Starting phenix.real_space_refine on Thu Jan 16 05:48:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qro_18621/01_2025/8qro_18621.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qro_18621/01_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_18621/01_2025/8qro_18621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qro_18621/01_2025/8qro_18621.map" model { file = "/net/cci-nas-00/data/ceres_data/8qro_18621/01_2025/8qro_18621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qro_18621/01_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-5571/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: 5.57, per 1000 atoms: 0.60 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: 2.64 Conformation dependent library (CDL) restraints added in 1.2 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: 0.87 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: 2.72 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: 0.06 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: 0.870 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.220 Find NCS groups from input model: 0.170 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:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.620 ------------------------------------------------------------------------------- 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 : 1.127 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: 1.1443 time to fit residues: 157.9395 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 : 1.006 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105387 restraints weight = 11370.290| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.98 r_work: 0.3275 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 : 0.944 Fit side-chains REVERT: A 85 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.5997 (mtp85) REVERT: A 179 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7187 (mm-30) REVERT: B 85 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.5611 (mtp85) REVERT: B 291 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7294 (mt-10) REVERT: C 85 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.5839 (mtp85) REVERT: C 274 MET cc_start: 0.8254 (mtm) cc_final: 0.7913 (mtt) REVERT: C 328 PHE cc_start: 0.8664 (m-80) cc_final: 0.8441 (m-80) REVERT: C 475 ASP cc_start: 0.6873 (m-30) cc_final: 0.6571 (m-30) outliers start: 21 outliers final: 3 residues processed: 130 average time/residue: 1.2168 time to fit residues: 169.7391 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 : 0.994 ------------------------------------------------------------------------------- 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: 6.9990 chunk 17 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.146025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.092825 restraints weight = 10710.589| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.01 r_work: 0.2905 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1716 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= 0.247 Angle : 0.525 5.628 12843 Z= 0.264 Chirality : 0.039 0.143 1611 Planarity : 0.005 0.043 1587 Dihedral : 3.519 13.532 1302 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.04 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: 2.19 (0.24), residues: 1224 helix: 1.90 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -0.82 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 275 HIS 0.002 0.001 HIS A 316 PHE 0.013 0.002 PHE C 237 TYR 0.010 0.001 TYR B 208 ARG 0.001 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 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.979 Fit side-chains REVERT: A 85 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5961 (mtp85) REVERT: A 179 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7133 (mm-30) REVERT: A 247 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7859 (mtpt) REVERT: A 330 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6640 (mpt180) REVERT: A 387 MET cc_start: 0.8557 (mmm) cc_final: 0.8047 (mtm) REVERT: B 85 ARG cc_start: 0.6311 (OUTLIER) cc_final: 0.5449 (mtp85) REVERT: B 291 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7369 (mt-10) REVERT: B 330 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6609 (mpt180) REVERT: B 387 MET cc_start: 0.8568 (mmm) cc_final: 0.7390 (mtm) REVERT: C 85 ARG cc_start: 0.6475 (OUTLIER) cc_final: 0.5851 (mtp85) REVERT: C 179 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7241 (mm-30) REVERT: C 274 MET cc_start: 0.8442 (mtm) cc_final: 0.8141 (mtt) REVERT: C 330 ARG cc_start: 0.6838 (OUTLIER) cc_final: 0.6546 (mpt180) REVERT: C 367 ASN cc_start: 0.8482 (m-40) cc_final: 0.8205 (m110) REVERT: C 475 ASP cc_start: 0.6863 (m-30) cc_final: 0.6530 (m-30) outliers start: 21 outliers final: 6 residues processed: 121 average time/residue: 1.2455 time to fit residues: 161.4678 Evaluate side-chains 111 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 330 ARG 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 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: 0.9980 chunk 106 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.146628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.094192 restraints weight = 10612.456| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.95 r_work: 0.2929 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1831 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= 0.205 Angle : 0.502 7.321 12843 Z= 0.250 Chirality : 0.038 0.140 1611 Planarity : 0.005 0.044 1587 Dihedral : 3.477 13.775 1302 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.45 % Allowed : 11.82 % Favored : 85.73 % 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: 2.51 (0.24), residues: 1224 helix: 2.09 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -0.46 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 130 HIS 0.001 0.000 HIS B 316 PHE 0.012 0.001 PHE C 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 130 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.949 Fit side-chains REVERT: A 85 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.5959 (mtp85) REVERT: A 179 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7205 (mm-30) REVERT: B 85 ARG cc_start: 0.6319 (OUTLIER) cc_final: 0.5458 (mtp85) REVERT: B 291 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7402 (mt-10) REVERT: B 330 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6812 (mpt180) REVERT: C 85 ARG cc_start: 0.6491 (OUTLIER) cc_final: 0.5835 (mtp85) REVERT: C 179 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7324 (mm-30) REVERT: C 367 ASN cc_start: 0.8521 (m-40) cc_final: 0.8258 (m110) REVERT: C 475 ASP cc_start: 0.6837 (m-30) cc_final: 0.6545 (m-30) outliers start: 24 outliers final: 8 residues processed: 126 average time/residue: 1.2667 time to fit residues: 170.9689 Evaluate side-chains 114 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 274 MET Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 330 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 0.0570 chunk 3 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- 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 = 0.146567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.093633 restraints weight = 10632.011| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.00 r_work: 0.2916 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1930 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= 0.213 Angle : 0.497 7.007 12843 Z= 0.249 Chirality : 0.038 0.138 1611 Planarity : 0.005 0.042 1587 Dihedral : 3.455 12.216 1302 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.85 % Allowed : 11.72 % Favored : 85.42 % 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: 2.59 (0.24), residues: 1224 helix: 2.14 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -0.36 (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 C 237 TYR 0.009 0.001 TYR B 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 137 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 1.008 Fit side-chains REVERT: A 85 ARG cc_start: 0.6303 (OUTLIER) cc_final: 0.5866 (mtp85) REVERT: A 179 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7120 (mm-30) REVERT: B 85 ARG cc_start: 0.6251 (OUTLIER) cc_final: 0.5413 (mtp85) REVERT: B 291 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7400 (mt-10) REVERT: C 85 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.5797 (mtp85) REVERT: C 179 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7249 (mm-30) REVERT: C 367 ASN cc_start: 0.8446 (m-40) cc_final: 0.8194 (m110) REVERT: C 475 ASP cc_start: 0.6777 (m-30) cc_final: 0.6469 (m-30) outliers start: 28 outliers final: 11 residues processed: 131 average time/residue: 1.1638 time to fit residues: 164.5180 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 : 1.005 ------------------------------------------------------------------------------- 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 274 MET 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: 7.9990 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.145816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.092970 restraints weight = 10591.905| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.94 r_work: 0.2909 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9429 Z= 0.252 Angle : 0.514 6.742 12843 Z= 0.255 Chirality : 0.039 0.141 1611 Planarity : 0.005 0.046 1587 Dihedral : 3.480 12.717 1302 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.73 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: 2.53 (0.24), residues: 1224 helix: 2.08 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.39 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 130 HIS 0.002 0.000 HIS B 316 PHE 0.014 0.002 PHE C 237 TYR 0.010 0.001 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 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.963 Fit side-chains REVERT: A 85 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.6024 (mtp85) REVERT: A 179 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7315 (mm-30) REVERT: B 85 ARG cc_start: 0.6363 (OUTLIER) cc_final: 0.5529 (mtp85) REVERT: C 85 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.5882 (mtp85) REVERT: C 179 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7452 (mm-30) REVERT: C 367 ASN cc_start: 0.8484 (m-40) cc_final: 0.8252 (m110) REVERT: C 475 ASP cc_start: 0.6964 (m-30) cc_final: 0.6687 (m-30) outliers start: 24 outliers final: 12 residues processed: 122 average time/residue: 1.0749 time to fit residues: 142.0454 Evaluate side-chains 119 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG 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 274 MET 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.0324 > 50: distance: 49 - 55: 20.900 distance: 55 - 56: 9.254 distance: 55 - 61: 18.321 distance: 56 - 57: 28.014 distance: 56 - 59: 33.581 distance: 57 - 58: 44.986 distance: 57 - 62: 20.339 distance: 58 - 96: 31.013 distance: 59 - 60: 29.820 distance: 60 - 61: 17.641 distance: 62 - 63: 41.980 distance: 63 - 66: 15.579 distance: 64 - 65: 7.153 distance: 64 - 74: 9.177 distance: 65 - 104: 41.239 distance: 66 - 67: 21.147 distance: 67 - 68: 40.726 distance: 67 - 69: 36.201 distance: 68 - 70: 32.833 distance: 69 - 71: 35.739 distance: 70 - 72: 23.112 distance: 71 - 72: 40.330 distance: 74 - 75: 17.407 distance: 75 - 76: 13.088 distance: 75 - 78: 25.600 distance: 76 - 77: 4.086 distance: 76 - 85: 5.572 distance: 77 - 118: 22.244 distance: 78 - 79: 14.824 distance: 79 - 80: 31.561 distance: 80 - 81: 24.717 distance: 81 - 82: 13.323 distance: 82 - 83: 3.099 distance: 82 - 84: 20.282 distance: 85 - 86: 3.479 distance: 86 - 87: 5.697 distance: 86 - 89: 9.355 distance: 87 - 88: 10.765 distance: 87 - 96: 7.987 distance: 89 - 90: 21.453 distance: 90 - 91: 10.629 distance: 90 - 92: 11.588 distance: 91 - 93: 41.788 distance: 92 - 94: 60.617 distance: 94 - 95: 10.299 distance: 96 - 97: 8.281 distance: 97 - 98: 10.369 distance: 97 - 100: 17.031 distance: 98 - 99: 17.301 distance: 98 - 104: 9.357 distance: 100 - 101: 18.634 distance: 101 - 102: 20.724 distance: 101 - 103: 16.467 distance: 104 - 105: 10.568 distance: 105 - 106: 16.693 distance: 105 - 108: 17.419 distance: 106 - 107: 9.206 distance: 106 - 118: 6.827 distance: 108 - 109: 20.552 distance: 109 - 110: 13.726 distance: 109 - 111: 17.764 distance: 110 - 112: 11.318 distance: 111 - 113: 18.962 distance: 111 - 114: 21.904 distance: 112 - 113: 18.970 distance: 113 - 115: 6.578 distance: 114 - 116: 12.997 distance: 115 - 117: 23.180 distance: 116 - 117: 5.754 distance: 118 - 119: 21.220 distance: 119 - 120: 14.263 distance: 120 - 121: 16.429 distance: 120 - 122: 25.809 distance: 122 - 123: 11.933 distance: 123 - 124: 28.674 distance: 123 - 126: 25.807 distance: 124 - 125: 15.647 distance: 124 - 130: 31.468 distance: 125 - 151: 15.610 distance: 126 - 127: 34.161 distance: 126 - 128: 24.199 distance: 127 - 129: 32.162 distance: 130 - 131: 18.385 distance: 131 - 132: 6.749 distance: 131 - 134: 24.580 distance: 132 - 133: 6.435 distance: 132 - 137: 14.462 distance: 133 - 159: 23.680 distance: 134 - 135: 24.373 distance: 134 - 136: 31.172 distance: 137 - 138: 21.510 distance: 138 - 139: 16.924 distance: 138 - 141: 14.159 distance: 139 - 140: 12.386 distance: 139 - 144: 11.157 distance: 140 - 164: 20.535 distance: 141 - 142: 15.150 distance: 141 - 143: 23.055