Starting phenix.real_space_refine on Thu Jul 2 04:34:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7li6_23361/07_2026/7li6_23361.cif Found real_map, /net/cci-nas-00/data/ceres_data/7li6_23361/07_2026/7li6_23361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7li6_23361/07_2026/7li6_23361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7li6_23361/07_2026/7li6_23361.map" model { file = "/net/cci-nas-00/data/ceres_data/7li6_23361/07_2026/7li6_23361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7li6_23361/07_2026/7li6_23361.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7li6_23361/07_2026/7li6_23361.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7li6_23361/07_2026/7li6_23361.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.040 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 34 5.16 5 Cl 1 4.86 5 C 4178 2.51 5 N 958 2.21 5 O 1078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6249 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4284 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 515} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 196 Unusual residues: {' CL': 1, 'D10': 6, 'D12': 3, 'HP6': 9, 'LNK': 4, 'R16': 1} Classifications: {'undetermined': 24} Link IDs: {None: 23} Time building chain proxies: 1.22, per 1000 atoms: 0.20 Number of scatterers: 6249 At special positions: 0 Unit cell: (70.066, 79.981, 123.607, 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) Cl 1 17.00 S 34 16.00 O 1078 8.00 N 958 7.00 C 4178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " distance=2.03 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 208 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 317.1 milliseconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 51.5% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.597A pdb=" N TYR A 107 " --> pdb=" O TRP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 129 through 143 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 159 through 190 removed outlier: 4.332A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 252 through 268 removed outlier: 4.324A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 285 through 301 removed outlier: 4.174A pdb=" N TYR A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.528A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 310 " --> pdb=" O TRP A 306 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 322 removed outlier: 3.763A pdb=" N LEU A 321 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 317 through 322' Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.909A pdb=" N GLY A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 removed outlier: 3.518A pdb=" N ALA A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 391 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.800A pdb=" N VAL A 397 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 415 removed outlier: 4.248A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 443 removed outlier: 4.000A pdb=" N ALA A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 454 removed outlier: 3.813A pdb=" N ILE A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 4.454A pdb=" N ARG A 461 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 462 " --> pdb=" O TRP A 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 462' Processing helix chain 'A' and resid 463 through 476 removed outlier: 3.521A pdb=" N ALA A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 490 removed outlier: 3.659A pdb=" N LYS A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 495 removed outlier: 4.402A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 515 Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 534 through 544 removed outlier: 4.105A pdb=" N TRP A 541 " --> pdb=" O TRP A 537 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 559 Processing helix chain 'A' and resid 572 through 585 removed outlier: 4.354A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.656A pdb=" N LEU A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 599 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 600 " --> pdb=" O ARG A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 613 removed outlier: 3.634A pdb=" N THR A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.987A pdb=" N TYR B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 51' Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.827A pdb=" N VAL B 37 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 79 removed outlier: 7.174A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 79 removed outlier: 7.174A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 113 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 25 through 26 removed outlier: 3.567A pdb=" N THR C 25 " --> pdb=" O ARG C 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.731A pdb=" N LEU C 31 " --> pdb=" O LYS C 127 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 126 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR C 110 " --> pdb=" O THR C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.538A pdb=" N TYR C 73 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU C 70 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLN C 61 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 89 265 hydrogen bonds defined for protein. 765 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: 0.67 Time building geometry restraints manager: 0.65 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: 1808 1.34 - 1.46: 1610 1.46 - 1.58: 2936 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6403 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C2 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 1.439 1.464 -0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.30e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.25e+00 ... (remaining 6398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 8224 1.11 - 2.22: 194 2.22 - 3.34: 91 3.34 - 4.45: 111 4.45 - 5.56: 12 Bond angle restraints: 8632 Sorted by residual: angle pdb=" N TYR A 495 " pdb=" CA TYR A 495 " pdb=" C TYR A 495 " ideal model delta sigma weight residual 114.04 110.66 3.38 1.24e+00 6.50e-01 7.43e+00 angle pdb=" N VAL A 102 " pdb=" CA VAL A 102 " pdb=" C VAL A 102 " ideal model delta sigma weight residual 113.39 109.50 3.89 1.47e+00 4.63e-01 7.01e+00 angle pdb=" C ALA C 74 " pdb=" N ALA C 75 " pdb=" CA ALA C 75 " ideal model delta sigma weight residual 121.54 126.36 -4.82 1.91e+00 2.74e-01 6.38e+00 angle pdb=" CA GLY C 90 " pdb=" C GLY C 90 " pdb=" O GLY C 90 " ideal model delta sigma weight residual 122.22 120.64 1.58 6.50e-01 2.37e+00 5.92e+00 angle pdb=" C ARG A 461 " pdb=" N ARG A 462 " pdb=" CA ARG A 462 " ideal model delta sigma weight residual 121.54 126.02 -4.48 1.91e+00 2.74e-01 5.51e+00 ... (remaining 8627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 3388 17.66 - 35.32: 223 35.32 - 52.98: 47 52.98 - 70.64: 5 70.64 - 88.30: 6 Dihedral angle restraints: 3669 sinusoidal: 1463 harmonic: 2206 Sorted by residual: dihedral pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " pdb=" SG CYS A 209 " pdb=" CB CYS A 209 " ideal model delta sinusoidal sigma weight residual -86.00 -150.26 64.26 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CB GLU A 606 " pdb=" CG GLU A 606 " pdb=" CD GLU A 606 " pdb=" OE1 GLU A 606 " ideal model delta sinusoidal sigma weight residual 0.00 88.30 -88.30 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A 412 " pdb=" CG GLU A 412 " pdb=" CD GLU A 412 " pdb=" OE1 GLU A 412 " ideal model delta sinusoidal sigma weight residual 0.00 83.56 -83.56 1 3.00e+01 1.11e-03 9.47e+00 ... (remaining 3666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.331: 941 0.331 - 0.661: 0 0.661 - 0.992: 0 0.992 - 1.322: 0 1.322 - 1.653: 1 Chirality restraints: 942 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-02 2.50e+03 6.83e+03 chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CB ILE C 99 " pdb=" CA ILE C 99 " pdb=" CG1 ILE C 99 " pdb=" CG2 ILE C 99 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 939 not shown) Planarity restraints: 1045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 338 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 339 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 287 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO A 288 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 88 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C PHE A 88 " 0.020 2.00e-02 2.50e+03 pdb=" O PHE A 88 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU A 89 " -0.007 2.00e-02 2.50e+03 ... (remaining 1042 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1963 2.83 - 3.35: 5435 3.35 - 3.86: 9805 3.86 - 4.38: 10688 4.38 - 4.90: 19047 Nonbonded interactions: 46938 Sorted by model distance: nonbonded pdb=" O SER A 190 " pdb=" OG SER A 190 " model vdw 2.310 3.040 nonbonded pdb=" O GLU A 229 " pdb=" OG1 THR A 233 " model vdw 2.311 3.040 nonbonded pdb=" NE2 GLN C 114 " pdb=" O SER C 119 " model vdw 2.312 3.120 nonbonded pdb=" O VAL A 297 " pdb=" OG1 THR A 301 " model vdw 2.328 3.040 nonbonded pdb=" OG SER C 87 " pdb=" OD1 ASN C 98 " model vdw 2.354 3.040 ... (remaining 46933 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.780 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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 0.065 6409 Z= 0.111 Angle : 0.744 28.058 8644 Z= 0.324 Chirality : 0.066 1.653 942 Planarity : 0.003 0.039 1044 Dihedral : 12.291 88.297 2260 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.72 % Allowed : 9.53 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.27), residues: 761 helix: -0.87 (0.25), residues: 343 sheet: -2.44 (0.62), residues: 76 loop : -3.22 (0.28), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 234 TYR 0.011 0.001 TYR A 175 PHE 0.003 0.000 PHE A 88 TRP 0.004 0.000 TRP A 282 HIS 0.001 0.000 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.10 ( 6403) covalent geometry : angle 0.66671 / 0.30 ( 8632) SS BOND : bond 0.00070 / 0.04 ( 3) SS BOND : angle 0.21395 / 0.12 ( 6) hydrogen bonds : bond 0.19283 / 13.29 ( 260) hydrogen bonds : angle 5.83562 / 4.27 ( 765) Misc. bond : bond 0.00064 / 0.03 ( 1) link_BETA1-4 : bond 0.06474 / 3.41 ( 1) link_BETA1-4 : angle 17.65278 / 6.87 ( 3) link_NAG-ASN : bond 0.00286 / 0.15 ( 1) link_NAG-ASN : angle 1.79528 / 0.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.215 Fit side-chains REVERT: A 306 TRP cc_start: 0.7018 (t-100) cc_final: 0.6154 (p-90) REVERT: A 514 TRP cc_start: 0.7063 (m-10) cc_final: 0.6686 (m100) REVERT: A 535 TRP cc_start: 0.6493 (t60) cc_final: 0.6135 (p-90) REVERT: A 607 ARG cc_start: 0.7332 (mtt180) cc_final: 0.7032 (mtt180) REVERT: B 99 TYR cc_start: 0.8296 (m-80) cc_final: 0.8051 (m-80) REVERT: C 69 LYS cc_start: 0.7459 (tttp) cc_final: 0.7254 (tttm) REVERT: C 71 LEU cc_start: 0.7884 (tp) cc_final: 0.7630 (tp) REVERT: C 116 LYS cc_start: 0.6969 (tttt) cc_final: 0.6637 (mttp) outliers start: 11 outliers final: 7 residues processed: 110 average time/residue: 0.1033 time to fit residues: 14.0462 Evaluate side-chains 73 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 82 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN A 145 ASN A 254 GLN A 318 GLN A 416 ASN A 520 GLN B 24 GLN C 98 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.165174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.143927 restraints weight = 7173.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143863 restraints weight = 6328.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145124 restraints weight = 6109.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145869 restraints weight = 4992.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.146053 restraints weight = 4488.977| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6409 Z= 0.208 Angle : 0.669 10.087 8644 Z= 0.341 Chirality : 0.045 0.243 942 Planarity : 0.005 0.034 1044 Dihedral : 5.495 59.111 967 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.06 % Allowed : 15.31 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.30), residues: 761 helix: -0.11 (0.27), residues: 354 sheet: -2.26 (0.52), residues: 104 loop : -2.83 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 85 TYR 0.025 0.002 TYR A 176 PHE 0.024 0.002 PHE A 213 TRP 0.018 0.002 TRP A 204 HIS 0.003 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 ( 6403) covalent geometry : angle 0.66566 / 0.34 ( 8632) SS BOND : bond 0.00305 / 0.15 ( 3) SS BOND : angle 1.82633 / 1.06 ( 6) hydrogen bonds : bond 0.04693 / 3.04 ( 260) hydrogen bonds : angle 4.38010 / 3.14 ( 765) Misc. bond : bond 0.00060 / 0.03 ( 1) link_BETA1-4 : bond 0.00678 / 0.36 ( 1) link_BETA1-4 : angle 1.78924 / 0.73 ( 3) link_NAG-ASN : bond 0.00225 / 0.12 ( 1) link_NAG-ASN : angle 2.06769 / 1.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 306 TRP cc_start: 0.7184 (t-100) cc_final: 0.6860 (p-90) REVERT: B 53 MET cc_start: 0.8208 (mmt) cc_final: 0.7985 (mmt) REVERT: C 116 LYS cc_start: 0.7736 (tttt) cc_final: 0.7135 (mtmt) outliers start: 26 outliers final: 19 residues processed: 97 average time/residue: 0.0660 time to fit residues: 8.6677 Evaluate side-chains 82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 72 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.155869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120424 restraints weight = 7569.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125800 restraints weight = 4456.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129397 restraints weight = 3175.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.131872 restraints weight = 2528.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.133425 restraints weight = 2157.710| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6409 Z= 0.140 Angle : 0.561 9.406 8644 Z= 0.285 Chirality : 0.042 0.261 942 Planarity : 0.004 0.034 1044 Dihedral : 4.902 58.418 963 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.22 % Allowed : 17.19 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.31), residues: 761 helix: 0.40 (0.28), residues: 353 sheet: -1.45 (0.60), residues: 89 loop : -2.76 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 38 TYR 0.025 0.002 TYR A 176 PHE 0.012 0.001 PHE A 213 TRP 0.026 0.001 TRP A 514 HIS 0.002 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 6403) covalent geometry : angle 0.55818 / 0.28 ( 8632) SS BOND : bond 0.00198 / 0.10 ( 3) SS BOND : angle 1.31581 / 0.76 ( 6) hydrogen bonds : bond 0.03945 / 2.52 ( 260) hydrogen bonds : angle 4.19659 / 3.05 ( 765) Misc. bond : bond 0.00034 / 0.02 ( 1) link_BETA1-4 : bond 0.00411 / 0.22 ( 1) link_BETA1-4 : angle 1.20099 / 0.66 ( 3) link_NAG-ASN : bond 0.00015 / 0.01 ( 1) link_NAG-ASN : angle 2.03921 / 1.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.132 Fit side-chains REVERT: A 306 TRP cc_start: 0.6931 (t-100) cc_final: 0.5718 (p-90) REVERT: A 385 TYR cc_start: 0.6603 (OUTLIER) cc_final: 0.6196 (t80) REVERT: A 564 ARG cc_start: 0.8263 (ttt90) cc_final: 0.7739 (ttt90) REVERT: C 116 LYS cc_start: 0.7743 (tttt) cc_final: 0.6364 (mtmt) outliers start: 27 outliers final: 17 residues processed: 91 average time/residue: 0.0619 time to fit residues: 7.6517 Evaluate side-chains 82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 47 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 0.0370 chunk 34 optimal weight: 0.0770 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.159745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.124257 restraints weight = 7472.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.129898 restraints weight = 4356.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.133682 restraints weight = 3063.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136081 restraints weight = 2419.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.137420 restraints weight = 2061.804| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6409 Z= 0.099 Angle : 0.520 9.454 8644 Z= 0.263 Chirality : 0.041 0.258 942 Planarity : 0.004 0.031 1044 Dihedral : 4.468 50.475 963 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.91 % Allowed : 18.75 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.31), residues: 761 helix: 0.67 (0.29), residues: 354 sheet: -1.46 (0.59), residues: 97 loop : -2.50 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 38 TYR 0.022 0.001 TYR A 176 PHE 0.012 0.001 PHE A 133 TRP 0.029 0.001 TRP A 514 HIS 0.002 0.000 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 6403) covalent geometry : angle 0.51712 / 0.26 ( 8632) SS BOND : bond 0.00130 / 0.06 ( 3) SS BOND : angle 1.80993 / 1.00 ( 6) hydrogen bonds : bond 0.03212 / 2.06 ( 260) hydrogen bonds : angle 4.07615 / 2.99 ( 765) Misc. bond : bond 0.00012 / 0.01 ( 1) link_BETA1-4 : bond 0.00338 / 0.18 ( 1) link_BETA1-4 : angle 0.62996 / 0.34 ( 3) link_NAG-ASN : bond 0.00196 / 0.10 ( 1) link_NAG-ASN : angle 2.01769 / 1.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.209 Fit side-chains REVERT: A 102 VAL cc_start: 0.8542 (p) cc_final: 0.8308 (t) REVERT: A 247 ASP cc_start: 0.8397 (t0) cc_final: 0.8103 (t0) REVERT: A 347 PHE cc_start: 0.6929 (m-80) cc_final: 0.6719 (m-80) REVERT: A 385 TYR cc_start: 0.6426 (OUTLIER) cc_final: 0.6124 (t80) REVERT: A 564 ARG cc_start: 0.8159 (ttt90) cc_final: 0.7665 (ttt90) REVERT: B 38 ARG cc_start: 0.8259 (ttt90) cc_final: 0.7552 (ttm-80) REVERT: B 53 MET cc_start: 0.8186 (tpt) cc_final: 0.7588 (mmt) REVERT: C 116 LYS cc_start: 0.7723 (tttt) cc_final: 0.6393 (mtmt) outliers start: 25 outliers final: 17 residues processed: 93 average time/residue: 0.0676 time to fit residues: 8.4655 Evaluate side-chains 84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 0.0570 chunk 44 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.165039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130210 restraints weight = 7880.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135510 restraints weight = 4647.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.139043 restraints weight = 3325.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141210 restraints weight = 2661.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.142923 restraints weight = 2298.866| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6409 Z= 0.107 Angle : 0.522 9.417 8644 Z= 0.263 Chirality : 0.041 0.263 942 Planarity : 0.003 0.031 1044 Dihedral : 4.150 28.412 960 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.38 % Allowed : 18.75 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.32), residues: 761 helix: 0.80 (0.29), residues: 353 sheet: -0.95 (0.62), residues: 92 loop : -2.47 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 38 TYR 0.023 0.001 TYR A 110 PHE 0.009 0.001 PHE A 133 TRP 0.017 0.001 TRP A 514 HIS 0.001 0.000 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 6403) covalent geometry : angle 0.51865 / 0.26 ( 8632) SS BOND : bond 0.00214 / 0.10 ( 3) SS BOND : angle 1.82300 / 1.01 ( 6) hydrogen bonds : bond 0.03247 / 2.09 ( 260) hydrogen bonds : angle 4.03097 / 2.95 ( 765) Misc. bond : bond 0.00022 / 0.01 ( 1) link_BETA1-4 : bond 0.00433 / 0.23 ( 1) link_BETA1-4 : angle 0.70945 / 0.39 ( 3) link_NAG-ASN : bond 0.00190 / 0.10 ( 1) link_NAG-ASN : angle 2.19749 / 1.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.215 Fit side-chains REVERT: A 102 VAL cc_start: 0.8834 (p) cc_final: 0.8586 (t) REVERT: A 306 TRP cc_start: 0.7210 (t-100) cc_final: 0.6215 (p-90) REVERT: A 385 TYR cc_start: 0.6671 (OUTLIER) cc_final: 0.6466 (t80) REVERT: A 494 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.6253 (pt0) REVERT: A 564 ARG cc_start: 0.8317 (ttt90) cc_final: 0.7881 (ttt90) REVERT: B 38 ARG cc_start: 0.8210 (ttt90) cc_final: 0.7859 (ttm-80) REVERT: B 53 MET cc_start: 0.8204 (tpt) cc_final: 0.7747 (mmt) REVERT: C 116 LYS cc_start: 0.8019 (tttt) cc_final: 0.6792 (mtmt) outliers start: 28 outliers final: 21 residues processed: 89 average time/residue: 0.0627 time to fit residues: 7.7739 Evaluate side-chains 90 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN A 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111800 restraints weight = 7605.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117017 restraints weight = 4419.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.120549 restraints weight = 3125.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122824 restraints weight = 2484.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.124221 restraints weight = 2143.004| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 6409 Z= 0.236 Angle : 0.656 9.468 8644 Z= 0.335 Chirality : 0.045 0.269 942 Planarity : 0.004 0.033 1044 Dihedral : 5.706 40.284 960 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 4.69 % Allowed : 18.91 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.31), residues: 761 helix: 0.38 (0.28), residues: 362 sheet: -1.59 (0.55), residues: 104 loop : -2.41 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 38 TYR 0.027 0.002 TYR A 176 PHE 0.019 0.002 PHE A 373 TRP 0.020 0.002 TRP A 514 HIS 0.002 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.24 ( 6403) covalent geometry : angle 0.65161 / 0.33 ( 8632) SS BOND : bond 0.00383 / 0.18 ( 3) SS BOND : angle 2.34212 / 1.32 ( 6) hydrogen bonds : bond 0.04829 / 3.07 ( 260) hydrogen bonds : angle 4.38153 / 3.17 ( 765) Misc. bond : bond 0.00093 / 0.05 ( 1) link_BETA1-4 : bond 0.00212 / 0.11 ( 1) link_BETA1-4 : angle 0.77194 / 0.41 ( 3) link_NAG-ASN : bond 0.00181 / 0.10 ( 1) link_NAG-ASN : angle 2.62534 / 1.35 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.154 Fit side-chains REVERT: A 107 TYR cc_start: 0.5938 (OUTLIER) cc_final: 0.5509 (t80) REVERT: A 145 ASN cc_start: 0.8565 (m110) cc_final: 0.8260 (m-40) REVERT: A 176 TYR cc_start: 0.7819 (t80) cc_final: 0.7383 (t80) REVERT: A 204 TRP cc_start: 0.1788 (OUTLIER) cc_final: -0.0158 (m-90) REVERT: A 306 TRP cc_start: 0.7027 (t-100) cc_final: 0.5738 (p-90) REVERT: A 385 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.5908 (t80) REVERT: A 388 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7323 (tm-30) REVERT: A 389 MET cc_start: 0.6020 (tpp) cc_final: 0.5744 (tpp) REVERT: B 38 ARG cc_start: 0.8378 (ttt90) cc_final: 0.8147 (ttt-90) REVERT: B 79 TYR cc_start: 0.8927 (m-80) cc_final: 0.8562 (m-80) REVERT: B 99 TYR cc_start: 0.8227 (m-80) cc_final: 0.7900 (m-80) outliers start: 30 outliers final: 18 residues processed: 96 average time/residue: 0.0501 time to fit residues: 6.7448 Evaluate side-chains 84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 4 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 72 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.153962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118402 restraints weight = 7401.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123933 restraints weight = 4294.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127723 restraints weight = 3020.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130111 restraints weight = 2377.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131891 restraints weight = 2036.053| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6409 Z= 0.117 Angle : 0.564 9.373 8644 Z= 0.283 Chirality : 0.042 0.260 942 Planarity : 0.004 0.033 1044 Dihedral : 4.993 35.893 960 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.75 % Allowed : 20.31 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.32), residues: 761 helix: 0.74 (0.28), residues: 355 sheet: -1.29 (0.58), residues: 97 loop : -2.30 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 38 TYR 0.027 0.001 TYR A 110 PHE 0.012 0.001 PHE A 133 TRP 0.016 0.001 TRP A 514 HIS 0.001 0.000 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 6403) covalent geometry : angle 0.55945 / 0.28 ( 8632) SS BOND : bond 0.00196 / 0.09 ( 3) SS BOND : angle 1.96047 / 1.08 ( 6) hydrogen bonds : bond 0.03541 / 2.27 ( 260) hydrogen bonds : angle 4.14454 / 3.01 ( 765) Misc. bond : bond 0.00023 / 0.01 ( 1) link_BETA1-4 : bond 0.00227 / 0.12 ( 1) link_BETA1-4 : angle 0.67472 / 0.34 ( 3) link_NAG-ASN : bond 0.00103 / 0.05 ( 1) link_NAG-ASN : angle 2.51408 / 1.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.146 Fit side-chains REVERT: A 107 TYR cc_start: 0.5738 (OUTLIER) cc_final: 0.5374 (t80) REVERT: A 145 ASN cc_start: 0.8507 (m110) cc_final: 0.8196 (m-40) REVERT: A 306 TRP cc_start: 0.7016 (t-100) cc_final: 0.5724 (p-90) REVERT: A 385 TYR cc_start: 0.6598 (OUTLIER) cc_final: 0.6008 (t80) REVERT: B 53 MET cc_start: 0.8227 (tpt) cc_final: 0.7561 (mmt) REVERT: B 79 TYR cc_start: 0.8909 (m-80) cc_final: 0.8467 (m-80) REVERT: B 99 TYR cc_start: 0.8183 (m-80) cc_final: 0.7864 (m-80) outliers start: 24 outliers final: 19 residues processed: 88 average time/residue: 0.0509 time to fit residues: 6.3104 Evaluate side-chains 84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 58 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 73 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 4 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.155166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.119442 restraints weight = 7476.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125076 restraints weight = 4303.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128892 restraints weight = 3021.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.131452 restraints weight = 2384.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132958 restraints weight = 2025.721| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6409 Z= 0.110 Angle : 0.568 9.362 8644 Z= 0.281 Chirality : 0.042 0.264 942 Planarity : 0.004 0.065 1044 Dihedral : 4.683 30.674 960 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.81 % Allowed : 21.88 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.32), residues: 761 helix: 0.77 (0.28), residues: 360 sheet: -1.18 (0.59), residues: 97 loop : -2.31 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 38 TYR 0.030 0.001 TYR A 176 PHE 0.021 0.001 PHE A 423 TRP 0.015 0.001 TRP A 514 HIS 0.001 0.000 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 6403) covalent geometry : angle 0.56404 / 0.28 ( 8632) SS BOND : bond 0.00203 / 0.10 ( 3) SS BOND : angle 1.84185 / 1.01 ( 6) hydrogen bonds : bond 0.03299 / 2.10 ( 260) hydrogen bonds : angle 4.12591 / 3.00 ( 765) Misc. bond : bond 0.00022 / 0.01 ( 1) link_BETA1-4 : bond 0.00374 / 0.20 ( 1) link_BETA1-4 : angle 0.71347 / 0.36 ( 3) link_NAG-ASN : bond 0.00232 / 0.12 ( 1) link_NAG-ASN : angle 2.46933 / 1.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.130 Fit side-chains REVERT: A 145 ASN cc_start: 0.8548 (m110) cc_final: 0.8229 (m-40) REVERT: A 306 TRP cc_start: 0.6997 (t-100) cc_final: 0.5752 (p-90) REVERT: A 385 TYR cc_start: 0.6460 (OUTLIER) cc_final: 0.6172 (t80) REVERT: B 53 MET cc_start: 0.8171 (tpt) cc_final: 0.7520 (mmt) REVERT: B 79 TYR cc_start: 0.8913 (m-80) cc_final: 0.8456 (m-80) REVERT: B 99 TYR cc_start: 0.8115 (m-80) cc_final: 0.7892 (m-80) outliers start: 18 outliers final: 15 residues processed: 84 average time/residue: 0.0540 time to fit residues: 6.4738 Evaluate side-chains 82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.0060 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.0000 chunk 72 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.158133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124041 restraints weight = 7790.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129153 restraints weight = 4638.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.132531 restraints weight = 3329.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.134641 restraints weight = 2666.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136250 restraints weight = 2302.538| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6409 Z= 0.109 Angle : 0.563 9.350 8644 Z= 0.278 Chirality : 0.041 0.261 942 Planarity : 0.003 0.032 1044 Dihedral : 4.507 29.948 960 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.66 % Allowed : 22.19 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.32), residues: 761 helix: 0.87 (0.29), residues: 361 sheet: -0.76 (0.61), residues: 92 loop : -2.31 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 462 TYR 0.023 0.001 TYR A 176 PHE 0.012 0.001 PHE A 133 TRP 0.023 0.001 TRP A 514 HIS 0.001 0.000 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 6403) covalent geometry : angle 0.55942 / 0.28 ( 8632) SS BOND : bond 0.00215 / 0.10 ( 3) SS BOND : angle 1.83175 / 1.00 ( 6) hydrogen bonds : bond 0.03197 / 2.05 ( 260) hydrogen bonds : angle 4.08207 / 2.97 ( 765) Misc. bond : bond 0.00022 / 0.01 ( 1) link_BETA1-4 : bond 0.00396 / 0.21 ( 1) link_BETA1-4 : angle 0.75541 / 0.38 ( 3) link_NAG-ASN : bond 0.00214 / 0.11 ( 1) link_NAG-ASN : angle 2.40282 / 1.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.153 Fit side-chains REVERT: A 145 ASN cc_start: 0.8700 (m110) cc_final: 0.8456 (m-40) REVERT: A 306 TRP cc_start: 0.7240 (t-100) cc_final: 0.6234 (p-90) REVERT: A 514 TRP cc_start: 0.7960 (m-10) cc_final: 0.7628 (m-10) REVERT: B 53 MET cc_start: 0.8209 (tpt) cc_final: 0.7780 (mmt) REVERT: B 79 TYR cc_start: 0.8910 (m-80) cc_final: 0.8604 (m-80) outliers start: 17 outliers final: 15 residues processed: 83 average time/residue: 0.0612 time to fit residues: 7.0981 Evaluate side-chains 82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 68 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.147499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116345 restraints weight = 7367.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.120000 restraints weight = 5104.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122212 restraints weight = 3996.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.123964 restraints weight = 3405.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.125227 restraints weight = 3039.169| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6409 Z= 0.130 Angle : 0.580 9.385 8644 Z= 0.289 Chirality : 0.042 0.266 942 Planarity : 0.004 0.032 1044 Dihedral : 4.727 30.057 960 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.50 % Allowed : 22.66 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.32), residues: 761 helix: 0.89 (0.29), residues: 360 sheet: -0.83 (0.61), residues: 92 loop : -2.29 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 38 TYR 0.028 0.002 TYR A 176 PHE 0.023 0.001 PHE A 423 TRP 0.023 0.001 TRP A 514 HIS 0.001 0.000 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 6403) covalent geometry : angle 0.57622 / 0.29 ( 8632) SS BOND : bond 0.00263 / 0.13 ( 3) SS BOND : angle 1.88728 / 1.04 ( 6) hydrogen bonds : bond 0.03476 / 2.21 ( 260) hydrogen bonds : angle 4.14680 / 3.01 ( 765) Misc. bond : bond 0.00035 / 0.02 ( 1) link_BETA1-4 : bond 0.00300 / 0.16 ( 1) link_BETA1-4 : angle 0.72703 / 0.36 ( 3) link_NAG-ASN : bond 0.00137 / 0.07 ( 1) link_NAG-ASN : angle 2.47487 / 1.30 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.156 Fit side-chains REVERT: A 306 TRP cc_start: 0.7304 (t-100) cc_final: 0.6443 (p-90) REVERT: A 389 MET cc_start: 0.6669 (tpp) cc_final: 0.6423 (mtt) REVERT: B 53 MET cc_start: 0.8198 (tpt) cc_final: 0.7879 (mmt) REVERT: B 79 TYR cc_start: 0.8849 (m-80) cc_final: 0.8616 (m-80) outliers start: 16 outliers final: 14 residues processed: 81 average time/residue: 0.0599 time to fit residues: 6.7516 Evaluate side-chains 80 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 57 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 31 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 20 optimal weight: 0.0020 chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.156176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121553 restraints weight = 7765.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126812 restraints weight = 4498.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130343 restraints weight = 3187.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132657 restraints weight = 2539.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134254 restraints weight = 2176.895| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6409 Z= 0.115 Angle : 0.573 9.344 8644 Z= 0.286 Chirality : 0.042 0.260 942 Planarity : 0.004 0.032 1044 Dihedral : 4.634 30.404 960 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.66 % Allowed : 22.66 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.32), residues: 761 helix: 0.96 (0.28), residues: 360 sheet: -0.77 (0.61), residues: 92 loop : -2.24 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 38 TYR 0.028 0.002 TYR A 176 PHE 0.013 0.001 PHE A 133 TRP 0.023 0.001 TRP A 514 HIS 0.001 0.001 HIS A 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 6403) covalent geometry : angle 0.56919 / 0.29 ( 8632) SS BOND : bond 0.00235 / 0.11 ( 3) SS BOND : angle 1.83567 / 1.00 ( 6) hydrogen bonds : bond 0.03248 / 2.06 ( 260) hydrogen bonds : angle 4.11728 / 2.99 ( 765) Misc. bond : bond 0.00024 / 0.01 ( 1) link_BETA1-4 : bond 0.00361 / 0.19 ( 1) link_BETA1-4 : angle 0.73381 / 0.36 ( 3) link_NAG-ASN : bond 0.00205 / 0.11 ( 1) link_NAG-ASN : angle 2.39585 / 1.29 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 998.56 seconds wall clock time: 17 minutes 55.90 seconds (1075.90 seconds total)