Starting phenix.real_space_refine on Tue Sep 24 02:30:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/09_2024/7li8_23363.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/09_2024/7li8_23363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/09_2024/7li8_23363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/09_2024/7li8_23363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/09_2024/7li8_23363.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7li8_23363/09_2024/7li8_23363.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4104 2.51 5 N 962 2.21 5 O 1081 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6181 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4303 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 515} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 109 Unusual residues: {'D10': 1, 'D12': 3, 'HP6': 6, 'LNK': 1, 'R16': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 5.48, per 1000 atoms: 0.89 Number of scatterers: 6181 At special positions: 0 Unit cell: (68.688, 77.112, 122.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1081 8.00 N 962 7.00 C 4104 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: 1.60 Conformation dependent library (CDL) restraints added in 810.5 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: 31 helices and 8 sheets defined 51.0% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.679A 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 148 through 153 Processing helix chain 'A' and resid 159 through 176 removed outlier: 4.107A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 4.028A 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: 3.628A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 removed outlier: 3.769A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 301 removed outlier: 4.317A pdb=" N SER A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.660A pdb=" N GLY A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 359 through 389 removed outlier: 3.988A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.802A pdb=" N VAL A 397 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 415 removed outlier: 4.411A pdb=" N PHE A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 448 removed outlier: 4.117A pdb=" N ALA A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.842A pdb=" N THR A 482 " --> pdb=" O VAL A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 removed outlier: 4.382A pdb=" N LEU A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 515 removed outlier: 3.769A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 534 through 558 removed outlier: 3.641A pdb=" N ARG A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP A 541 " --> pdb=" O TRP A 537 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Proline residue: A 546 - end of helix Processing helix chain 'A' and resid 571 through 585 removed outlier: 4.187A pdb=" N ILE A 575 " --> pdb=" O PRO A 571 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 598 removed outlier: 3.813A pdb=" N ILE A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 613 removed outlier: 3.743A pdb=" N THR A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 4.165A pdb=" N TYR B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.956A 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 helix chain 'C' and resid 103 through 107 removed outlier: 3.519A pdb=" N THR C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.633A pdb=" N GLN B 24 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B 42 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 100 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.526A pdb=" N ILE B 67 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.526A pdb=" N ILE B 67 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.774A pdb=" N TYR C 73 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.774A pdb=" N TYR C 73 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 90 removed outlier: 3.561A pdb=" N SER C 89 " --> pdb=" O SER C 96 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 756 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: 1.60 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1811 1.34 - 1.46: 1452 1.46 - 1.58: 3037 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6349 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+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 1.56e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.50e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.33e+00 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.24e+00 ... (remaining 6344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 8193 1.08 - 2.16: 247 2.16 - 3.24: 65 3.24 - 4.32: 79 4.32 - 5.40: 12 Bond angle restraints: 8596 Sorted by residual: angle pdb=" N VAL A 102 " pdb=" CA VAL A 102 " pdb=" C VAL A 102 " ideal model delta sigma weight residual 113.53 109.27 4.26 9.80e-01 1.04e+00 1.89e+01 angle pdb=" N VAL A 92 " pdb=" CA VAL A 92 " pdb=" C VAL A 92 " ideal model delta sigma weight residual 113.71 110.54 3.17 9.50e-01 1.11e+00 1.11e+01 angle pdb=" N VAL A 446 " pdb=" CA VAL A 446 " pdb=" C VAL A 446 " ideal model delta sigma weight residual 112.96 109.70 3.26 1.00e+00 1.00e+00 1.07e+01 angle pdb=" C GLY B 121 " pdb=" N SER B 122 " pdb=" CA SER B 122 " ideal model delta sigma weight residual 120.38 124.54 -4.16 1.37e+00 5.33e-01 9.22e+00 angle pdb=" C MET B 127 " pdb=" N ASP B 128 " pdb=" CA ASP B 128 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.79e+00 ... (remaining 8591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.73: 3326 14.73 - 29.46: 272 29.46 - 44.19: 59 44.19 - 58.91: 9 58.91 - 73.64: 2 Dihedral angle restraints: 3668 sinusoidal: 1462 harmonic: 2206 Sorted by residual: dihedral pdb=" CB CYS B 41 " pdb=" SG CYS B 41 " pdb=" SG CYS B 115 " pdb=" CB CYS B 115 " ideal model delta sinusoidal sigma weight residual 93.00 166.64 -73.64 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CA TRP A 204 " pdb=" C TRP A 204 " pdb=" N ASN A 205 " pdb=" CA ASN A 205 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ASP A 87 " pdb=" CB ASP A 87 " pdb=" CG ASP A 87 " pdb=" OD1 ASP A 87 " ideal model delta sinusoidal sigma weight residual -30.00 -82.66 52.66 1 2.00e+01 2.50e-03 9.44e+00 ... (remaining 3665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 929 0.103 - 0.206: 12 0.206 - 0.309: 0 0.309 - 0.413: 0 0.413 - 0.516: 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 -1.88 -0.52 2.00e-02 2.50e+03 6.65e+02 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 7.05e-01 chirality pdb=" CB THR C 107 " pdb=" CA THR C 107 " pdb=" OG1 THR C 107 " pdb=" CG2 THR C 107 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 939 not shown) Planarity restraints: 1048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 338 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 339 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 130 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A 131 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 128 " -0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C ASP B 128 " 0.019 2.00e-02 2.50e+03 pdb=" O ASP B 128 " -0.007 2.00e-02 2.50e+03 pdb=" N TYR B 129 " -0.006 2.00e-02 2.50e+03 ... (remaining 1045 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1068 2.76 - 3.30: 5736 3.30 - 3.83: 9932 3.83 - 4.37: 10836 4.37 - 4.90: 19149 Nonbonded interactions: 46721 Sorted by model distance: nonbonded pdb=" OH TYR A 110 " pdb=" O VAL A 394 " model vdw 2.230 3.040 nonbonded pdb=" OG SER B 49 " pdb=" O PRO B 72 " model vdw 2.256 3.040 nonbonded pdb=" O LYS A 201 " pdb=" NE1 TRP B 52 " model vdw 2.296 3.120 nonbonded pdb=" O SER A 477 " pdb=" OG SER A 477 " model vdw 2.303 3.040 nonbonded pdb=" OG SER B 36 " pdb=" O LEU B 102 " model vdw 2.330 3.040 ... (remaining 46716 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.910 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 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 0.031 6349 Z= 0.132 Angle : 0.601 5.403 8596 Z= 0.300 Chirality : 0.041 0.516 942 Planarity : 0.003 0.033 1047 Dihedral : 10.905 69.682 2259 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.27), residues: 761 helix: -1.23 (0.23), residues: 353 sheet: -2.94 (0.51), residues: 82 loop : -2.92 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.000 TRP A 204 HIS 0.001 0.000 HIS A 223 PHE 0.013 0.000 PHE B 125 TYR 0.011 0.001 TYR A 175 ARG 0.001 0.000 ARG A 298 *********************** 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 153 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6008 (mmpt) cc_final: 0.5241 (ptmt) REVERT: A 152 ARG cc_start: 0.8690 (mmm-85) cc_final: 0.8428 (mmt90) REVERT: A 222 LEU cc_start: 0.7905 (tp) cc_final: 0.7315 (tp) REVERT: B 58 GLN cc_start: 0.8476 (tt0) cc_final: 0.8096 (tt0) REVERT: C 62 GLN cc_start: 0.8044 (tt0) cc_final: 0.7838 (tt0) REVERT: C 110 TYR cc_start: 0.7845 (m-80) cc_final: 0.7568 (m-80) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2079 time to fit residues: 40.1641 Evaluate side-chains 117 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 194 GLN A 354 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6349 Z= 0.317 Angle : 0.642 9.650 8596 Z= 0.323 Chirality : 0.042 0.230 942 Planarity : 0.004 0.032 1047 Dihedral : 4.993 57.891 946 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.58 % Allowed : 12.60 % Favored : 83.83 % 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: -1.99 (0.30), residues: 761 helix: -0.28 (0.26), residues: 349 sheet: -2.64 (0.51), residues: 92 loop : -2.00 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 271 HIS 0.004 0.001 HIS C 100 PHE 0.030 0.002 PHE A 287 TYR 0.024 0.002 TYR A 358 ARG 0.006 0.001 ARG B 59 *********************** 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 144 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6052 (mmpt) cc_final: 0.5220 (ptmt) REVERT: A 145 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7782 (t0) REVERT: A 222 LEU cc_start: 0.8051 (tp) cc_final: 0.7796 (tp) REVERT: A 548 PHE cc_start: 0.7931 (m-80) cc_final: 0.7675 (t80) REVERT: A 592 TYR cc_start: 0.8671 (t80) cc_final: 0.8380 (t80) REVERT: B 53 MET cc_start: 0.7489 (ttm) cc_final: 0.7189 (ttm) REVERT: C 110 TYR cc_start: 0.8023 (m-80) cc_final: 0.7761 (m-80) outliers start: 23 outliers final: 19 residues processed: 134 average time/residue: 0.1935 time to fit residues: 33.6638 Evaluate side-chains 124 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 54 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6349 Z= 0.183 Angle : 0.578 9.424 8596 Z= 0.287 Chirality : 0.040 0.240 942 Planarity : 0.004 0.030 1047 Dihedral : 4.795 57.602 946 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.89 % Allowed : 16.64 % Favored : 79.47 % 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: -1.36 (0.31), residues: 761 helix: 0.27 (0.28), residues: 348 sheet: -1.87 (0.56), residues: 86 loop : -1.90 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 271 HIS 0.002 0.000 HIS A 223 PHE 0.017 0.001 PHE A 377 TYR 0.037 0.002 TYR A 358 ARG 0.006 0.001 ARG C 85 *********************** 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 142 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6074 (mmpt) cc_final: 0.5201 (ptmt) REVERT: A 222 LEU cc_start: 0.8050 (tp) cc_final: 0.7812 (tp) REVERT: A 260 MET cc_start: 0.7573 (tmm) cc_final: 0.7190 (tmt) REVERT: A 370 MET cc_start: 0.8157 (tpp) cc_final: 0.7907 (tpp) REVERT: A 548 PHE cc_start: 0.7863 (m-80) cc_final: 0.7648 (t80) REVERT: A 592 TYR cc_start: 0.8673 (t80) cc_final: 0.8409 (t80) REVERT: B 53 MET cc_start: 0.7436 (ttm) cc_final: 0.7191 (ttm) REVERT: C 110 TYR cc_start: 0.7956 (m-80) cc_final: 0.7567 (m-10) outliers start: 25 outliers final: 16 residues processed: 134 average time/residue: 0.1731 time to fit residues: 31.0683 Evaluate side-chains 118 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6349 Z= 0.221 Angle : 0.587 9.424 8596 Z= 0.293 Chirality : 0.041 0.239 942 Planarity : 0.004 0.032 1047 Dihedral : 4.936 58.612 946 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.51 % Allowed : 17.73 % Favored : 77.76 % 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: -1.25 (0.31), residues: 761 helix: 0.31 (0.28), residues: 351 sheet: -1.58 (0.56), residues: 86 loop : -1.88 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 204 HIS 0.001 0.000 HIS A 235 PHE 0.021 0.001 PHE A 377 TYR 0.026 0.002 TYR B 120 ARG 0.005 0.001 ARG B 38 *********************** 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 141 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6074 (mmpt) cc_final: 0.5175 (ptmt) REVERT: A 260 MET cc_start: 0.7703 (tmm) cc_final: 0.7275 (tmt) REVERT: A 370 MET cc_start: 0.8256 (tpp) cc_final: 0.8036 (tpp) REVERT: A 548 PHE cc_start: 0.7969 (m-80) cc_final: 0.7749 (t80) REVERT: B 53 MET cc_start: 0.7564 (ttm) cc_final: 0.7148 (ttm) REVERT: C 27 SER cc_start: 0.6637 (OUTLIER) cc_final: 0.6099 (m) REVERT: C 102 MET cc_start: 0.7482 (tmm) cc_final: 0.7084 (tmm) REVERT: C 105 ASP cc_start: 0.8066 (t0) cc_final: 0.7842 (t0) REVERT: C 110 TYR cc_start: 0.8087 (m-80) cc_final: 0.7582 (m-10) outliers start: 29 outliers final: 23 residues processed: 133 average time/residue: 0.1878 time to fit residues: 33.1328 Evaluate side-chains 132 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6349 Z= 0.219 Angle : 0.586 9.403 8596 Z= 0.291 Chirality : 0.041 0.238 942 Planarity : 0.004 0.032 1047 Dihedral : 4.956 58.098 946 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.98 % Allowed : 17.73 % Favored : 77.29 % 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: -1.09 (0.31), residues: 761 helix: 0.52 (0.28), residues: 351 sheet: -1.46 (0.57), residues: 86 loop : -1.91 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 204 HIS 0.001 0.001 HIS A 223 PHE 0.021 0.001 PHE A 377 TYR 0.028 0.002 TYR B 120 ARG 0.002 0.000 ARG B 59 *********************** 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 146 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6066 (mmpt) cc_final: 0.5125 (ptmt) REVERT: A 260 MET cc_start: 0.7723 (tmm) cc_final: 0.7330 (tmt) REVERT: A 370 MET cc_start: 0.8300 (tpp) cc_final: 0.8095 (tpp) REVERT: A 385 TYR cc_start: 0.7477 (t80) cc_final: 0.7156 (t80) REVERT: A 464 ARG cc_start: 0.7180 (mmp80) cc_final: 0.4799 (tpp-160) REVERT: A 548 PHE cc_start: 0.7984 (m-80) cc_final: 0.7776 (t80) REVERT: C 62 GLN cc_start: 0.8781 (tt0) cc_final: 0.8225 (tt0) REVERT: C 71 LEU cc_start: 0.8540 (tp) cc_final: 0.8198 (tt) REVERT: C 105 ASP cc_start: 0.8039 (t0) cc_final: 0.7808 (t0) REVERT: C 110 TYR cc_start: 0.8108 (m-80) cc_final: 0.7550 (m-10) outliers start: 32 outliers final: 25 residues processed: 139 average time/residue: 0.1816 time to fit residues: 33.0540 Evaluate side-chains 129 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6349 Z= 0.193 Angle : 0.590 9.825 8596 Z= 0.292 Chirality : 0.041 0.240 942 Planarity : 0.003 0.032 1047 Dihedral : 4.898 58.206 946 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.51 % Allowed : 21.00 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.31), residues: 761 helix: 0.63 (0.28), residues: 351 sheet: -1.32 (0.58), residues: 86 loop : -1.86 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 204 HIS 0.002 0.001 HIS A 223 PHE 0.021 0.001 PHE A 377 TYR 0.030 0.001 TYR B 120 ARG 0.004 0.000 ARG C 38 *********************** 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 144 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6097 (mmpt) cc_final: 0.5163 (ptmt) REVERT: A 260 MET cc_start: 0.7672 (tmm) cc_final: 0.7282 (tmt) REVERT: A 301 THR cc_start: 0.7161 (p) cc_final: 0.6950 (p) REVERT: A 385 TYR cc_start: 0.7479 (t80) cc_final: 0.7149 (t80) REVERT: A 464 ARG cc_start: 0.7174 (mmp80) cc_final: 0.4818 (tpp-160) REVERT: C 71 LEU cc_start: 0.8532 (tp) cc_final: 0.8174 (tt) REVERT: C 99 ILE cc_start: 0.7559 (pt) cc_final: 0.6776 (tt) REVERT: C 105 ASP cc_start: 0.7996 (t0) cc_final: 0.7763 (t0) REVERT: C 110 TYR cc_start: 0.8069 (m-80) cc_final: 0.7473 (m-10) outliers start: 29 outliers final: 25 residues processed: 136 average time/residue: 0.1748 time to fit residues: 31.5035 Evaluate side-chains 134 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6349 Z= 0.217 Angle : 0.619 10.150 8596 Z= 0.305 Chirality : 0.041 0.239 942 Planarity : 0.003 0.031 1047 Dihedral : 4.980 57.781 946 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.82 % Allowed : 21.62 % Favored : 73.56 % 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: -0.89 (0.32), residues: 761 helix: 0.62 (0.28), residues: 351 sheet: -1.31 (0.54), residues: 97 loop : -1.73 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 204 HIS 0.003 0.001 HIS C 100 PHE 0.023 0.001 PHE A 377 TYR 0.038 0.002 TYR A 358 ARG 0.005 0.000 ARG B 38 *********************** 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 150 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6101 (mmpt) cc_final: 0.5184 (ptmt) REVERT: A 260 MET cc_start: 0.7701 (tmm) cc_final: 0.7332 (tmt) REVERT: A 410 TYR cc_start: 0.7631 (m-80) cc_final: 0.7421 (m-80) REVERT: A 464 ARG cc_start: 0.7191 (mmp80) cc_final: 0.4889 (tpp-160) REVERT: A 548 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6681 (t80) REVERT: B 47 ARG cc_start: 0.7602 (mtm180) cc_final: 0.7279 (mtm-85) REVERT: B 53 MET cc_start: 0.7389 (ttt) cc_final: 0.7133 (ttm) REVERT: C 71 LEU cc_start: 0.8538 (tp) cc_final: 0.8302 (tt) REVERT: C 99 ILE cc_start: 0.7279 (pt) cc_final: 0.6411 (tt) outliers start: 31 outliers final: 28 residues processed: 140 average time/residue: 0.1902 time to fit residues: 35.4938 Evaluate side-chains 141 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 0.0050 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6349 Z= 0.206 Angle : 0.641 10.773 8596 Z= 0.312 Chirality : 0.041 0.240 942 Planarity : 0.004 0.031 1047 Dihedral : 5.003 58.202 946 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.51 % Allowed : 22.24 % Favored : 73.25 % 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: -0.84 (0.31), residues: 761 helix: 0.67 (0.28), residues: 351 sheet: -1.22 (0.56), residues: 86 loop : -1.73 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 204 HIS 0.005 0.001 HIS C 100 PHE 0.023 0.001 PHE A 377 TYR 0.037 0.002 TYR A 358 ARG 0.006 0.000 ARG B 38 *********************** 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 145 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6095 (mmpt) cc_final: 0.5165 (ptmt) REVERT: A 103 TRP cc_start: 0.7627 (t60) cc_final: 0.7357 (t60) REVERT: A 260 MET cc_start: 0.7701 (tmm) cc_final: 0.7328 (tmt) REVERT: A 385 TYR cc_start: 0.7489 (t80) cc_final: 0.7188 (t80) REVERT: A 410 TYR cc_start: 0.7617 (m-80) cc_final: 0.7394 (m-80) REVERT: A 464 ARG cc_start: 0.7130 (mmp80) cc_final: 0.4875 (tpp-160) REVERT: B 38 ARG cc_start: 0.8122 (tpp80) cc_final: 0.7851 (tpp80) REVERT: B 47 ARG cc_start: 0.7608 (mtm180) cc_final: 0.7297 (mtm-85) REVERT: C 71 LEU cc_start: 0.8487 (tp) cc_final: 0.8200 (tt) outliers start: 29 outliers final: 27 residues processed: 136 average time/residue: 0.1318 time to fit residues: 24.0654 Evaluate side-chains 138 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6349 Z= 0.206 Angle : 0.649 11.762 8596 Z= 0.315 Chirality : 0.041 0.228 942 Planarity : 0.004 0.031 1047 Dihedral : 4.963 57.735 946 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.67 % Allowed : 22.08 % Favored : 73.25 % 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: -0.81 (0.31), residues: 761 helix: 0.73 (0.28), residues: 350 sheet: -1.13 (0.54), residues: 98 loop : -1.79 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 204 HIS 0.004 0.001 HIS C 100 PHE 0.023 0.001 PHE A 377 TYR 0.035 0.002 TYR A 358 ARG 0.005 0.000 ARG B 38 *********************** 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 147 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6086 (mmpt) cc_final: 0.5150 (ptmt) REVERT: A 260 MET cc_start: 0.7722 (tmm) cc_final: 0.7347 (tmt) REVERT: A 301 THR cc_start: 0.7289 (p) cc_final: 0.7072 (p) REVERT: A 328 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7821 (t0) REVERT: A 385 TYR cc_start: 0.7524 (t80) cc_final: 0.7124 (t80) REVERT: A 410 TYR cc_start: 0.7626 (m-80) cc_final: 0.7395 (m-80) REVERT: A 464 ARG cc_start: 0.7095 (mmp80) cc_final: 0.4852 (tpp-160) REVERT: A 548 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6576 (t80) REVERT: B 38 ARG cc_start: 0.8026 (tpp80) cc_final: 0.7738 (tpp80) REVERT: B 47 ARG cc_start: 0.7630 (mtm180) cc_final: 0.7374 (mtm-85) REVERT: C 71 LEU cc_start: 0.8514 (tp) cc_final: 0.8228 (tt) outliers start: 30 outliers final: 28 residues processed: 136 average time/residue: 0.1821 time to fit residues: 33.1008 Evaluate side-chains 141 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 6 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6349 Z= 0.214 Angle : 0.669 12.044 8596 Z= 0.324 Chirality : 0.041 0.236 942 Planarity : 0.004 0.031 1047 Dihedral : 4.960 57.753 946 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.82 % Allowed : 22.08 % Favored : 73.09 % 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: -0.76 (0.32), residues: 761 helix: 0.73 (0.28), residues: 351 sheet: -1.04 (0.55), residues: 98 loop : -1.75 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 59 HIS 0.004 0.001 HIS C 100 PHE 0.023 0.001 PHE A 377 TYR 0.035 0.002 TYR A 358 ARG 0.005 0.000 ARG B 38 ********************** 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 147 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6087 (mmpt) cc_final: 0.5169 (ptmt) REVERT: A 260 MET cc_start: 0.7740 (tmm) cc_final: 0.7361 (tmt) REVERT: A 301 THR cc_start: 0.7327 (p) cc_final: 0.7105 (p) REVERT: A 328 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7791 (t0) REVERT: A 385 TYR cc_start: 0.7563 (t80) cc_final: 0.7078 (t80) REVERT: A 410 TYR cc_start: 0.7638 (m-80) cc_final: 0.7401 (m-80) REVERT: A 464 ARG cc_start: 0.7064 (mmp80) cc_final: 0.4834 (tpp-160) REVERT: A 548 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6698 (t80) REVERT: B 38 ARG cc_start: 0.8027 (tpp80) cc_final: 0.7710 (tpp80) REVERT: B 47 ARG cc_start: 0.7687 (mtm180) cc_final: 0.7433 (mtm-85) REVERT: B 53 MET cc_start: 0.7348 (ttt) cc_final: 0.7027 (ttm) REVERT: C 71 LEU cc_start: 0.8486 (tp) cc_final: 0.8216 (tt) outliers start: 31 outliers final: 28 residues processed: 136 average time/residue: 0.1850 time to fit residues: 33.2118 Evaluate side-chains 144 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 204 TRP Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.171817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144870 restraints weight = 8647.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147110 restraints weight = 6457.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.148744 restraints weight = 5353.387| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6349 Z= 0.216 Angle : 0.670 11.795 8596 Z= 0.324 Chirality : 0.041 0.234 942 Planarity : 0.004 0.031 1047 Dihedral : 4.979 57.896 946 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.82 % Allowed : 22.40 % Favored : 72.78 % 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: -0.72 (0.32), residues: 761 helix: 0.76 (0.28), residues: 351 sheet: -1.04 (0.54), residues: 99 loop : -1.72 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 59 HIS 0.004 0.001 HIS C 100 PHE 0.023 0.001 PHE A 377 TYR 0.035 0.002 TYR A 358 ARG 0.005 0.000 ARG B 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1688.69 seconds wall clock time: 33 minutes 43.48 seconds (2023.48 seconds total)