Starting phenix.real_space_refine on Tue Mar 11 21:03:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7li6_23361/03_2025/7li6_23361.cif Found real_map, /net/cci-nas-00/data/ceres_data/7li6_23361/03_2025/7li6_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_23361/03_2025/7li6_23361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7li6_23361/03_2025/7li6_23361.map" model { file = "/net/cci-nas-00/data/ceres_data/7li6_23361/03_2025/7li6_23361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7li6_23361/03_2025/7li6_23361.cif" } resolution = 3.5 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLU:plan': 1, 'ARG: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 dihedrals: 6 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: 5.46, per 1000 atoms: 0.87 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: 1.71 Conformation dependent library (CDL) restraints added in 854.8 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: 0.73 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: 1.71 Time building geometry restraints manager: 2.00 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: 3426 17.66 - 35.32: 225 35.32 - 52.98: 48 52.98 - 70.64: 6 70.64 - 88.30: 6 Dihedral angle restraints: 3711 sinusoidal: 1505 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 3708 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: 2.780 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.820 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 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 0.030 6403 Z= 0.130 Angle : 0.667 5.560 8632 Z= 0.305 Chirality : 0.066 1.653 942 Planarity : 0.003 0.039 1044 Dihedral : 12.312 88.297 2302 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.37 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (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 TRP 0.004 0.000 TRP A 282 HIS 0.001 0.000 HIS A 223 PHE 0.003 0.000 PHE A 88 TYR 0.011 0.001 TYR A 175 ARG 0.001 0.000 ARG A 234 *********************** 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 : 0.672 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: 0.7629 (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: 0.2636 time to fit residues: 35.5341 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 : 0.688 ------------------------------------------------------------------------------- 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 63 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 chunk 22 optimal weight: 0.0470 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 145 ASN A 254 GLN A 416 ASN A 520 GLN B 24 GLN C 98 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.185224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.163780 restraints weight = 6857.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.165458 restraints weight = 5033.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.166610 restraints weight = 4259.962| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6403 Z= 0.149 Angle : 0.517 10.116 8632 Z= 0.261 Chirality : 0.040 0.246 942 Planarity : 0.004 0.035 1044 Dihedral : 5.160 56.724 1009 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.97 % Allowed : 14.22 % Favored : 82.81 % 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: -1.84 (0.30), residues: 761 helix: 0.29 (0.28), residues: 350 sheet: -1.79 (0.61), residues: 86 loop : -2.83 (0.31), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 59 HIS 0.001 0.000 HIS A 235 PHE 0.008 0.001 PHE A 380 TYR 0.022 0.001 TYR A 358 ARG 0.007 0.001 ARG A 564 *********************** 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 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 301 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7474 (p) REVERT: A 370 MET cc_start: 0.7106 (mmp) cc_final: 0.6717 (mmt) REVERT: C 69 LYS cc_start: 0.7987 (tttp) cc_final: 0.7771 (tttm) outliers start: 19 outliers final: 11 residues processed: 93 average time/residue: 0.2206 time to fit residues: 26.3401 Evaluate side-chains 75 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU 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 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 B residue 137 THR Chi-restraints excluded: chain C residue 82 VAL 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 56 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.162694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128684 restraints weight = 7623.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133813 restraints weight = 4564.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.137181 restraints weight = 3278.939| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6403 Z= 0.238 Angle : 0.557 9.394 8632 Z= 0.286 Chirality : 0.042 0.268 942 Planarity : 0.004 0.030 1044 Dihedral : 5.181 57.282 1003 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.38 % Allowed : 15.31 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.61 (0.31), residues: 761 helix: 0.46 (0.28), residues: 355 sheet: -1.81 (0.56), residues: 98 loop : -2.68 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 204 HIS 0.002 0.001 HIS A 223 PHE 0.017 0.001 PHE A 334 TYR 0.023 0.002 TYR A 176 ARG 0.005 0.001 ARG A 462 *********************** 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 97 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 306 TRP cc_start: 0.7177 (t-100) cc_final: 0.6288 (p-90) REVERT: A 370 MET cc_start: 0.7239 (mmp) cc_final: 0.6839 (mmt) REVERT: A 386 MET cc_start: 0.7359 (ttp) cc_final: 0.7079 (mtm) REVERT: A 458 TRP cc_start: 0.8275 (m100) cc_final: 0.7863 (m100) REVERT: B 53 MET cc_start: 0.8271 (tpt) cc_final: 0.8009 (mmt) outliers start: 28 outliers final: 19 residues processed: 89 average time/residue: 0.1858 time to fit residues: 22.2986 Evaluate side-chains 83 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 396 GLU 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 481 LEU Chi-restraints excluded: chain A residue 482 THR 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 33 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 82 VAL 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 54 optimal weight: 5.9990 chunk 14 optimal weight: 0.1980 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 68 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.162480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126753 restraints weight = 7503.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132493 restraints weight = 4332.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136362 restraints weight = 3033.244| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6403 Z= 0.169 Angle : 0.530 9.471 8632 Z= 0.267 Chirality : 0.041 0.257 942 Planarity : 0.004 0.030 1044 Dihedral : 4.976 56.930 1003 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.22 % Allowed : 17.03 % Favored : 78.75 % 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: -1.28 (0.31), residues: 761 helix: 0.66 (0.28), residues: 354 sheet: -1.22 (0.60), residues: 92 loop : -2.56 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 514 HIS 0.001 0.000 HIS A 235 PHE 0.010 0.001 PHE A 133 TYR 0.023 0.001 TYR A 176 ARG 0.004 0.000 ARG A 462 *********************** 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 91 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.605 Fit side-chains REVERT: A 152 ARG cc_start: 0.8424 (tpp80) cc_final: 0.7999 (tpp80) REVERT: A 347 PHE cc_start: 0.6898 (m-80) cc_final: 0.6662 (m-80) REVERT: A 370 MET cc_start: 0.6664 (mmp) cc_final: 0.6305 (mmt) REVERT: A 386 MET cc_start: 0.6802 (ttp) cc_final: 0.6577 (mtm) REVERT: A 564 ARG cc_start: 0.7999 (ttt-90) cc_final: 0.7478 (ttt-90) outliers start: 27 outliers final: 21 residues processed: 84 average time/residue: 0.1813 time to fit residues: 20.4895 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 : 0.651 ------------------------------------------------------------------------------- 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 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 482 THR 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 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 137 THR Chi-restraints excluded: chain C residue 40 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 59 optimal weight: 0.0270 chunk 4 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.159314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123800 restraints weight = 7383.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129308 restraints weight = 4333.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.133043 restraints weight = 3068.293| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6403 Z= 0.182 Angle : 0.531 9.428 8632 Z= 0.268 Chirality : 0.041 0.263 942 Planarity : 0.003 0.032 1044 Dihedral : 5.071 57.176 1003 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.53 % Allowed : 17.34 % Favored : 78.12 % 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: -1.16 (0.32), residues: 761 helix: 0.72 (0.28), residues: 355 sheet: -1.29 (0.59), residues: 97 loop : -2.41 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 514 HIS 0.002 0.001 HIS C 100 PHE 0.010 0.001 PHE A 213 TYR 0.023 0.001 TYR A 176 ARG 0.003 0.000 ARG A 462 *********************** 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: 29 poor density : 66 time to evaluate : 0.637 Fit side-chains REVERT: A 107 TYR cc_start: 0.5751 (OUTLIER) cc_final: 0.5083 (t80) REVERT: A 247 ASP cc_start: 0.8410 (t0) cc_final: 0.8081 (t0) REVERT: A 370 MET cc_start: 0.6700 (mmp) cc_final: 0.6366 (mmt) REVERT: A 493 GLU cc_start: 0.7852 (tt0) cc_final: 0.7639 (tt0) REVERT: A 564 ARG cc_start: 0.7892 (ttt-90) cc_final: 0.7401 (ttt-90) REVERT: B 53 MET cc_start: 0.8272 (tpt) cc_final: 0.7631 (mmt) outliers start: 29 outliers final: 22 residues processed: 88 average time/residue: 0.1840 time to fit residues: 21.8041 Evaluate side-chains 84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 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 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 482 THR 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 70 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 40 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 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.161007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125976 restraints weight = 7747.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.131209 restraints weight = 4569.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134704 restraints weight = 3265.567| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6403 Z= 0.203 Angle : 0.544 9.391 8632 Z= 0.275 Chirality : 0.042 0.262 942 Planarity : 0.004 0.033 1044 Dihedral : 5.283 57.091 1003 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.59 % Allowed : 18.59 % Favored : 77.81 % 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: -1.11 (0.32), residues: 761 helix: 0.75 (0.28), residues: 354 sheet: -1.23 (0.59), residues: 97 loop : -2.38 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 514 HIS 0.001 0.001 HIS A 235 PHE 0.015 0.001 PHE A 423 TYR 0.022 0.001 TYR A 176 ARG 0.008 0.001 ARG A 152 *********************** 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 94 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.681 Fit side-chains REVERT: A 102 VAL cc_start: 0.8887 (p) cc_final: 0.8662 (t) REVERT: A 107 TYR cc_start: 0.6458 (OUTLIER) cc_final: 0.5814 (t80) REVERT: A 185 TYR cc_start: 0.8384 (t80) cc_final: 0.8136 (t80) REVERT: A 306 TRP cc_start: 0.7224 (t-100) cc_final: 0.6281 (p-90) REVERT: A 370 MET cc_start: 0.7252 (mmp) cc_final: 0.6943 (mmt) REVERT: A 385 TYR cc_start: 0.6885 (OUTLIER) cc_final: 0.6495 (t80) outliers start: 23 outliers final: 19 residues processed: 90 average time/residue: 0.1751 time to fit residues: 21.4804 Evaluate side-chains 87 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 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 23 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 103 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 63 optimal weight: 0.0370 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.158508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123068 restraints weight = 7330.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128670 restraints weight = 4284.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.132450 restraints weight = 3010.635| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6403 Z= 0.149 Angle : 0.520 9.385 8632 Z= 0.263 Chirality : 0.041 0.259 942 Planarity : 0.003 0.033 1044 Dihedral : 4.821 57.329 1001 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.28 % Allowed : 19.06 % Favored : 77.66 % 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 (0.32), residues: 761 helix: 0.80 (0.28), residues: 360 sheet: -0.75 (0.61), residues: 92 loop : -2.38 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 514 HIS 0.001 0.000 HIS A 235 PHE 0.009 0.001 PHE A 133 TYR 0.023 0.001 TYR A 176 ARG 0.006 0.000 ARG A 152 *********************** 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: 21 poor density : 71 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.8051 (t80) cc_final: 0.7684 (t80) REVERT: A 306 TRP cc_start: 0.6971 (t-100) cc_final: 0.5801 (p-90) REVERT: A 370 MET cc_start: 0.6647 (mmp) cc_final: 0.6331 (mmt) REVERT: B 38 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7346 (ttm-80) REVERT: B 53 MET cc_start: 0.8260 (tpt) cc_final: 0.7601 (mmt) outliers start: 21 outliers final: 18 residues processed: 88 average time/residue: 0.1817 time to fit residues: 21.9011 Evaluate side-chains 86 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 191 PHE Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 209 CYS 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 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 70 ILE 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 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.223790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.190997 restraints weight = 7640.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.195165 restraints weight = 5044.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.197713 restraints weight = 3837.403| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6403 Z= 0.203 Angle : 0.540 9.387 8632 Z= 0.274 Chirality : 0.042 0.263 942 Planarity : 0.003 0.033 1044 Dihedral : 5.010 57.343 1001 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.44 % Allowed : 19.53 % Favored : 77.03 % 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: -0.91 (0.32), residues: 761 helix: 0.85 (0.28), residues: 354 sheet: -0.93 (0.60), residues: 97 loop : -2.27 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 514 HIS 0.001 0.001 HIS A 223 PHE 0.015 0.001 PHE A 423 TYR 0.021 0.001 TYR A 176 ARG 0.005 0.000 ARG A 152 *********************** 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 92 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.8383 (t80) cc_final: 0.8180 (t80) REVERT: A 306 TRP cc_start: 0.7276 (t-100) cc_final: 0.6321 (p-90) REVERT: A 370 MET cc_start: 0.7226 (mmp) cc_final: 0.6954 (mmt) REVERT: A 385 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.6522 (t80) REVERT: B 53 MET cc_start: 0.8226 (tpt) cc_final: 0.7899 (mmt) REVERT: B 79 TYR cc_start: 0.8869 (m-80) cc_final: 0.8649 (m-80) outliers start: 22 outliers final: 19 residues processed: 88 average time/residue: 0.1800 time to fit residues: 21.6972 Evaluate side-chains 89 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 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 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 70 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 40 THR 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 62 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.164284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.141887 restraints weight = 7164.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.142067 restraints weight = 5808.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142848 restraints weight = 5644.766| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6403 Z= 0.201 Angle : 0.560 9.372 8632 Z= 0.283 Chirality : 0.042 0.259 942 Planarity : 0.003 0.034 1044 Dihedral : 5.124 57.480 1001 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.91 % Allowed : 19.38 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.32), residues: 761 helix: 0.78 (0.28), residues: 361 sheet: -0.86 (0.60), residues: 97 loop : -2.24 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 514 HIS 0.001 0.000 HIS A 235 PHE 0.011 0.001 PHE A 133 TYR 0.024 0.001 TYR A 176 ARG 0.006 0.000 ARG A 152 *********************** 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 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 306 TRP cc_start: 0.7313 (t-100) cc_final: 0.6653 (p-90) REVERT: A 370 MET cc_start: 0.7328 (mmp) cc_final: 0.7089 (mmt) REVERT: A 385 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.6467 (t80) REVERT: B 53 MET cc_start: 0.8181 (tpt) cc_final: 0.7950 (mmt) outliers start: 25 outliers final: 21 residues processed: 93 average time/residue: 0.1761 time to fit residues: 22.3006 Evaluate side-chains 93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 175 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 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 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 70 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 40 THR 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 2 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 0.0060 chunk 69 optimal weight: 0.0040 chunk 67 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.157568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121979 restraints weight = 7393.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127535 restraints weight = 4328.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131282 restraints weight = 3048.882| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6403 Z= 0.163 Angle : 0.553 9.349 8632 Z= 0.280 Chirality : 0.041 0.257 942 Planarity : 0.003 0.034 1044 Dihedral : 4.984 57.505 1001 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.44 % Allowed : 20.00 % Favored : 76.56 % 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: -0.78 (0.32), residues: 761 helix: 0.89 (0.28), residues: 361 sheet: -0.93 (0.59), residues: 99 loop : -2.15 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 514 HIS 0.001 0.000 HIS A 235 PHE 0.013 0.001 PHE A 133 TYR 0.024 0.001 TYR A 176 ARG 0.005 0.000 ARG A 152 ********************** 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 87 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 306 TRP cc_start: 0.6970 (t-100) cc_final: 0.5707 (p-90) REVERT: A 370 MET cc_start: 0.6627 (mmp) cc_final: 0.6309 (mmt) REVERT: A 385 TYR cc_start: 0.6416 (OUTLIER) cc_final: 0.6066 (t80) REVERT: B 53 MET cc_start: 0.8208 (tpt) cc_final: 0.7571 (mmt) outliers start: 22 outliers final: 20 residues processed: 84 average time/residue: 0.1805 time to fit residues: 20.6438 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 : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 175 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 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 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 70 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.119088 restraints weight = 7565.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.124642 restraints weight = 4358.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128340 restraints weight = 3052.562| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6403 Z= 0.218 Angle : 0.584 9.401 8632 Z= 0.296 Chirality : 0.042 0.262 942 Planarity : 0.003 0.034 1044 Dihedral : 5.221 57.744 1001 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.59 % Allowed : 20.00 % 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 (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: -0.82 (0.32), residues: 761 helix: 0.81 (0.28), residues: 361 sheet: -0.88 (0.60), residues: 97 loop : -2.14 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 514 HIS 0.002 0.001 HIS A 235 PHE 0.010 0.001 PHE A 133 TYR 0.025 0.002 TYR A 176 ARG 0.005 0.000 ARG A 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2311.60 seconds wall clock time: 40 minutes 55.66 seconds (2455.66 seconds total)