Starting phenix.real_space_refine on Fri Oct 11 04:20:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qro_18621/10_2024/8qro_18621.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qro_18621/10_2024/8qro_18621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qro_18621/10_2024/8qro_18621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qro_18621/10_2024/8qro_18621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qro_18621/10_2024/8qro_18621.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qro_18621/10_2024/8qro_18621.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians S 45 5.16 5 Na 9 4.78 5 C 6093 2.51 5 N 1509 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 9273 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3078 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 16, 'TRANS': 397} Chain breaks: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 13 Unusual residues: {' NA': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Restraints were copied for chains: C, B Time building chain proxies: 5.81, per 1000 atoms: 0.63 Number of scatterers: 9273 At special positions: 0 Unit cell: (102.828, 101.992, 71.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 Na 9 11.00 O 1617 8.00 N 1509 7.00 C 6093 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: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 3 sheets defined 86.6% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 49 through 75 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 90 through 118 removed outlier: 3.521A pdb=" N GLU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 120 through 154 Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 230 through 249 Processing helix chain 'A' and resid 252 through 291 removed outlier: 3.889A pdb=" N TRP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 294 through 319 removed outlier: 3.669A pdb=" N LEU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LYS A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 329 Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.660A pdb=" N PHE A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 352 through 367 Proline residue: A 358 - end of helix Processing helix chain 'A' and resid 371 through 386 Proline residue: A 380 - end of helix removed outlier: 3.802A pdb=" N THR A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 405 Processing helix chain 'A' and resid 410 through 428 removed outlier: 3.921A pdb=" N VAL A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.853A pdb=" N ALA A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 removed outlier: 3.883A pdb=" N ILE A 456 " --> pdb=" O HIS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 487 removed outlier: 4.137A pdb=" N ARG A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 90 through 118 removed outlier: 3.520A pdb=" N GLU B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Proline residue: B 106 - end of helix Processing helix chain 'B' and resid 120 through 154 Processing helix chain 'B' and resid 179 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 230 through 249 Processing helix chain 'B' and resid 252 through 291 removed outlier: 3.889A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 294 through 319 removed outlier: 3.669A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.660A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 352 through 367 Proline residue: B 358 - end of helix Processing helix chain 'B' and resid 371 through 386 Proline residue: B 380 - end of helix removed outlier: 3.803A pdb=" N THR B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 405 Processing helix chain 'B' and resid 410 through 428 removed outlier: 3.921A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 removed outlier: 3.854A pdb=" N ALA B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 removed outlier: 3.884A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 487 removed outlier: 4.137A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 75 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 90 through 118 removed outlier: 3.520A pdb=" N GLU C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Proline residue: C 106 - end of helix Processing helix chain 'C' and resid 120 through 154 Processing helix chain 'C' and resid 179 through 192 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 230 through 249 Processing helix chain 'C' and resid 252 through 291 removed outlier: 3.889A pdb=" N TRP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Proline residue: C 278 - end of helix Processing helix chain 'C' and resid 294 through 319 removed outlier: 3.669A pdb=" N LEU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 329 Processing helix chain 'C' and resid 332 through 339 removed outlier: 3.660A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 352 through 367 Proline residue: C 358 - end of helix Processing helix chain 'C' and resid 371 through 386 Proline residue: C 380 - end of helix removed outlier: 3.803A pdb=" N THR C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 405 Processing helix chain 'C' and resid 410 through 428 removed outlier: 3.921A pdb=" N VAL C 426 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 removed outlier: 3.853A pdb=" N ALA C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 removed outlier: 3.884A pdb=" N ILE C 456 " --> pdb=" O HIS C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 487 removed outlier: 4.137A pdb=" N ARG C 465 " --> pdb=" O TRP C 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 209 Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 209 Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 209 775 hydrogen bonds defined for protein. 2316 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: 2.95 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2928 1.34 - 1.46: 1858 1.46 - 1.58: 4571 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 9429 Sorted by residual: bond pdb=" N LEU B 49 " pdb=" CA LEU B 49 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N LEU A 49 " pdb=" CA LEU A 49 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N LEU C 49 " pdb=" CA LEU C 49 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N GLN A 604 " pdb=" CA GLN A 604 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N GLN B 604 " pdb=" CA GLN B 604 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 ... (remaining 9424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.89: 12055 0.89 - 1.78: 604 1.78 - 2.67: 104 2.67 - 3.56: 47 3.56 - 4.44: 33 Bond angle restraints: 12843 Sorted by residual: angle pdb=" CA PHE A 299 " pdb=" C PHE A 299 " pdb=" O PHE A 299 " ideal model delta sigma weight residual 120.70 118.49 2.21 1.03e+00 9.43e-01 4.59e+00 angle pdb=" CA PHE B 299 " pdb=" C PHE B 299 " pdb=" O PHE B 299 " ideal model delta sigma weight residual 120.70 118.52 2.18 1.03e+00 9.43e-01 4.46e+00 angle pdb=" CA PHE C 299 " pdb=" C PHE C 299 " pdb=" O PHE C 299 " ideal model delta sigma weight residual 120.70 118.54 2.16 1.03e+00 9.43e-01 4.41e+00 angle pdb=" N VAL C 90 " pdb=" CA VAL C 90 " pdb=" C VAL C 90 " ideal model delta sigma weight residual 109.34 113.24 -3.90 2.08e+00 2.31e-01 3.52e+00 angle pdb=" N PHE B 299 " pdb=" CA PHE B 299 " pdb=" C PHE B 299 " ideal model delta sigma weight residual 111.14 113.16 -2.02 1.08e+00 8.57e-01 3.50e+00 ... (remaining 12838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.48: 4821 12.48 - 24.97: 525 24.97 - 37.45: 126 37.45 - 49.94: 39 49.94 - 62.42: 15 Dihedral angle restraints: 5526 sinusoidal: 2022 harmonic: 3504 Sorted by residual: dihedral pdb=" CA LEU C 455 " pdb=" CB LEU C 455 " pdb=" CG LEU C 455 " pdb=" CD1 LEU C 455 " ideal model delta sinusoidal sigma weight residual 60.00 114.43 -54.43 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CA LEU A 455 " pdb=" CB LEU A 455 " pdb=" CG LEU A 455 " pdb=" CD1 LEU A 455 " ideal model delta sinusoidal sigma weight residual 60.00 114.42 -54.42 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CA LEU B 455 " pdb=" CB LEU B 455 " pdb=" CG LEU B 455 " pdb=" CD1 LEU B 455 " ideal model delta sinusoidal sigma weight residual 60.00 114.40 -54.40 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 5523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1092 0.026 - 0.053: 232 0.053 - 0.079: 189 0.079 - 0.105: 69 0.105 - 0.131: 29 Chirality restraints: 1611 Sorted by residual: chirality pdb=" CB ILE B 289 " pdb=" CA ILE B 289 " pdb=" CG1 ILE B 289 " pdb=" CG2 ILE B 289 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA VAL B 220 " pdb=" N VAL B 220 " pdb=" C VAL B 220 " pdb=" CB VAL B 220 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CB ILE C 289 " pdb=" CA ILE C 289 " pdb=" CG1 ILE C 289 " pdb=" CG2 ILE C 289 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1608 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 357 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 358 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 358 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 358 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 357 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO C 358 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 358 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 358 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 357 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO B 358 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " -0.022 5.00e-02 4.00e+02 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1734 2.76 - 3.30: 9812 3.30 - 3.83: 16750 3.83 - 4.37: 19125 4.37 - 4.90: 33800 Nonbonded interactions: 81221 Sorted by model distance: nonbonded pdb=" CD1 PHE A 393 " pdb=" CG1 VAL A 463 " model vdw 2.231 3.760 nonbonded pdb=" CD1 PHE B 393 " pdb=" CG1 VAL B 463 " model vdw 2.231 3.760 nonbonded pdb=" CD1 PHE C 393 " pdb=" CG1 VAL C 463 " model vdw 2.231 3.760 nonbonded pdb=" OG1 THR B 138 " pdb="NA NA B 603 " model vdw 2.241 2.470 nonbonded pdb=" OG1 THR A 138 " pdb="NA NA A 603 " model vdw 2.241 2.470 ... (remaining 81216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.080 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:16.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9429 Z= 0.148 Angle : 0.519 4.445 12843 Z= 0.291 Chirality : 0.037 0.131 1611 Planarity : 0.004 0.040 1587 Dihedral : 11.990 62.424 3276 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.31 % Allowed : 7.34 % Favored : 92.35 % 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 (0.24), residues: 1224 helix: 1.19 (0.16), residues: 981 sheet: -1.43 (0.65), residues: 60 loop : -1.37 (0.38), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 275 HIS 0.001 0.001 HIS C 313 PHE 0.009 0.001 PHE A 299 TYR 0.007 0.001 TYR A 208 ARG 0.003 0.000 ARG C 330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.036 Fit side-chains REVERT: A 224 GLN cc_start: 0.8159 (pm20) cc_final: 0.7761 (pm20) REVERT: A 400 PHE cc_start: 0.7795 (t80) cc_final: 0.7498 (t80) REVERT: B 400 PHE cc_start: 0.7759 (t80) cc_final: 0.7497 (t80) REVERT: C 224 GLN cc_start: 0.8192 (pm20) cc_final: 0.7897 (pm20) REVERT: C 274 MET cc_start: 0.8267 (mtm) cc_final: 0.7965 (mtt) REVERT: C 387 MET cc_start: 0.8842 (mtt) cc_final: 0.8622 (mtt) REVERT: C 400 PHE cc_start: 0.7650 (t80) cc_final: 0.7422 (t80) REVERT: C 475 ASP cc_start: 0.7561 (m-30) cc_final: 0.7205 (m-30) outliers start: 3 outliers final: 0 residues processed: 128 average time/residue: 1.0493 time to fit residues: 145.7834 Evaluate side-chains 105 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN A 452 HIS B 367 ASN C 367 ASN C 452 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9429 Z= 0.247 Angle : 0.551 5.701 12843 Z= 0.277 Chirality : 0.040 0.143 1611 Planarity : 0.005 0.041 1587 Dihedral : 3.555 12.615 1302 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.14 % Allowed : 9.68 % Favored : 88.18 % 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: 1.98 (0.24), residues: 1224 helix: 1.78 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -1.06 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 275 HIS 0.002 0.001 HIS B 316 PHE 0.013 0.002 PHE C 237 TYR 0.011 0.001 TYR B 208 ARG 0.002 0.000 ARG C 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.154 Fit side-chains REVERT: A 85 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6265 (mtp85) REVERT: A 179 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7304 (mm-30) REVERT: B 85 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.5818 (mtp85) REVERT: B 455 LEU cc_start: 0.8063 (mp) cc_final: 0.7859 (mt) REVERT: C 85 ARG cc_start: 0.6888 (OUTLIER) cc_final: 0.6092 (mtp85) REVERT: C 274 MET cc_start: 0.8376 (mtm) cc_final: 0.8059 (mtt) REVERT: C 475 ASP cc_start: 0.7168 (m-30) cc_final: 0.6880 (m-30) outliers start: 21 outliers final: 3 residues processed: 130 average time/residue: 1.2103 time to fit residues: 168.5013 Evaluate side-chains 108 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 367 ASN B 263 ASN C 367 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9429 Z= 0.372 Angle : 0.583 5.887 12843 Z= 0.293 Chirality : 0.042 0.148 1611 Planarity : 0.005 0.043 1587 Dihedral : 3.686 13.806 1302 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.24 % Allowed : 11.21 % Favored : 86.54 % 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: 1.90 (0.24), residues: 1224 helix: 1.64 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -0.55 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 275 HIS 0.002 0.001 HIS A 316 PHE 0.016 0.002 PHE C 237 TYR 0.016 0.002 TYR B 334 ARG 0.003 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 1.047 Fit side-chains REVERT: A 85 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.6399 (mtp85) REVERT: A 179 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7245 (mm-30) REVERT: B 85 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.5842 (mtp85) REVERT: B 330 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6264 (mtm-85) REVERT: B 387 MET cc_start: 0.8822 (mmm) cc_final: 0.7368 (mtm) REVERT: B 455 LEU cc_start: 0.8221 (mp) cc_final: 0.7990 (mt) REVERT: C 85 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6210 (mtp85) REVERT: C 179 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7382 (mm-30) REVERT: C 330 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.6512 (mpt180) REVERT: C 475 ASP cc_start: 0.7260 (m-30) cc_final: 0.6934 (m-30) outliers start: 22 outliers final: 7 residues processed: 119 average time/residue: 1.2481 time to fit residues: 159.1621 Evaluate side-chains 110 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 330 ARG Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 393 PHE Chi-restraints excluded: chain C residue 466 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN B 367 ASN C 367 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9429 Z= 0.195 Angle : 0.499 7.492 12843 Z= 0.250 Chirality : 0.038 0.141 1611 Planarity : 0.005 0.047 1587 Dihedral : 3.521 13.804 1302 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.75 % Allowed : 11.93 % Favored : 85.32 % 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: 2.42 (0.24), residues: 1224 helix: 2.03 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -0.52 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 275 HIS 0.001 0.000 HIS A 316 PHE 0.011 0.001 PHE A 237 TYR 0.008 0.001 TYR B 208 ARG 0.001 0.000 ARG C 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 1.043 Fit side-chains REVERT: A 85 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6327 (mtp85) REVERT: A 179 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7224 (mm-30) REVERT: A 247 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8014 (mptt) REVERT: B 85 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.5720 (mtp85) REVERT: B 455 LEU cc_start: 0.8024 (mp) cc_final: 0.7821 (mt) REVERT: C 85 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6064 (mtp85) REVERT: C 330 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6475 (mpt180) REVERT: C 367 ASN cc_start: 0.8723 (m-40) cc_final: 0.8503 (m110) REVERT: C 475 ASP cc_start: 0.7101 (m-30) cc_final: 0.6811 (m-30) outliers start: 27 outliers final: 8 residues processed: 124 average time/residue: 1.1705 time to fit residues: 156.3406 Evaluate side-chains 115 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 466 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 367 ASN B 484 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9429 Z= 0.172 Angle : 0.481 6.767 12843 Z= 0.240 Chirality : 0.037 0.135 1611 Planarity : 0.005 0.048 1587 Dihedral : 3.399 12.050 1302 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.45 % Allowed : 13.15 % Favored : 84.40 % 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: 2.72 (0.24), residues: 1224 helix: 2.18 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.28 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 130 HIS 0.001 0.000 HIS B 316 PHE 0.011 0.001 PHE C 400 TYR 0.007 0.001 TYR B 208 ARG 0.001 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.109 Fit side-chains REVERT: A 85 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.6288 (mtp85) REVERT: A 179 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 247 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7970 (mptt) REVERT: B 85 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5685 (mtp85) REVERT: C 85 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6006 (mtp85) REVERT: C 179 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7330 (mm-30) REVERT: C 274 MET cc_start: 0.8390 (mtm) cc_final: 0.8051 (mtt) REVERT: C 367 ASN cc_start: 0.8612 (m-40) cc_final: 0.8410 (m110) REVERT: C 475 ASP cc_start: 0.7082 (m-30) cc_final: 0.6798 (m-30) outliers start: 24 outliers final: 6 residues processed: 130 average time/residue: 1.1261 time to fit residues: 158.2306 Evaluate side-chains 117 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 384 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 0.0770 chunk 98 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 367 ASN B 452 HIS B 484 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9429 Z= 0.173 Angle : 0.485 6.788 12843 Z= 0.240 Chirality : 0.037 0.136 1611 Planarity : 0.005 0.050 1587 Dihedral : 3.380 12.227 1302 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.34 % Allowed : 14.27 % Favored : 83.38 % 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: 2.83 (0.24), residues: 1224 helix: 2.25 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.25 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 130 HIS 0.001 0.000 HIS B 316 PHE 0.010 0.001 PHE A 237 TYR 0.007 0.001 TYR B 208 ARG 0.001 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.154 Fit side-chains REVERT: A 179 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7218 (mm-30) REVERT: A 247 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7967 (mptt) REVERT: B 85 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.5660 (mtp85) REVERT: C 85 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.5991 (mtp85) REVERT: C 179 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7395 (mm-30) REVERT: C 274 MET cc_start: 0.8393 (mtm) cc_final: 0.8049 (mtt) REVERT: C 388 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: C 475 ASP cc_start: 0.7065 (m-30) cc_final: 0.6815 (m-30) outliers start: 23 outliers final: 7 residues processed: 132 average time/residue: 1.0663 time to fit residues: 152.7413 Evaluate side-chains 122 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 384 THR Chi-restraints excluded: chain C residue 388 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 367 ASN C 367 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9429 Z= 0.203 Angle : 0.496 6.673 12843 Z= 0.246 Chirality : 0.038 0.138 1611 Planarity : 0.005 0.050 1587 Dihedral : 3.390 12.465 1302 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.83 % Allowed : 14.48 % Favored : 83.69 % 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: 2.80 (0.24), residues: 1224 helix: 2.23 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.24 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 130 HIS 0.001 0.000 HIS A 316 PHE 0.012 0.001 PHE B 237 TYR 0.008 0.001 TYR C 334 ARG 0.001 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.341 Fit side-chains REVERT: A 179 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7223 (mm-30) REVERT: B 85 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5678 (mtp85) REVERT: C 85 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.5995 (mtp85) REVERT: C 179 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7388 (mm-30) REVERT: C 475 ASP cc_start: 0.7054 (m-30) cc_final: 0.6778 (m-30) outliers start: 18 outliers final: 7 residues processed: 127 average time/residue: 1.0705 time to fit residues: 147.1701 Evaluate side-chains 121 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 384 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.2980 chunk 35 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 367 ASN B 367 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9429 Z= 0.212 Angle : 0.509 6.936 12843 Z= 0.251 Chirality : 0.038 0.137 1611 Planarity : 0.005 0.050 1587 Dihedral : 3.409 12.566 1302 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.73 % Allowed : 14.78 % Favored : 83.49 % 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: 2.75 (0.24), residues: 1224 helix: 2.19 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.24 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 130 HIS 0.001 0.000 HIS B 316 PHE 0.012 0.001 PHE B 237 TYR 0.008 0.001 TYR C 334 ARG 0.001 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 1.097 Fit side-chains REVERT: A 179 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7247 (mm-30) REVERT: B 85 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.5685 (mtp85) REVERT: C 85 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.5997 (mtp85) REVERT: C 179 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7374 (mm-30) REVERT: C 475 ASP cc_start: 0.7074 (m-30) cc_final: 0.6800 (m-30) outliers start: 17 outliers final: 7 residues processed: 119 average time/residue: 1.0815 time to fit residues: 139.2863 Evaluate side-chains 118 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 384 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 367 ASN B 367 ASN C 367 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9429 Z= 0.269 Angle : 0.536 8.291 12843 Z= 0.265 Chirality : 0.039 0.139 1611 Planarity : 0.005 0.050 1587 Dihedral : 3.499 12.544 1302 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.73 % Allowed : 14.88 % Favored : 83.38 % 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: 2.50 (0.24), residues: 1224 helix: 2.05 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -0.36 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 130 HIS 0.002 0.000 HIS B 316 PHE 0.014 0.002 PHE C 237 TYR 0.012 0.002 TYR C 334 ARG 0.002 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 1.081 Fit side-chains REVERT: A 179 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7295 (mm-30) REVERT: A 482 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8138 (mm) REVERT: B 85 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.5637 (mtp85) REVERT: C 85 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6081 (mtp85) REVERT: C 179 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7366 (mm-30) REVERT: C 475 ASP cc_start: 0.7162 (m-30) cc_final: 0.6866 (m-30) outliers start: 17 outliers final: 10 residues processed: 121 average time/residue: 1.0937 time to fit residues: 143.5541 Evaluate side-chains 120 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 384 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 367 ASN B 367 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9429 Z= 0.195 Angle : 0.508 9.629 12843 Z= 0.250 Chirality : 0.038 0.138 1611 Planarity : 0.005 0.050 1587 Dihedral : 3.450 12.900 1302 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.33 % Allowed : 15.60 % Favored : 83.08 % 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: 2.68 (0.24), residues: 1224 helix: 2.22 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -0.47 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 130 HIS 0.001 0.000 HIS B 316 PHE 0.011 0.001 PHE A 237 TYR 0.008 0.001 TYR A 334 ARG 0.001 0.000 ARG A 376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.083 Fit side-chains REVERT: A 179 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7286 (mm-30) REVERT: B 85 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.5638 (mtp85) REVERT: C 85 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6009 (mtp85) REVERT: C 179 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7321 (mm-30) REVERT: C 475 ASP cc_start: 0.7073 (m-30) cc_final: 0.6791 (m-30) outliers start: 13 outliers final: 9 residues processed: 119 average time/residue: 1.0881 time to fit residues: 140.4467 Evaluate side-chains 115 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 384 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN B 367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.148213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096053 restraints weight = 10558.812| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.94 r_work: 0.2959 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9429 Z= 0.169 Angle : 0.503 8.638 12843 Z= 0.246 Chirality : 0.037 0.133 1611 Planarity : 0.005 0.050 1587 Dihedral : 3.420 14.004 1302 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.33 % Allowed : 15.70 % Favored : 82.98 % 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: 2.81 (0.24), residues: 1224 helix: 2.33 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -0.52 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 130 HIS 0.001 0.000 HIS B 316 PHE 0.010 0.001 PHE B 400 TYR 0.007 0.001 TYR B 334 ARG 0.001 0.000 ARG A 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3261.34 seconds wall clock time: 59 minutes 17.40 seconds (3557.40 seconds total)