Starting phenix.real_space_refine on Thu Mar 13 08:07:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rga_19131/03_2025/8rga_19131.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rga_19131/03_2025/8rga_19131.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/8rga_19131/03_2025/8rga_19131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rga_19131/03_2025/8rga_19131.map" model { file = "/net/cci-nas-00/data/ceres_data/8rga_19131/03_2025/8rga_19131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rga_19131/03_2025/8rga_19131.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= 0.002 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 36 5.16 5 C 5650 2.51 5 N 1468 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8802 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4401 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 17, 'TRANS': 554} Chain: "B" Number of atoms: 4401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4401 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 17, 'TRANS': 554} Time building chain proxies: 5.33, per 1000 atoms: 0.61 Number of scatterers: 8802 At special positions: 0 Unit cell: (71.315, 113.265, 132.562, 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 36 16.00 O 1648 8.00 N 1468 7.00 C 5650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 68.1% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 26 through 56 Proline residue: A 47 - end of helix Processing helix chain 'A' and resid 62 through 110 removed outlier: 3.707A pdb=" N GLN A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.874A pdb=" N ALA A 119 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 140 Processing helix chain 'A' and resid 140 through 163 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.511A pdb=" N VAL A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 210 Proline residue: A 183 - end of helix Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 221 through 275 Proline residue: A 252 - end of helix removed outlier: 3.824A pdb=" N SER A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 Processing helix chain 'A' and resid 295 through 322 removed outlier: 4.497A pdb=" N GLN A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 387 Processing helix chain 'A' and resid 409 through 416 Processing helix chain 'A' and resid 430 through 437 Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.710A pdb=" N ARG A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN A 496 " --> pdb=" O ALA A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 525 Processing helix chain 'A' and resid 537 through 542 removed outlier: 3.893A pdb=" N VAL A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 537 through 542' Processing helix chain 'A' and resid 560 through 567 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'B' and resid 12 through 21 Processing helix chain 'B' and resid 26 through 57 Proline residue: B 47 - end of helix Processing helix chain 'B' and resid 60 through 110 Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.774A pdb=" N ASP B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 140 removed outlier: 4.021A pdb=" N ASP B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 163 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.500A pdb=" N VAL B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 210 Proline residue: B 183 - end of helix Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 221 through 275 removed outlier: 3.615A pdb=" N GLU B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Proline residue: B 252 - end of helix Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 296 through 321 removed outlier: 4.401A pdb=" N GLN B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 409 through 416 removed outlier: 3.504A pdb=" N ARG B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 437 Processing helix chain 'B' and resid 447 through 455 Processing helix chain 'B' and resid 480 through 496 removed outlier: 3.642A pdb=" N ARG B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN B 496 " --> pdb=" O ALA B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 525 removed outlier: 4.116A pdb=" N SER B 516 " --> pdb=" O GLN B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 567 Processing helix chain 'B' and resid 570 through 581 Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 364 removed outlier: 7.466A pdb=" N ALA A 362 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ASP A 344 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE A 364 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLN A 342 " --> pdb=" O ILE A 364 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 420 removed outlier: 5.832A pdb=" N GLY A 418 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR A 370 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL A 369 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LEU A 547 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 371 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL A 549 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 360 through 364 removed outlier: 7.667A pdb=" N ALA B 362 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP B 344 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE B 364 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLN B 342 " --> pdb=" O ILE B 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 417 through 418 removed outlier: 3.719A pdb=" N GLY B 418 " --> pdb=" O ILE B 499 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET B 501 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR B 370 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL B 369 " --> pdb=" O GLN B 545 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N LEU B 547 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 371 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL B 549 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 546 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG B 557 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE B 548 " --> pdb=" O THR B 555 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1752 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: 2.90 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1452 1.31 - 1.44: 2161 1.44 - 1.57: 5252 1.57 - 1.69: 1 1.69 - 1.82: 70 Bond restraints: 8936 Sorted by residual: bond pdb=" C SER A 511 " pdb=" O SER A 511 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.21e-02 6.83e+03 1.77e+01 bond pdb=" CG PRO A 175 " pdb=" CD PRO A 175 " ideal model delta sigma weight residual 1.503 1.364 0.139 3.40e-02 8.65e+02 1.67e+01 bond pdb=" CB PRO A 175 " pdb=" CG PRO A 175 " ideal model delta sigma weight residual 1.492 1.652 -0.160 5.00e-02 4.00e+02 1.03e+01 bond pdb=" N ASP B 510 " pdb=" CA ASP B 510 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 8.97e+00 bond pdb=" N ASP A 510 " pdb=" CA ASP A 510 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.13e+00 ... (remaining 8931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 11947 3.64 - 7.27: 125 7.27 - 10.91: 19 10.91 - 14.55: 1 14.55 - 18.19: 2 Bond angle restraints: 12094 Sorted by residual: angle pdb=" CA PRO A 175 " pdb=" N PRO A 175 " pdb=" CD PRO A 175 " ideal model delta sigma weight residual 112.00 93.81 18.19 1.40e+00 5.10e-01 1.69e+02 angle pdb=" N PRO A 175 " pdb=" CD PRO A 175 " pdb=" CG PRO A 175 " ideal model delta sigma weight residual 103.20 92.20 11.00 1.50e+00 4.44e-01 5.37e+01 angle pdb=" CA PRO B 404 " pdb=" N PRO B 404 " pdb=" CD PRO B 404 " ideal model delta sigma weight residual 112.00 103.96 8.04 1.40e+00 5.10e-01 3.30e+01 angle pdb=" N ALA A 505 " pdb=" CA ALA A 505 " pdb=" C ALA A 505 " ideal model delta sigma weight residual 113.19 106.95 6.24 1.19e+00 7.06e-01 2.75e+01 angle pdb=" N PRO B 404 " pdb=" CA PRO B 404 " pdb=" C PRO B 404 " ideal model delta sigma weight residual 112.47 102.07 10.40 2.06e+00 2.36e-01 2.55e+01 ... (remaining 12089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 4633 17.25 - 34.50: 602 34.50 - 51.75: 138 51.75 - 69.00: 24 69.00 - 86.25: 11 Dihedral angle restraints: 5408 sinusoidal: 2132 harmonic: 3276 Sorted by residual: dihedral pdb=" C GLU B 403 " pdb=" N GLU B 403 " pdb=" CA GLU B 403 " pdb=" CB GLU B 403 " ideal model delta harmonic sigma weight residual -122.60 -139.39 16.79 0 2.50e+00 1.60e-01 4.51e+01 dihedral pdb=" N GLU B 403 " pdb=" C GLU B 403 " pdb=" CA GLU B 403 " pdb=" CB GLU B 403 " ideal model delta harmonic sigma weight residual 122.80 139.07 -16.27 0 2.50e+00 1.60e-01 4.23e+01 dihedral pdb=" CA GLY B 401 " pdb=" C GLY B 401 " pdb=" N ASP B 402 " pdb=" CA ASP B 402 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 5405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1429 0.122 - 0.244: 34 0.244 - 0.366: 0 0.366 - 0.487: 0 0.487 - 0.609: 1 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CA GLU B 403 " pdb=" N GLU B 403 " pdb=" C GLU B 403 " pdb=" CB GLU B 403 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.28e+00 chirality pdb=" CA ASP B 510 " pdb=" N ASP B 510 " pdb=" C ASP B 510 " pdb=" CB ASP B 510 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA LEU B 439 " pdb=" N LEU B 439 " pdb=" C LEU B 439 " pdb=" CB LEU B 439 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1461 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 174 " -0.108 5.00e-02 4.00e+02 1.49e-01 3.53e+01 pdb=" N PRO A 175 " 0.256 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 403 " -0.023 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C GLU B 403 " 0.076 2.00e-02 2.50e+03 pdb=" O GLU B 403 " -0.027 2.00e-02 2.50e+03 pdb=" N PRO B 404 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 403 " -0.060 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO B 404 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " -0.047 5.00e-02 4.00e+02 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 116 2.65 - 3.21: 8892 3.21 - 3.78: 14091 3.78 - 4.34: 17511 4.34 - 4.90: 28388 Nonbonded interactions: 68998 Sorted by model distance: nonbonded pdb=" OG1 THR B 40 " pdb=" OG1 THR B 147 " model vdw 2.091 3.040 nonbonded pdb=" N GLU B 222 " pdb=" OE1 GLU B 222 " model vdw 2.208 3.120 nonbonded pdb=" OH TYR A 226 " pdb=" OE1 GLU B 101 " model vdw 2.245 3.040 nonbonded pdb=" N GLU A 440 " pdb=" OE1 GLU A 440 " model vdw 2.257 3.120 nonbonded pdb=" NZ LYS A 358 " pdb=" O LYS A 551 " model vdw 2.297 3.120 ... (remaining 68993 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.100 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 0.005 0.160 8936 Z= 0.325 Angle : 0.926 18.185 12094 Z= 0.526 Chirality : 0.049 0.609 1464 Planarity : 0.007 0.149 1518 Dihedral : 16.160 86.253 3304 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.96 % Allowed : 6.23 % Favored : 92.81 % Rotamer: Outliers : 1.04 % Allowed : 25.73 % Favored : 73.24 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.25), residues: 1140 helix: 1.56 (0.19), residues: 750 sheet: 0.96 (0.65), residues: 70 loop : -3.85 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP B 413 HIS 0.003 0.001 HIS B 141 PHE 0.020 0.001 PHE A 348 TYR 0.024 0.002 TYR B 408 ARG 0.007 0.001 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 MET cc_start: 0.8502 (tpt) cc_final: 0.8168 (tpt) REVERT: B 439 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6999 (tt) outliers start: 10 outliers final: 4 residues processed: 137 average time/residue: 0.1785 time to fit residues: 35.4814 Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 439 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.205645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.138622 restraints weight = 12724.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.139334 restraints weight = 7351.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.141993 restraints weight = 4438.191| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8936 Z= 0.208 Angle : 0.705 13.024 12094 Z= 0.358 Chirality : 0.043 0.220 1464 Planarity : 0.005 0.079 1518 Dihedral : 6.084 59.892 1232 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.84 % Favored : 92.46 % Rotamer: Outliers : 3.53 % Allowed : 23.03 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.78 (0.26), residues: 1140 helix: 2.09 (0.19), residues: 760 sheet: 0.85 (0.64), residues: 70 loop : -3.88 (0.28), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 413 HIS 0.003 0.001 HIS B 141 PHE 0.014 0.001 PHE B 390 TYR 0.029 0.002 TYR B 408 ARG 0.004 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8151 (ttpp) cc_final: 0.7805 (ttpp) REVERT: A 368 LYS cc_start: 0.6485 (tptp) cc_final: 0.6205 (tptp) REVERT: A 580 MET cc_start: 0.4747 (mpp) cc_final: 0.3888 (mpp) REVERT: B 61 ASN cc_start: 0.4500 (OUTLIER) cc_final: 0.4104 (t0) REVERT: B 109 LYS cc_start: 0.8199 (tmmt) cc_final: 0.7969 (tmmt) REVERT: B 439 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7051 (tt) outliers start: 34 outliers final: 18 residues processed: 153 average time/residue: 0.1774 time to fit residues: 39.4309 Evaluate side-chains 144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.4599 r_free = 0.4599 target = 0.204339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.132844 restraints weight = 13020.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.137159 restraints weight = 6514.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.139975 restraints weight = 4270.708| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8936 Z= 0.226 Angle : 0.681 12.689 12094 Z= 0.343 Chirality : 0.042 0.224 1464 Planarity : 0.005 0.085 1518 Dihedral : 5.858 56.999 1230 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.93 % Favored : 92.54 % Rotamer: Outliers : 5.08 % Allowed : 22.20 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.26), residues: 1140 helix: 2.22 (0.19), residues: 760 sheet: 0.68 (0.63), residues: 70 loop : -3.76 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 413 HIS 0.003 0.001 HIS B 560 PHE 0.007 0.001 PHE B 384 TYR 0.024 0.002 TYR B 408 ARG 0.003 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 130 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7750 (ttpp) REVERT: A 169 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8931 (mm) REVERT: A 335 GLU cc_start: 0.7862 (pm20) cc_final: 0.7619 (pm20) REVERT: A 368 LYS cc_start: 0.6678 (tptp) cc_final: 0.6394 (tptp) REVERT: A 385 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8466 (mtmm) REVERT: A 483 GLN cc_start: 0.6562 (OUTLIER) cc_final: 0.6278 (mp10) REVERT: B 61 ASN cc_start: 0.4258 (OUTLIER) cc_final: 0.3883 (t0) REVERT: B 126 ARG cc_start: 0.7232 (mtp180) cc_final: 0.6859 (mtm110) REVERT: B 160 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: B 225 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8292 (mm-30) REVERT: B 259 MET cc_start: 0.8650 (tpp) cc_final: 0.8206 (tpp) REVERT: B 294 ILE cc_start: 0.7323 (OUTLIER) cc_final: 0.6825 (mm) REVERT: B 439 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7054 (tp) outliers start: 49 outliers final: 29 residues processed: 167 average time/residue: 0.1739 time to fit residues: 42.5862 Evaluate side-chains 160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 485 GLN Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 40 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 39 optimal weight: 0.4980 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.203436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.132027 restraints weight = 12847.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.136378 restraints weight = 6482.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.139171 restraints weight = 4272.370| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8936 Z= 0.218 Angle : 0.688 10.455 12094 Z= 0.345 Chirality : 0.042 0.261 1464 Planarity : 0.005 0.089 1518 Dihedral : 5.776 55.154 1230 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.75 % Favored : 92.72 % Rotamer: Outliers : 5.71 % Allowed : 24.38 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.03 (0.26), residues: 1140 helix: 2.28 (0.19), residues: 760 sheet: 0.70 (0.64), residues: 70 loop : -3.74 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 413 HIS 0.002 0.001 HIS B 560 PHE 0.012 0.001 PHE A 390 TYR 0.027 0.002 TYR A 114 ARG 0.002 0.000 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8155 (ttpp) cc_final: 0.7630 (tptt) REVERT: A 169 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8920 (mm) REVERT: A 271 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8113 (mmm) REVERT: A 385 LYS cc_start: 0.8950 (mtmm) cc_final: 0.8500 (mtmm) REVERT: A 411 GLU cc_start: 0.9324 (tm-30) cc_final: 0.9105 (tm-30) REVERT: A 483 GLN cc_start: 0.6672 (OUTLIER) cc_final: 0.6464 (mp10) REVERT: B 61 ASN cc_start: 0.4236 (OUTLIER) cc_final: 0.3848 (t0) REVERT: B 126 ARG cc_start: 0.7219 (mtp180) cc_final: 0.6856 (mtm110) REVERT: B 160 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: B 225 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8366 (mm-30) REVERT: B 259 MET cc_start: 0.8651 (tpp) cc_final: 0.8269 (tpp) REVERT: B 294 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.6776 (mm) REVERT: B 439 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6998 (tp) outliers start: 55 outliers final: 32 residues processed: 171 average time/residue: 0.1642 time to fit residues: 41.6966 Evaluate side-chains 160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 23 optimal weight: 0.9980 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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 = 0.4626 r_free = 0.4626 target = 0.206597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.140942 restraints weight = 12795.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.142752 restraints weight = 7096.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.145931 restraints weight = 4135.916| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8936 Z= 0.200 Angle : 0.675 10.491 12094 Z= 0.337 Chirality : 0.042 0.226 1464 Planarity : 0.005 0.088 1518 Dihedral : 5.657 53.631 1229 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.58 % Favored : 92.89 % Rotamer: Outliers : 6.12 % Allowed : 24.48 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.26), residues: 1140 helix: 2.39 (0.19), residues: 754 sheet: 0.75 (0.63), residues: 70 loop : -3.63 (0.30), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 413 HIS 0.003 0.001 HIS B 560 PHE 0.018 0.001 PHE A 348 TYR 0.022 0.001 TYR B 114 ARG 0.001 0.000 ARG B 571 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 126 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7612 (tptt) REVERT: A 169 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8870 (mm) REVERT: A 271 MET cc_start: 0.8510 (mmt) cc_final: 0.8084 (mmm) REVERT: A 390 PHE cc_start: 0.8501 (m-10) cc_final: 0.8297 (m-10) REVERT: A 428 SER cc_start: 0.8576 (t) cc_final: 0.7681 (p) REVERT: A 454 MET cc_start: 0.8160 (mmm) cc_final: 0.7935 (mmp) REVERT: B 61 ASN cc_start: 0.4470 (OUTLIER) cc_final: 0.3981 (t0) REVERT: B 109 LYS cc_start: 0.8290 (tmmt) cc_final: 0.8049 (tmmt) REVERT: B 126 ARG cc_start: 0.7168 (mtp180) cc_final: 0.6814 (mtm110) REVERT: B 160 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: B 249 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7230 (mp) REVERT: B 259 MET cc_start: 0.8590 (tpp) cc_final: 0.8248 (tpp) REVERT: B 294 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.6514 (mm) REVERT: B 439 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7044 (tp) outliers start: 59 outliers final: 39 residues processed: 171 average time/residue: 0.1583 time to fit residues: 40.3098 Evaluate side-chains 168 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 102 optimal weight: 0.1980 chunk 76 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 93 optimal weight: 40.0000 chunk 98 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.207226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.138656 restraints weight = 12626.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.143271 restraints weight = 6205.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.146169 restraints weight = 4014.595| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8936 Z= 0.193 Angle : 0.678 10.037 12094 Z= 0.335 Chirality : 0.041 0.224 1464 Planarity : 0.005 0.087 1518 Dihedral : 5.580 52.236 1229 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.84 % Favored : 92.63 % Rotamer: Outliers : 5.91 % Allowed : 26.14 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.26), residues: 1140 helix: 2.37 (0.19), residues: 754 sheet: 0.91 (0.64), residues: 70 loop : -3.66 (0.30), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 413 HIS 0.003 0.001 HIS B 560 PHE 0.018 0.001 PHE A 348 TYR 0.021 0.001 TYR B 114 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7644 (tptt) REVERT: A 130 ASP cc_start: 0.7555 (m-30) cc_final: 0.7186 (m-30) REVERT: A 156 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8377 (mt) REVERT: A 169 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8829 (mm) REVERT: A 271 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8016 (mmm) REVERT: A 428 SER cc_start: 0.8422 (t) cc_final: 0.7488 (p) REVERT: B 61 ASN cc_start: 0.4113 (OUTLIER) cc_final: 0.3744 (t0) REVERT: B 126 ARG cc_start: 0.7122 (mtp180) cc_final: 0.6613 (mtm110) REVERT: B 160 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: B 249 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7275 (mp) REVERT: B 259 MET cc_start: 0.8654 (tpp) cc_final: 0.8364 (tpp) REVERT: B 290 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7042 (mp) REVERT: B 294 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6508 (mm) REVERT: B 439 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6980 (tp) outliers start: 57 outliers final: 35 residues processed: 166 average time/residue: 0.1634 time to fit residues: 40.2595 Evaluate side-chains 167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 5 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 15 optimal weight: 0.0980 chunk 98 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 30.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.204971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.137615 restraints weight = 12817.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.140484 restraints weight = 7032.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.143053 restraints weight = 4406.431| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8936 Z= 0.255 Angle : 0.708 9.413 12094 Z= 0.350 Chirality : 0.042 0.227 1464 Planarity : 0.005 0.085 1518 Dihedral : 5.553 48.364 1229 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.32 % Favored : 93.16 % Rotamer: Outliers : 7.05 % Allowed : 24.48 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.26), residues: 1140 helix: 2.30 (0.19), residues: 758 sheet: 0.89 (0.64), residues: 70 loop : -3.66 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 164 HIS 0.003 0.001 HIS B 560 PHE 0.019 0.001 PHE A 348 TYR 0.021 0.001 TYR B 114 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 128 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7715 (tptt) REVERT: A 169 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 271 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8076 (mmm) REVERT: A 428 SER cc_start: 0.8650 (t) cc_final: 0.7839 (p) REVERT: B 61 ASN cc_start: 0.4348 (OUTLIER) cc_final: 0.3899 (t0) REVERT: B 126 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6636 (mtm110) REVERT: B 160 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: B 249 LEU cc_start: 0.8289 (tt) cc_final: 0.7302 (mp) REVERT: B 259 MET cc_start: 0.8640 (tpp) cc_final: 0.8210 (tpp) REVERT: B 290 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.6980 (mp) REVERT: B 294 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.6591 (mm) REVERT: B 436 CYS cc_start: 0.7789 (t) cc_final: 0.6734 (p) REVERT: B 439 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.6912 (tp) outliers start: 68 outliers final: 47 residues processed: 177 average time/residue: 0.1712 time to fit residues: 45.0114 Evaluate side-chains 182 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 126 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 0.0670 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.206649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.140588 restraints weight = 12901.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.142175 restraints weight = 7047.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.144889 restraints weight = 4224.895| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8936 Z= 0.207 Angle : 0.719 16.671 12094 Z= 0.350 Chirality : 0.042 0.226 1464 Planarity : 0.005 0.084 1518 Dihedral : 5.522 46.368 1229 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.40 % Favored : 92.98 % Rotamer: Outliers : 5.91 % Allowed : 26.35 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1140 helix: 2.32 (0.19), residues: 756 sheet: 1.03 (0.65), residues: 70 loop : -3.59 (0.30), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 413 HIS 0.003 0.001 HIS B 560 PHE 0.017 0.001 PHE A 348 TYR 0.021 0.001 TYR B 114 ARG 0.001 0.000 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 130 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7685 (tptt) REVERT: A 169 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8758 (mm) REVERT: A 271 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8063 (mmm) REVERT: A 428 SER cc_start: 0.8615 (t) cc_final: 0.7867 (p) REVERT: B 61 ASN cc_start: 0.4541 (OUTLIER) cc_final: 0.4027 (t0) REVERT: B 126 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6672 (mtm110) REVERT: B 160 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: B 249 LEU cc_start: 0.8290 (tt) cc_final: 0.7314 (mp) REVERT: B 259 MET cc_start: 0.8562 (tpp) cc_final: 0.8186 (tpp) REVERT: B 439 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.6927 (tp) outliers start: 57 outliers final: 40 residues processed: 172 average time/residue: 0.1636 time to fit residues: 42.6940 Evaluate side-chains 172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 125 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 485 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 = 0.4595 r_free = 0.4595 target = 0.202655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.132154 restraints weight = 12941.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.136678 restraints weight = 6412.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.139520 restraints weight = 4164.525| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8936 Z= 0.297 Angle : 0.787 15.259 12094 Z= 0.385 Chirality : 0.044 0.271 1464 Planarity : 0.005 0.083 1518 Dihedral : 5.575 46.863 1229 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.14 % Favored : 93.33 % Rotamer: Outliers : 6.12 % Allowed : 26.87 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1140 helix: 2.17 (0.19), residues: 750 sheet: 1.00 (0.66), residues: 70 loop : -3.51 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 413 HIS 0.003 0.001 HIS B 560 PHE 0.017 0.002 PHE A 348 TYR 0.021 0.002 TYR A 114 ARG 0.004 0.000 ARG A 484 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 126 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7773 (tptt) REVERT: A 122 GLU cc_start: 0.7885 (tp30) cc_final: 0.7360 (tp30) REVERT: A 169 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8748 (mm) REVERT: A 271 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8076 (mmm) REVERT: A 428 SER cc_start: 0.8594 (t) cc_final: 0.7956 (p) REVERT: B 61 ASN cc_start: 0.4211 (OUTLIER) cc_final: 0.3788 (t0) REVERT: B 126 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6669 (mtm110) REVERT: B 160 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: B 249 LEU cc_start: 0.8332 (tt) cc_final: 0.7377 (mp) REVERT: B 259 MET cc_start: 0.8715 (tpp) cc_final: 0.8301 (tpp) REVERT: B 294 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.6977 (mm) REVERT: B 436 CYS cc_start: 0.7795 (t) cc_final: 0.6610 (p) outliers start: 59 outliers final: 45 residues processed: 166 average time/residue: 0.2113 time to fit residues: 54.6630 Evaluate side-chains 174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 102 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 55 optimal weight: 40.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 485 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 = 0.4634 r_free = 0.4634 target = 0.206054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.143536 restraints weight = 12811.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.143490 restraints weight = 6857.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.144476 restraints weight = 4554.127| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8936 Z= 0.245 Angle : 0.760 15.344 12094 Z= 0.370 Chirality : 0.043 0.300 1464 Planarity : 0.005 0.082 1518 Dihedral : 5.437 46.764 1227 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.14 % Favored : 93.33 % Rotamer: Outliers : 5.71 % Allowed : 27.49 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.26), residues: 1140 helix: 2.22 (0.19), residues: 744 sheet: 1.06 (0.66), residues: 70 loop : -3.43 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 413 HIS 0.002 0.001 HIS B 560 PHE 0.017 0.001 PHE A 348 TYR 0.021 0.001 TYR B 114 ARG 0.003 0.000 ARG B 486 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 127 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7687 (tptt) REVERT: A 122 GLU cc_start: 0.7833 (tp30) cc_final: 0.7361 (tp30) REVERT: A 169 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8767 (mm) REVERT: A 271 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8077 (mmm) REVERT: A 324 GLU cc_start: 0.7980 (pm20) cc_final: 0.7608 (mp0) REVERT: A 428 SER cc_start: 0.8613 (t) cc_final: 0.8027 (p) REVERT: B 61 ASN cc_start: 0.4562 (OUTLIER) cc_final: 0.4004 (t0) REVERT: B 126 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6676 (mtm110) REVERT: B 160 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: B 249 LEU cc_start: 0.8330 (tt) cc_final: 0.7355 (mp) REVERT: B 259 MET cc_start: 0.8685 (tpp) cc_final: 0.8321 (tpp) REVERT: B 436 CYS cc_start: 0.7764 (t) cc_final: 0.6559 (p) outliers start: 55 outliers final: 48 residues processed: 167 average time/residue: 0.1839 time to fit residues: 46.0147 Evaluate side-chains 176 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 122 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 437 TYR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 561 HIS Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 160 PHE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 TYR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 559 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 485 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 = 0.4647 r_free = 0.4647 target = 0.207626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.146760 restraints weight = 12726.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.145935 restraints weight = 7664.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.146909 restraints weight = 4911.842| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8936 Z= 0.207 Angle : 0.761 14.413 12094 Z= 0.370 Chirality : 0.043 0.309 1464 Planarity : 0.005 0.082 1518 Dihedral : 5.404 46.739 1227 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.40 % Favored : 93.07 % Rotamer: Outliers : 4.88 % Allowed : 28.42 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.26), residues: 1140 helix: 2.21 (0.19), residues: 748 sheet: 1.25 (0.66), residues: 70 loop : -3.48 (0.30), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 413 HIS 0.003 0.001 HIS B 560 PHE 0.017 0.001 PHE A 348 TYR 0.022 0.001 TYR B 114 ARG 0.002 0.000 ARG B 486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2962.21 seconds wall clock time: 53 minutes 45.43 seconds (3225.43 seconds total)