Starting phenix.real_space_refine on Fri Jul 19 05:16:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsq_18639/07_2024/8qsq_18639.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsq_18639/07_2024/8qsq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsq_18639/07_2024/8qsq_18639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsq_18639/07_2024/8qsq_18639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsq_18639/07_2024/8qsq_18639.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsq_18639/07_2024/8qsq_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 Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.25, per 1000 atoms: 0.65 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 - 3.50 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 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: 2.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.68 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: 1.96 Time building geometry restraints manager: 2.83 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: 100.67 - 107.34: 286 107.34 - 114.01: 3644 114.01 - 120.68: 2860 120.68 - 127.35: 2216 127.35 - 134.02: 103 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 2.440 nonbonded pdb=" NZ LYS B 288 " pdb=" OD2 ASP B 431 " model vdw 2.276 2.520 nonbonded pdb=" O ASP B 499 " pdb=" OG SER B 502 " model vdw 2.293 2.440 nonbonded pdb=" OG1 THR B 276 " pdb=" OG1 THR B 445 " model vdw 2.318 2.440 nonbonded pdb=" NZ LYS B 31 " pdb=" OE2 GLU B 35 " model vdw 2.330 2.520 ... (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 ========== 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: 1.530 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.210 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.240 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.846 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: 0.2250 time to fit residues: 26.2743 Evaluate side-chains 42 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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: 9.9990 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6701 Z= 0.330 Angle : 0.739 7.386 9109 Z= 0.396 Chirality : 0.045 0.184 965 Planarity : 0.006 0.057 1171 Dihedral : 6.441 54.852 991 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.30 % Allowed : 10.22 % Favored : 87.48 % 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: -0.21 (0.28), residues: 787 helix: 0.17 (0.24), residues: 398 sheet: 0.07 (0.73), residues: 48 loop : -0.37 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 328 HIS 0.008 0.002 HIS A 336 PHE 0.021 0.002 PHE B 315 TYR 0.027 0.002 TYR B 385 ARG 0.009 0.001 ARG A 494 *********************** 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 52 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 36 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 GLN cc_start: 0.9582 (tt0) cc_final: 0.9340 (tp-100) REVERT: B 123 MET cc_start: 0.4955 (mtp) cc_final: 0.4734 (ptm) REVERT: B 323 MET cc_start: 0.8001 (mmp) cc_final: 0.7565 (mmt) REVERT: B 455 MET cc_start: 0.5639 (tmt) cc_final: 0.4446 (ttp) REVERT: B 572 ASN cc_start: 0.8399 (m-40) cc_final: 0.7979 (t0) outliers start: 16 outliers final: 9 residues processed: 51 average time/residue: 0.1896 time to fit residues: 14.2535 Evaluate side-chains 40 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 322 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 39 optimal weight: 0.0170 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN B 508 ASN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6701 Z= 0.214 Angle : 0.573 7.543 9109 Z= 0.303 Chirality : 0.041 0.215 965 Planarity : 0.004 0.037 1171 Dihedral : 5.204 34.354 986 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.88 % Allowed : 9.93 % Favored : 87.19 % 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: 0.31 (0.29), residues: 787 helix: 0.65 (0.26), residues: 396 sheet: 0.34 (0.76), residues: 48 loop : -0.22 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 478 HIS 0.008 0.002 HIS A 501 PHE 0.015 0.002 PHE B 315 TYR 0.017 0.001 TYR B 516 ARG 0.006 0.001 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 50 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 30 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.9051 (mpp) cc_final: 0.8485 (ppp) REVERT: B 98 GLN cc_start: 0.9602 (tt0) cc_final: 0.9354 (tp-100) REVERT: B 152 MET cc_start: 0.1120 (mmp) cc_final: 0.0917 (mmp) REVERT: B 323 MET cc_start: 0.7765 (mmp) cc_final: 0.7468 (mmp) REVERT: B 455 MET cc_start: 0.5380 (tmt) cc_final: 0.4851 (ttp) REVERT: B 474 MET cc_start: 0.0529 (mmm) cc_final: -0.0035 (mmt) REVERT: B 572 ASN cc_start: 0.8242 (m-40) cc_final: 0.7841 (t0) outliers start: 20 outliers final: 14 residues processed: 47 average time/residue: 0.1463 time to fit residues: 10.4788 Evaluate side-chains 44 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 30 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 367 ASN Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 60 GLN 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 341 LYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 504 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 40.0000 chunk 75 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN B 305 GLN B 472 GLN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.5966 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= 0.196 Angle : 0.555 7.918 9109 Z= 0.292 Chirality : 0.041 0.212 965 Planarity : 0.004 0.030 1171 Dihedral : 4.918 34.727 986 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.88 % Allowed : 10.07 % Favored : 86.04 % 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: 0.42 (0.30), residues: 787 helix: 0.77 (0.26), residues: 397 sheet: 1.31 (0.77), residues: 43 loop : -0.33 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 478 HIS 0.007 0.002 HIS B 535 PHE 0.016 0.002 PHE B 315 TYR 0.017 0.001 TYR B 516 ARG 0.006 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 57 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 30 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8935 (mpp) cc_final: 0.8502 (ppp) REVERT: B 98 GLN cc_start: 0.9616 (tt0) cc_final: 0.9362 (tp-100) REVERT: B 271 TRP cc_start: 0.0349 (OUTLIER) cc_final: -0.1321 (m-90) REVERT: B 323 MET cc_start: 0.7342 (mmp) cc_final: 0.7034 (mmt) REVERT: B 455 MET cc_start: 0.6619 (tmt) cc_final: 0.6009 (ttp) outliers start: 27 outliers final: 19 residues processed: 56 average time/residue: 0.1518 time to fit residues: 12.6212 Evaluate side-chains 49 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 29 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 367 ASN 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 60 GLN 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 341 LYS 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 504 PHE Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 0.0370 chunk 67 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN B 472 GLN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.6447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6701 Z= 0.197 Angle : 0.555 6.895 9109 Z= 0.293 Chirality : 0.042 0.195 965 Planarity : 0.004 0.035 1171 Dihedral : 4.834 35.971 986 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.59 % Allowed : 11.94 % 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: 0.44 (0.30), residues: 787 helix: 0.75 (0.26), residues: 403 sheet: 1.46 (0.77), residues: 43 loop : -0.31 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 478 HIS 0.007 0.001 HIS B 535 PHE 0.015 0.002 PHE B 315 TYR 0.018 0.001 TYR B 516 ARG 0.005 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 46 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 28 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8973 (mpp) cc_final: 0.8588 (ppp) REVERT: B 98 GLN cc_start: 0.9625 (tt0) cc_final: 0.9375 (tp-100) REVERT: B 323 MET cc_start: 0.7621 (mmp) cc_final: 0.7374 (mmp) REVERT: B 339 VAL cc_start: 0.3229 (OUTLIER) cc_final: 0.2810 (m) REVERT: B 455 MET cc_start: 0.5962 (tmt) cc_final: 0.5663 (ttp) REVERT: B 474 MET cc_start: -0.0674 (mmp) cc_final: -0.1228 (mmp) outliers start: 18 outliers final: 15 residues processed: 44 average time/residue: 0.1551 time to fit residues: 10.3511 Evaluate side-chains 43 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 27 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 367 ASN 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 271 TRP Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.6920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6701 Z= 0.213 Angle : 0.569 7.575 9109 Z= 0.303 Chirality : 0.042 0.210 965 Planarity : 0.004 0.036 1171 Dihedral : 4.808 35.507 986 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.02 % Allowed : 11.51 % 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: 0.36 (0.30), residues: 787 helix: 0.64 (0.26), residues: 404 sheet: 1.48 (0.77), residues: 43 loop : -0.30 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 478 HIS 0.007 0.002 HIS B 535 PHE 0.011 0.002 PHE B 523 TYR 0.017 0.001 TYR B 516 ARG 0.005 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 48 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 27 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: B 82 MET cc_start: 0.8861 (mpp) cc_final: 0.8561 (ppp) REVERT: B 98 GLN cc_start: 0.9518 (tt0) cc_final: 0.9244 (tp-100) REVERT: B 271 TRP cc_start: -0.0579 (OUTLIER) cc_final: -0.2041 (m-90) REVERT: B 339 VAL cc_start: 0.3675 (OUTLIER) cc_final: 0.3231 (m) REVERT: B 474 MET cc_start: 0.0484 (mmp) cc_final: 0.0150 (mmp) REVERT: B 485 VAL cc_start: 0.6208 (OUTLIER) cc_final: 0.5603 (t) outliers start: 21 outliers final: 15 residues processed: 47 average time/residue: 0.1972 time to fit residues: 13.5561 Evaluate side-chains 44 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 26 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 367 ASN 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 322 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 45 optimal weight: 0.0570 chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 0.0000 chunk 44 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 overall best weight: 3.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.7079 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= 0.178 Angle : 0.560 9.181 9109 Z= 0.293 Chirality : 0.042 0.199 965 Planarity : 0.004 0.037 1171 Dihedral : 4.565 32.912 986 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.88 % Allowed : 12.52 % Favored : 84.60 % 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: 0.45 (0.30), residues: 787 helix: 0.71 (0.26), residues: 403 sheet: 1.62 (0.76), residues: 43 loop : -0.27 (0.35), residues: 341 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 0.009 0.001 PHE B 523 TYR 0.016 0.001 TYR B 516 ARG 0.004 0.001 ARG B 460 *********************** 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 47 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 27 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8821 (mpp) cc_final: 0.8596 (ppp) REVERT: B 98 GLN cc_start: 0.9502 (tt0) cc_final: 0.9220 (tp-100) REVERT: B 222 LEU cc_start: 0.8968 (tp) cc_final: 0.8570 (mt) REVERT: B 339 VAL cc_start: 0.3606 (OUTLIER) cc_final: 0.3145 (t) outliers start: 20 outliers final: 14 residues processed: 44 average time/residue: 0.1693 time to fit residues: 10.9863 Evaluate side-chains 41 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 26 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 367 ASN Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 402 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 341 LYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 ASN B 81 GLN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 GLN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.7564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6701 Z= 0.220 Angle : 0.613 9.151 9109 Z= 0.319 Chirality : 0.042 0.218 965 Planarity : 0.004 0.034 1171 Dihedral : 4.802 34.229 986 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 24.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.59 % Allowed : 12.81 % Favored : 84.60 % 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: 0.31 (0.30), residues: 787 helix: 0.62 (0.26), residues: 402 sheet: 1.47 (0.76), residues: 43 loop : -0.35 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 478 HIS 0.007 0.002 HIS B 535 PHE 0.026 0.002 PHE B 315 TYR 0.015 0.001 TYR B 516 ARG 0.005 0.001 ARG B 460 *********************** 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 43 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 25 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8824 (mpp) cc_final: 0.8606 (ppp) REVERT: B 98 GLN cc_start: 0.9525 (tt0) cc_final: 0.9231 (tp-100) REVERT: B 222 LEU cc_start: 0.9009 (tp) cc_final: 0.8617 (mt) REVERT: B 323 MET cc_start: 0.7611 (mmt) cc_final: 0.7297 (mmt) REVERT: B 339 VAL cc_start: 0.3662 (OUTLIER) cc_final: 0.3431 (t) REVERT: B 474 MET cc_start: -0.1226 (mmp) cc_final: -0.1503 (mmp) outliers start: 18 outliers final: 15 residues processed: 41 average time/residue: 0.1844 time to fit residues: 10.8305 Evaluate side-chains 40 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 24 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 367 ASN 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 271 TRP Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 534 LYS Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.7905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6701 Z= 0.207 Angle : 0.598 9.541 9109 Z= 0.311 Chirality : 0.042 0.228 965 Planarity : 0.004 0.035 1171 Dihedral : 4.789 34.600 986 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.88 % Allowed : 12.52 % Favored : 84.60 % 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: 0.27 (0.30), residues: 787 helix: 0.66 (0.26), residues: 403 sheet: 1.36 (0.76), residues: 45 loop : -0.48 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 165 HIS 0.007 0.001 HIS B 535 PHE 0.015 0.002 PHE B 315 TYR 0.015 0.001 TYR B 516 ARG 0.006 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 45 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 25 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 98 GLN cc_start: 0.9568 (tt0) cc_final: 0.9231 (tp-100) REVERT: B 222 LEU cc_start: 0.9006 (tp) cc_final: 0.8590 (mt) REVERT: B 271 TRP cc_start: 0.0056 (OUTLIER) cc_final: -0.1409 (m-90) REVERT: B 512 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7360 (t80) outliers start: 20 outliers final: 13 residues processed: 44 average time/residue: 0.1697 time to fit residues: 10.9409 Evaluate side-chains 40 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 25 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 367 ASN 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 271 TRP Chi-restraints excluded: chain B residue 322 ASN Chi-restraints excluded: chain B residue 341 LYS 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 Chi-restraints excluded: chain B residue 581 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.8146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6701 Z= 0.227 Angle : 0.627 8.962 9109 Z= 0.327 Chirality : 0.043 0.234 965 Planarity : 0.004 0.033 1171 Dihedral : 5.000 31.988 986 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 26.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.45 % Allowed : 13.38 % Favored : 84.17 % 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: 0.19 (0.30), residues: 787 helix: 0.59 (0.26), residues: 404 sheet: 1.33 (0.75), residues: 45 loop : -0.52 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 275 HIS 0.007 0.002 HIS B 535 PHE 0.016 0.002 PHE B 40 TYR 0.017 0.002 TYR B 516 ARG 0.006 0.001 ARG B 460 ********************** 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 43 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 26 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 98 GLN cc_start: 0.9574 (tt0) cc_final: 0.9263 (tp-100) REVERT: B 222 LEU cc_start: 0.9013 (tp) cc_final: 0.8588 (mt) REVERT: B 474 MET cc_start: -0.1355 (mmp) cc_final: -0.1675 (mmp) REVERT: B 512 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.7388 (t80) outliers start: 17 outliers final: 13 residues processed: 42 average time/residue: 0.1821 time to fit residues: 11.3317 Evaluate side-chains 39 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 25 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 367 ASN 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 341 LYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 3 optimal weight: 0.0970 chunk 44 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 overall best weight: 2.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN ** B 552 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 = 0.3926 r_free = 0.3926 target = 0.046707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.039061 restraints weight = 90052.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.039882 restraints weight = 53512.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.040429 restraints weight = 35866.698| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.8051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6701 Z= 0.168 Angle : 0.601 9.505 9109 Z= 0.310 Chirality : 0.042 0.206 965 Planarity : 0.004 0.036 1171 Dihedral : 4.612 19.564 984 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.30 % Allowed : 13.09 % Favored : 84.60 % 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: 0.46 (0.31), residues: 787 helix: 0.84 (0.26), residues: 396 sheet: 1.51 (0.77), residues: 45 loop : -0.41 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 165 HIS 0.006 0.001 HIS A 501 PHE 0.011 0.001 PHE B 315 TYR 0.015 0.001 TYR B 516 ARG 0.006 0.001 ARG B 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1445.99 seconds wall clock time: 26 minutes 50.95 seconds (1610.95 seconds total)