Starting phenix.real_space_refine on Thu Mar 13 18:42:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qro_18621/03_2025/8qro_18621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qro_18621/03_2025/8qro_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/cci-nas-00/data/ceres_data/8qro_18621/03_2025/8qro_18621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qro_18621/03_2025/8qro_18621.map" model { file = "/net/cci-nas-00/data/ceres_data/8qro_18621/03_2025/8qro_18621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qro_18621/03_2025/8qro_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.63, per 1000 atoms: 0.61 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: 2.53 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: 0.86 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: 2.62 Time building geometry restraints manager: 2.96 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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 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: 0.820 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.650 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.680 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.919 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: 1.1284 time to fit residues: 155.8860 Evaluate side-chains 105 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.153287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105411 restraints weight = 11370.292| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.98 r_work: 0.3276 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.999 Fit side-chains REVERT: A 85 ARG cc_start: 0.6498 (OUTLIER) cc_final: 0.5991 (mtp85) REVERT: A 179 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7185 (mm-30) REVERT: B 85 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.5605 (mtp85) REVERT: B 291 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7291 (mt-10) REVERT: C 85 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.5835 (mtp85) REVERT: C 274 MET cc_start: 0.8252 (mtm) cc_final: 0.7911 (mtt) REVERT: C 328 PHE cc_start: 0.8662 (m-80) cc_final: 0.8439 (m-80) REVERT: C 475 ASP cc_start: 0.6867 (m-30) cc_final: 0.6564 (m-30) outliers start: 21 outliers final: 3 residues processed: 130 average time/residue: 1.2208 time to fit residues: 170.2262 Evaluate side-chains 108 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 107 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.147903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095170 restraints weight = 10688.220| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.02 r_work: 0.2944 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1639 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 : 0.502 5.505 12843 Z= 0.252 Chirality : 0.038 0.138 1611 Planarity : 0.005 0.044 1587 Dihedral : 3.439 12.872 1302 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.14 % Allowed : 11.11 % Favored : 86.75 % 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: 2.39 (0.24), residues: 1224 helix: 2.06 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.86 (0.38), residues: 204 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 C 237 TYR 0.010 0.001 TYR B 208 ARG 0.001 0.000 ARG C 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 128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.104 Fit side-chains REVERT: A 85 ARG cc_start: 0.6339 (OUTLIER) cc_final: 0.5890 (mtp85) REVERT: A 179 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7125 (mm-30) REVERT: A 387 MET cc_start: 0.8550 (mmm) cc_final: 0.7994 (mtm) REVERT: B 85 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5407 (mtp85) REVERT: B 291 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7373 (mt-10) REVERT: C 85 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.5800 (mtp85) REVERT: C 179 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7250 (mm-30) REVERT: C 274 MET cc_start: 0.8348 (mtm) cc_final: 0.8043 (mtt) REVERT: C 330 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.6543 (mpt180) REVERT: C 367 ASN cc_start: 0.8501 (m-40) cc_final: 0.8201 (m110) REVERT: C 475 ASP cc_start: 0.6865 (m-30) cc_final: 0.6559 (m-30) outliers start: 21 outliers final: 6 residues processed: 123 average time/residue: 1.1560 time to fit residues: 152.8506 Evaluate side-chains 111 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 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 466 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 106 optimal weight: 0.0980 chunk 99 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.146570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.093557 restraints weight = 10598.867| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.01 r_work: 0.2919 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9429 Z= 0.227 Angle : 0.509 7.473 12843 Z= 0.254 Chirality : 0.038 0.140 1611 Planarity : 0.005 0.044 1587 Dihedral : 3.465 13.558 1302 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.04 % Allowed : 11.82 % Favored : 86.14 % 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: 2.08 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.48 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 275 HIS 0.001 0.000 HIS B 316 PHE 0.013 0.002 PHE C 237 TYR 0.009 0.001 TYR C 334 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 124 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.324 Fit side-chains REVERT: A 85 ARG cc_start: 0.6343 (OUTLIER) cc_final: 0.5922 (mtp85) REVERT: A 179 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7094 (mm-30) REVERT: B 85 ARG cc_start: 0.6270 (OUTLIER) cc_final: 0.5408 (mtp85) REVERT: B 291 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7396 (mt-10) REVERT: C 85 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.5824 (mtp85) REVERT: C 179 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7314 (mm-30) REVERT: C 274 MET cc_start: 0.8422 (mtm) cc_final: 0.8115 (mtt) REVERT: C 330 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6651 (mpt180) REVERT: C 367 ASN cc_start: 0.8501 (m-40) cc_final: 0.8236 (m110) REVERT: C 475 ASP cc_start: 0.6849 (m-30) cc_final: 0.6546 (m-30) outliers start: 20 outliers final: 8 residues processed: 122 average time/residue: 1.6270 time to fit residues: 214.9828 Evaluate side-chains 117 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.093652 restraints weight = 10622.182| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.02 r_work: 0.2916 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1909 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= 0.215 Angle : 0.496 6.881 12843 Z= 0.249 Chirality : 0.038 0.139 1611 Planarity : 0.005 0.047 1587 Dihedral : 3.454 12.519 1302 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.96 % Allowed : 11.52 % Favored : 85.52 % 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: 2.62 (0.24), residues: 1224 helix: 2.15 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -0.37 (0.43), residues: 207 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 0.012 0.002 PHE B 237 TYR 0.009 0.001 TYR C 334 ARG 0.001 0.000 ARG C 376 *********************** 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 146 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 1.044 Fit side-chains REVERT: A 85 ARG cc_start: 0.6247 (OUTLIER) cc_final: 0.5814 (mtp85) REVERT: A 179 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7046 (mm-30) REVERT: B 85 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.5346 (mtp85) REVERT: B 291 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7371 (mt-10) REVERT: C 85 ARG cc_start: 0.6373 (OUTLIER) cc_final: 0.5756 (mtp85) REVERT: C 179 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7187 (mm-30) REVERT: C 367 ASN cc_start: 0.8344 (m-40) cc_final: 0.8095 (m110) REVERT: C 475 ASP cc_start: 0.6730 (m-30) cc_final: 0.6430 (m-30) outliers start: 29 outliers final: 10 residues processed: 141 average time/residue: 1.0730 time to fit residues: 163.6363 Evaluate side-chains 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 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 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 393 PHE Chi-restraints excluded: chain C residue 466 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.144780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.091325 restraints weight = 10606.154| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.02 r_work: 0.2885 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9429 Z= 0.298 Angle : 0.535 6.878 12843 Z= 0.266 Chirality : 0.040 0.144 1611 Planarity : 0.005 0.048 1587 Dihedral : 3.536 13.015 1302 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 2.41 (0.24), residues: 1224 helix: 1.98 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -0.33 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 130 HIS 0.002 0.001 HIS B 316 PHE 0.015 0.002 PHE C 237 TYR 0.013 0.002 TYR C 334 ARG 0.002 0.000 ARG C 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 131 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.923 Fit side-chains REVERT: A 85 ARG cc_start: 0.6285 (OUTLIER) cc_final: 0.5922 (mtp85) REVERT: A 179 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7103 (mm-30) REVERT: A 482 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7715 (mm) REVERT: B 85 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5371 (mtp85) REVERT: B 291 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7387 (mt-10) REVERT: C 85 ARG cc_start: 0.6381 (OUTLIER) cc_final: 0.5755 (mtp85) REVERT: C 179 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7253 (mm-30) REVERT: C 367 ASN cc_start: 0.8332 (m-40) cc_final: 0.8082 (m110) REVERT: C 475 ASP cc_start: 0.6809 (m-30) cc_final: 0.6514 (m-30) outliers start: 24 outliers final: 10 residues processed: 127 average time/residue: 0.9787 time to fit residues: 135.1509 Evaluate side-chains 121 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG 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 308 CYS Chi-restraints excluded: chain B residue 384 THR 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 384 THR Chi-restraints excluded: chain C residue 393 PHE Chi-restraints excluded: chain C residue 466 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 111 optimal weight: 0.1980 chunk 63 optimal weight: 0.0010 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.148650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096295 restraints weight = 10655.381| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.00 r_work: 0.2960 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9429 Z= 0.154 Angle : 0.471 6.182 12843 Z= 0.235 Chirality : 0.037 0.137 1611 Planarity : 0.005 0.049 1587 Dihedral : 3.384 12.451 1302 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.24 % Allowed : 13.56 % Favored : 84.20 % 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: 2.89 (0.24), residues: 1224 helix: 2.29 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.20 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 130 HIS 0.001 0.000 HIS A 373 PHE 0.010 0.001 PHE C 258 TYR 0.007 0.001 TYR B 208 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 140 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.966 Fit side-chains REVERT: A 85 ARG cc_start: 0.6240 (OUTLIER) cc_final: 0.5877 (mtp85) REVERT: A 179 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6996 (mm-30) REVERT: B 85 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5336 (mtp85) REVERT: B 291 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7327 (mt-10) REVERT: C 85 ARG cc_start: 0.6375 (OUTLIER) cc_final: 0.5690 (mtp85) REVERT: C 179 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7211 (mm-30) REVERT: C 367 ASN cc_start: 0.8360 (m-40) cc_final: 0.8094 (m110) REVERT: C 475 ASP cc_start: 0.6758 (m-30) cc_final: 0.6501 (m-30) outliers start: 22 outliers final: 10 residues processed: 134 average time/residue: 1.0010 time to fit residues: 145.7457 Evaluate side-chains 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 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 384 THR Chi-restraints excluded: chain C residue 393 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 100 optimal weight: 0.7980 chunk 37 optimal weight: 0.0970 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.147993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.095469 restraints weight = 10737.080| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.01 r_work: 0.2949 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2144 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= 0.169 Angle : 0.485 6.484 12843 Z= 0.239 Chirality : 0.037 0.135 1611 Planarity : 0.005 0.050 1587 Dihedral : 3.381 12.692 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 : 1.63 % Allowed : 15.19 % Favored : 83.18 % 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: 2.94 (0.24), residues: 1224 helix: 2.32 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.19 (0.44), residues: 189 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 393 TYR 0.007 0.001 TYR A 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 135 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.911 Fit side-chains REVERT: A 179 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7047 (mm-30) REVERT: A 385 VAL cc_start: 0.8480 (t) cc_final: 0.8261 (m) REVERT: B 85 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5321 (mtp85) REVERT: B 291 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7376 (mt-10) REVERT: C 85 ARG cc_start: 0.6373 (OUTLIER) cc_final: 0.5697 (mtp85) REVERT: C 179 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7302 (mm-30) REVERT: C 367 ASN cc_start: 0.8362 (m-40) cc_final: 0.8108 (m110) REVERT: C 475 ASP cc_start: 0.6749 (m-30) cc_final: 0.6461 (m-30) outliers start: 16 outliers final: 8 residues processed: 130 average time/residue: 1.0232 time to fit residues: 144.3741 Evaluate side-chains 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 384 THR Chi-restraints excluded: chain C residue 393 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.146847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.094212 restraints weight = 10611.590| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.95 r_work: 0.2927 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2168 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= 0.218 Angle : 0.506 6.589 12843 Z= 0.249 Chirality : 0.038 0.137 1611 Planarity : 0.005 0.050 1587 Dihedral : 3.424 12.649 1302 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.73 % Allowed : 15.09 % Favored : 83.18 % 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: 2.82 (0.24), residues: 1224 helix: 2.29 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -0.30 (0.43), residues: 207 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 0.012 0.002 PHE C 237 TYR 0.008 0.001 TYR A 334 ARG 0.001 0.000 ARG C 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 131 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.995 Fit side-chains REVERT: A 179 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7293 (mm-30) REVERT: B 85 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.5481 (mtp85) REVERT: B 291 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7424 (mt-10) REVERT: C 85 ARG cc_start: 0.6502 (OUTLIER) cc_final: 0.5829 (mtp85) REVERT: C 179 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7460 (mm-30) REVERT: C 366 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7204 (mm-30) REVERT: C 367 ASN cc_start: 0.8454 (m-40) cc_final: 0.8212 (m110) REVERT: C 475 ASP cc_start: 0.6917 (m-30) cc_final: 0.6643 (m-30) outliers start: 17 outliers final: 9 residues processed: 125 average time/residue: 1.0606 time to fit residues: 144.9483 Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 384 THR Chi-restraints excluded: chain C residue 393 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 0.3980 chunk 37 optimal weight: 30.0000 chunk 115 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 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 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.148028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.095582 restraints weight = 10778.240| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.97 r_work: 0.2952 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2202 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 : 0.490 7.079 12843 Z= 0.242 Chirality : 0.037 0.134 1611 Planarity : 0.005 0.050 1587 Dihedral : 3.394 13.280 1302 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.22 % Allowed : 15.80 % 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: 2.91 (0.24), residues: 1224 helix: 2.31 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.23 (0.44), residues: 189 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 0.010 0.001 PHE B 237 TYR 0.007 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 128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.933 Fit side-chains REVERT: A 179 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7097 (mm-30) REVERT: B 85 ARG cc_start: 0.6208 (OUTLIER) cc_final: 0.5359 (mtp85) REVERT: B 291 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7398 (mt-10) REVERT: C 179 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7362 (mm-30) REVERT: C 366 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7209 (mm-30) REVERT: C 367 ASN cc_start: 0.8396 (m-40) cc_final: 0.8148 (m110) REVERT: C 475 ASP cc_start: 0.6802 (m-30) cc_final: 0.6543 (m-30) outliers start: 12 outliers final: 8 residues processed: 125 average time/residue: 1.1448 time to fit residues: 155.5080 Evaluate side-chains 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 384 THR Chi-restraints excluded: chain C residue 56 LEU 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 46 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 96 optimal weight: 0.0970 chunk 103 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 332 ASN A 367 ASN B 367 ASN B 484 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.149533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097452 restraints weight = 10638.639| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.95 r_work: 0.2980 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9429 Z= 0.156 Angle : 0.486 8.012 12843 Z= 0.238 Chirality : 0.037 0.134 1611 Planarity : 0.005 0.050 1587 Dihedral : 3.338 14.168 1302 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.33 % Allowed : 15.90 % Favored : 82.77 % 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: 3.04 (0.24), residues: 1224 helix: 2.40 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -0.24 (0.43), residues: 189 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 0.012 0.001 PHE C 393 TYR 0.006 0.001 TYR B 208 ARG 0.001 0.000 ARG A 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7628.99 seconds wall clock time: 133 minutes 45.38 seconds (8025.38 seconds total)