restraints weight = 51432.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.042507 restraints weight = 34488.058| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6701 Z= 0.170 Angle : 0.545 8.006 9109 Z= 0.285 Chirality : 0.041 0.163 965 Planarity : 0.004 0.031 1171 Dihedral : 4.436 23.073 984 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.73 % Allowed : 10.22 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.48 (0.29), residues: 787 helix: 0.83 (0.26), residues: 393 sheet: 0.48 (0.75), residues: 51 loop : -0.18 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 328 HIS 0.007 0.001 HIS A 501 PHE 0.015 0.001 PHE B 315 TYR 0.016 0.001 TYR B 50 ARG 0.003 0.000 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8435 (mpp) cc_final: 0.7874 (ppp) REVERT: B 455 MET cc_start: 0.3856 (tmt) cc_final: 0.3372 (ttp) REVERT: B 494 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7980 (p0) REVERT: B 557 MET cc_start: 0.6009 (tmm) cc_final: 0.5759 (tmm) REVERT: B 572 ASN cc_start: 0.8632 (m-40) cc_final: 0.8051 (t0) outliers start: 12 outliers final: 6 residues processed: 41 average time/residue: 0.1562 time to fit residues: 9.8836 Evaluate side-chains 35 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 494 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 58 optimal weight: 50.0000 chunk 59 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN B 305 GLN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.047154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.039179 restraints weight = 89110.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.040015 restraints weight = 52998.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.040572 restraints weight = 35625.591| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6701 Z= 0.227 Angle : 0.592 6.543 9109 Z= 0.311 Chirality : 0.042 0.211 965 Planarity : 0.004 0.032 1171 Dihedral : 4.915 29.498 984 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.45 % Allowed : 9.93 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.28 (0.29), residues: 787 helix: 0.58 (0.25), residues: 402 sheet: 0.61 (0.80), residues: 48 loop : -0.22 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 478 HIS 0.007 0.002 HIS B 535 PHE 0.017 0.002 PHE B 315 TYR 0.017 0.002 TYR B 385 ARG 0.007 0.001 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: B 82 MET cc_start: 0.8343 (mpp) cc_final: 0.7882 (ppp) REVERT: B 323 MET cc_start: 0.7809 (mmt) cc_final: 0.7529 (mmt) REVERT: B 455 MET cc_start: 0.4063 (tmt) cc_final: 0.3596 (ttp) REVERT: B 474 MET cc_start: -0.2265 (mmp) cc_final: -0.2745 (mmp) REVERT: B 485 VAL cc_start: 0.6592 (OUTLIER) cc_final: 0.5940 (t) REVERT: B 494 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8105 (p0) REVERT: B 572 ASN cc_start: 0.8742 (m-40) cc_final: 0.8325 (t0) outliers start: 17 outliers final: 10 residues processed: 45 average time/residue: 0.1746 time to fit residues: 12.7949 Evaluate side-chains 40 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 504 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 40.0000 chunk 8 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.045274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.037473 restraints weight = 91666.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.038311 restraints weight = 53140.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.038880 restraints weight = 35271.054| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.7276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6701 Z= 0.357 Angle : 0.760 8.018 9109 Z= 0.402 Chirality : 0.047 0.296 965 Planarity : 0.006 0.041 1171 Dihedral : 5.950 30.861 984 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 26.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.59 % Allowed : 10.50 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.71 (0.28), residues: 787 helix: -0.22 (0.24), residues: 402 sheet: 0.63 (0.72), residues: 45 loop : -0.78 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 275 HIS 0.010 0.002 HIS B 535 PHE 0.023 0.003 PHE B 315 TYR 0.028 0.002 TYR B 50 ARG 0.008 0.001 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 27 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: B 82 MET cc_start: 0.8383 (mpp) cc_final: 0.7726 (ppp) REVERT: B 332 MET cc_start: 0.8029 (tpp) cc_final: 0.7600 (tpt) REVERT: B 339 VAL cc_start: 0.2970 (OUTLIER) cc_final: 0.2378 (m) REVERT: B 462 MET cc_start: 0.6246 (mmp) cc_final: 0.5844 (mmp) REVERT: B 485 VAL cc_start: 0.6683 (OUTLIER) cc_final: 0.5777 (t) REVERT: B 572 ASN cc_start: 0.8991 (m-40) cc_final: 0.8595 (t0) outliers start: 18 outliers final: 11 residues processed: 44 average time/residue: 0.1551 time to fit residues: 10.6432 Evaluate side-chains 37 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 534 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.045781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.038046 restraints weight = 90498.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.038879 restraints weight = 52370.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.039424 restraints weight = 34543.430| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.7413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6701 Z= 0.257 Angle : 0.647 9.275 9109 Z= 0.341 Chirality : 0.044 0.269 965 Planarity : 0.005 0.040 1171 Dihedral : 5.293 23.701 984 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.59 % Allowed : 11.22 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.41 (0.29), residues: 787 helix: 0.08 (0.25), residues: 397 sheet: 0.96 (0.74), residues: 45 loop : -0.75 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 478 HIS 0.008 0.002 HIS A 501 PHE 0.013 0.002 PHE A 374 TYR 0.023 0.002 TYR B 237 ARG 0.006 0.001 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 25 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: B 82 MET cc_start: 0.8372 (mpp) cc_final: 0.8032 (ppp) REVERT: B 271 TRP cc_start: 0.0368 (OUTLIER) cc_final: -0.1667 (m-90) REVERT: B 323 MET cc_start: 0.7995 (mmt) cc_final: 0.7460 (mmt) REVERT: B 339 VAL cc_start: 0.2905 (OUTLIER) cc_final: 0.2385 (m) REVERT: B 462 MET cc_start: 0.5842 (mmp) cc_final: 0.5476 (mmp) REVERT: B 512 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7374 (t80) REVERT: B 572 ASN cc_start: 0.9035 (m-40) cc_final: 0.8609 (t0) outliers start: 18 outliers final: 12 residues processed: 42 average time/residue: 0.1607 time to fit residues: 10.1740 Evaluate side-chains 38 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 23 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 271 TRP Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 534 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 HIS B 277 ASN B 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.046026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.038375 restraints weight = 90599.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.039226 restraints weight = 51873.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.039774 restraints weight = 34120.537| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.7588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6701 Z= 0.219 Angle : 0.619 9.378 9109 Z= 0.321 Chirality : 0.043 0.236 965 Planarity : 0.004 0.037 1171 Dihedral : 4.915 19.284 984 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.73 % Allowed : 11.51 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.24 (0.30), residues: 787 helix: 0.15 (0.25), residues: 407 sheet: 1.15 (0.75), residues: 45 loop : -0.59 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 478 HIS 0.007 0.002 HIS A 501 PHE 0.017 0.002 PHE B 315 TYR 0.024 0.002 TYR B 237 ARG 0.005 0.001 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 23 time to evaluate : 0.671 Fit side-chains REVERT: B 474 MET cc_start: -0.3146 (mmp) cc_final: -0.3466 (mmp) REVERT: B 480 MET cc_start: 0.6818 (ptt) cc_final: 0.5945 (ttt) REVERT: B 494 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8110 (p0) REVERT: B 512 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7378 (t80) REVERT: B 572 ASN cc_start: 0.9034 (m-40) cc_final: 0.8707 (t0) outliers start: 19 outliers final: 10 residues processed: 40 average time/residue: 0.1415 time to fit residues: 8.9279 Evaluate side-chains 35 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 23 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.0270 chunk 59 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 51 optimal weight: 50.0000 chunk 70 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 overall best weight: 3.8044 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.046064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.038461 restraints weight = 90040.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.039314 restraints weight = 51362.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.039855 restraints weight = 33695.302| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.7744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6701 Z= 0.213 Angle : 0.634 15.540 9109 Z= 0.324 Chirality : 0.043 0.231 965 Planarity : 0.004 0.033 1171 Dihedral : 4.896 19.388 984 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.16 % Allowed : 12.23 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.16 (0.30), residues: 787 helix: 0.26 (0.25), residues: 404 sheet: 1.21 (0.75), residues: 45 loop : -0.62 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 478 HIS 0.006 0.001 HIS A 501 PHE 0.019 0.002 PHE B 315 TYR 0.017 0.001 TYR B 237 ARG 0.004 0.001 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 24 time to evaluate : 0.800 Fit side-chains REVERT: B 222 LEU cc_start: 0.8631 (tp) cc_final: 0.8331 (mt) REVERT: B 271 TRP cc_start: 0.0617 (OUTLIER) cc_final: -0.1793 (m-90) REVERT: B 480 MET cc_start: 0.6863 (ptt) cc_final: 0.6028 (ttm) REVERT: B 494 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8110 (p0) REVERT: B 572 ASN cc_start: 0.9024 (m-40) cc_final: 0.8716 (t0) outliers start: 15 outliers final: 11 residues processed: 38 average time/residue: 0.1591 time to fit residues: 9.3512 Evaluate side-chains 37 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 271 TRP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.046006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.038258 restraints weight = 90572.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.039089 restraints weight = 53149.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.039643 restraints weight = 35350.308| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.7741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6701 Z= 0.178 Angle : 0.587 9.179 9109 Z= 0.306 Chirality : 0.043 0.207 965 Planarity : 0.004 0.032 1171 Dihedral : 4.605 18.718 984 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.87 % Allowed : 12.66 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.02 (0.30), residues: 787 helix: 0.34 (0.25), residues: 403 sheet: 1.45 (0.77), residues: 45 loop : -0.53 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 478 HIS 0.006 0.001 HIS A 501 PHE 0.010 0.001 PHE B 315 TYR 0.014 0.001 TYR B 454 ARG 0.005 0.001 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.605 Fit side-chains REVERT: B 222 LEU cc_start: 0.8594 (tp) cc_final: 0.8244 (mt) REVERT: B 271 TRP cc_start: 0.0569 (OUTLIER) cc_final: -0.1898 (m-90) REVERT: B 494 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8097 (p0) REVERT: B 572 ASN cc_start: 0.9083 (m-40) cc_final: 0.8734 (t0) outliers start: 13 outliers final: 11 residues processed: 36 average time/residue: 0.1636 time to fit residues: 9.0279 Evaluate side-chains 37 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 271 TRP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 42 optimal weight: 40.0000 chunk 63 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.045426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.037845 restraints weight = 92185.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.038659 restraints weight = 53693.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.039185 restraints weight = 35705.239| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.8368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6701 Z= 0.272 Angle : 0.686 10.758 9109 Z= 0.361 Chirality : 0.045 0.270 965 Planarity : 0.005 0.035 1171 Dihedral : 5.315 24.914 984 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 22.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.01 % Allowed : 12.52 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.41 (0.29), residues: 787 helix: -0.03 (0.25), residues: 407 sheet: 1.00 (0.74), residues: 45 loop : -0.60 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 275 HIS 0.008 0.002 HIS A 501 PHE 0.014 0.002 PHE A 368 TYR 0.024 0.002 TYR B 454 ARG 0.006 0.001 ARG A 494 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 25 time to evaluate : 0.720 Fit side-chains REVERT: B 222 LEU cc_start: 0.8612 (tp) cc_final: 0.8301 (mt) REVERT: B 494 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8514 (p0) REVERT: B 572 ASN cc_start: 0.9056 (m-40) cc_final: 0.8705 (t0) outliers start: 14 outliers final: 12 residues processed: 38 average time/residue: 0.1576 time to fit residues: 9.0680 Evaluate side-chains 37 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 24 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 402 ASN Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 40.0000 chunk 21 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.046292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.038699 restraints weight = 92036.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.039511 restraints weight = 54167.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.040048 restraints weight = 36182.331| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.8182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6701 Z= 0.172 Angle : 0.606 9.013 9109 Z= 0.316 Chirality : 0.043 0.231 965 Planarity : 0.004 0.032 1171 Dihedral : 4.896 29.381 984 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.73 % Allowed : 12.81 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.11 (0.30), residues: 787 helix: 0.26 (0.26), residues: 407 sheet: 1.36 (0.77), residues: 45 loop : -0.57 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 473 HIS 0.006 0.001 HIS B 535 PHE 0.013 0.001 PHE B 400 TYR 0.018 0.001 TYR B 454 ARG 0.003 0.001 ARG A 494 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2624.22 seconds wall clock time: 47 minutes 50.24 seconds (2870.24 seconds total)