Starting phenix.real_space_refine on Tue Mar 11 20:27:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7li8_23363/03_2025/7li8_23363.cif Found real_map, /net/cci-nas-00/data/ceres_data/7li8_23363/03_2025/7li8_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/cci-nas-00/data/ceres_data/7li8_23363/03_2025/7li8_23363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7li8_23363/03_2025/7li8_23363.map" model { file = "/net/cci-nas-00/data/ceres_data/7li8_23363/03_2025/7li8_23363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7li8_23363/03_2025/7li8_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-5624/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: 5.05, per 1000 atoms: 0.82 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: 1.75 Conformation dependent library (CDL) restraints added in 866.3 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: 0.64 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: 1.58 Time building geometry restraints manager: 2.01 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: 3.940 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.970 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.290 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.644 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: 0.2132 time to fit residues: 41.5558 Evaluate side-chains 117 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.154069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.119939 restraints weight = 10121.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.123940 restraints weight = 6353.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.126687 restraints weight = 4715.007| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6349 Z= 0.316 Angle : 0.650 9.750 8596 Z= 0.325 Chirality : 0.042 0.228 942 Planarity : 0.004 0.032 1047 Dihedral : 5.017 57.905 946 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.58 % Allowed : 12.29 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.30), residues: 761 helix: -0.35 (0.26), residues: 353 sheet: -2.64 (0.50), residues: 92 loop : -2.11 (0.36), residues: 316 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 0.032 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 145 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6020 (mmpt) cc_final: 0.5201 (ptmt) REVERT: A 145 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7818 (t0) REVERT: A 548 PHE cc_start: 0.7924 (m-80) cc_final: 0.7660 (t80) REVERT: A 592 TYR cc_start: 0.8678 (t80) cc_final: 0.8423 (t80) REVERT: B 53 MET cc_start: 0.7443 (ttm) cc_final: 0.7196 (ttm) REVERT: C 110 TYR cc_start: 0.7913 (m-80) cc_final: 0.7700 (m-80) outliers start: 23 outliers final: 19 residues processed: 135 average time/residue: 0.1884 time to fit residues: 33.4793 Evaluate side-chains 126 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 42 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.152536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.118083 restraints weight = 10381.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.122005 restraints weight = 6692.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.124643 restraints weight = 5052.154| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6349 Z= 0.229 Angle : 0.594 9.317 8596 Z= 0.296 Chirality : 0.041 0.236 942 Planarity : 0.004 0.032 1047 Dihedral : 4.931 57.430 946 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.67 % Allowed : 16.64 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.47 (0.31), residues: 761 helix: 0.17 (0.27), residues: 352 sheet: -1.83 (0.56), residues: 87 loop : -2.00 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 204 HIS 0.003 0.001 HIS A 223 PHE 0.019 0.001 PHE A 377 TYR 0.040 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 147 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.6017 (mmpt) cc_final: 0.5147 (ptmt) REVERT: A 260 MET cc_start: 0.7762 (tmm) cc_final: 0.7369 (tmt) REVERT: A 538 ARG cc_start: 0.8658 (mtp180) cc_final: 0.8443 (mtm110) REVERT: A 548 PHE cc_start: 0.7979 (m-80) cc_final: 0.7704 (t80) REVERT: A 592 TYR cc_start: 0.8690 (t80) cc_final: 0.8459 (t80) REVERT: B 53 MET cc_start: 0.7521 (ttm) cc_final: 0.7305 (ttm) REVERT: C 110 TYR cc_start: 0.7880 (m-80) cc_final: 0.7435 (m-10) outliers start: 30 outliers final: 22 residues processed: 137 average time/residue: 0.1913 time to fit residues: 34.8839 Evaluate side-chains 125 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 130 ILE 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 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 24 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 65 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 24 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.148102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.116799 restraints weight = 10248.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120376 restraints weight = 6810.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.122831 restraints weight = 5226.996| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6349 Z= 0.166 Angle : 0.568 9.480 8596 Z= 0.281 Chirality : 0.040 0.242 942 Planarity : 0.003 0.031 1047 Dihedral : 4.783 58.714 946 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.11 % Allowed : 19.13 % 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: -1.23 (0.31), residues: 761 helix: 0.38 (0.28), residues: 352 sheet: -1.66 (0.56), residues: 85 loop : -1.91 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 151 HIS 0.002 0.000 HIS A 223 PHE 0.020 0.001 PHE A 377 TYR 0.029 0.001 TYR B 120 ARG 0.004 0.000 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 136 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5960 (mmpt) cc_final: 0.5110 (ptmt) REVERT: A 260 MET cc_start: 0.7703 (tmm) cc_final: 0.7331 (tmt) REVERT: A 385 TYR cc_start: 0.7321 (t80) cc_final: 0.6951 (t80) REVERT: A 548 PHE cc_start: 0.7923 (m-80) cc_final: 0.7714 (t80) REVERT: C 110 TYR cc_start: 0.7827 (m-80) cc_final: 0.7439 (m-10) outliers start: 20 outliers final: 16 residues processed: 132 average time/residue: 0.1858 time to fit residues: 32.4326 Evaluate side-chains 121 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 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 446 VAL Chi-restraints excluded: chain A residue 604 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 21 optimal weight: 0.3980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** A 111 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.159485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132578 restraints weight = 9133.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.134559 restraints weight = 6962.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.136309 restraints weight = 5813.849| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6349 Z= 0.254 Angle : 0.612 9.384 8596 Z= 0.305 Chirality : 0.041 0.238 942 Planarity : 0.004 0.032 1047 Dihedral : 5.055 57.935 946 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.82 % Allowed : 17.73 % Favored : 77.45 % 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: -1.15 (0.31), residues: 761 helix: 0.49 (0.28), residues: 352 sheet: -1.57 (0.54), residues: 86 loop : -1.95 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 204 HIS 0.004 0.001 HIS A 223 PHE 0.022 0.001 PHE A 377 TYR 0.028 0.002 TYR B 120 ARG 0.002 0.000 ARG A 152 *********************** 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 144 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5432 (mmpt) cc_final: 0.4833 (ptmt) REVERT: A 260 MET cc_start: 0.7928 (tmm) cc_final: 0.7655 (tmt) REVERT: C 71 LEU cc_start: 0.8637 (tp) cc_final: 0.8344 (tt) outliers start: 31 outliers final: 26 residues processed: 134 average time/residue: 0.1670 time to fit residues: 30.3213 Evaluate side-chains 127 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 421 THR 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 553 ILE Chi-restraints excluded: chain A residue 566 PHE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.160349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133364 restraints weight = 9218.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.135740 restraints weight = 7027.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137392 restraints weight = 5855.086| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3778 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= 0.181 Angle : 0.598 9.807 8596 Z= 0.295 Chirality : 0.041 0.240 942 Planarity : 0.003 0.032 1047 Dihedral : 4.922 58.306 946 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.20 % Allowed : 21.15 % Favored : 74.65 % 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 (0.31), residues: 761 helix: 0.65 (0.28), residues: 351 sheet: -1.40 (0.56), residues: 86 loop : -1.84 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 204 HIS 0.003 0.001 HIS A 223 PHE 0.021 0.001 PHE A 377 TYR 0.042 0.002 TYR A 358 ARG 0.002 0.000 ARG A 462 *********************** 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 139 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5519 (mmpt) cc_final: 0.4905 (ptmt) REVERT: A 260 MET cc_start: 0.7848 (tmm) cc_final: 0.7612 (tmt) REVERT: A 464 ARG cc_start: 0.7272 (mmp80) cc_final: 0.5124 (tpp-160) REVERT: A 548 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.5969 (t80) REVERT: C 71 LEU cc_start: 0.8611 (tp) cc_final: 0.8321 (tt) outliers start: 27 outliers final: 22 residues processed: 132 average time/residue: 0.1814 time to fit residues: 32.1674 Evaluate side-chains 126 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 548 PHE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 604 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 68 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.171208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.144916 restraints weight = 8852.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.147529 restraints weight = 6459.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.149169 restraints weight = 5208.877| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6349 Z= 0.205 Angle : 0.627 10.204 8596 Z= 0.306 Chirality : 0.041 0.241 942 Planarity : 0.003 0.031 1047 Dihedral : 4.907 57.901 946 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.89 % Allowed : 22.71 % Favored : 73.41 % 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: -0.89 (0.31), residues: 761 helix: 0.67 (0.28), residues: 352 sheet: -1.37 (0.56), residues: 87 loop : -1.79 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 59 HIS 0.003 0.001 HIS A 223 PHE 0.022 0.001 PHE A 377 TYR 0.024 0.001 TYR A 385 ARG 0.006 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 139 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5405 (mmpt) cc_final: 0.4871 (ptmt) REVERT: A 260 MET cc_start: 0.7859 (tmm) cc_final: 0.7650 (tmt) REVERT: A 464 ARG cc_start: 0.7275 (mmp80) cc_final: 0.5193 (tpp-160) REVERT: A 548 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.5989 (t80) REVERT: C 71 LEU cc_start: 0.8630 (tp) cc_final: 0.8342 (tt) outliers start: 25 outliers final: 23 residues processed: 131 average time/residue: 0.1775 time to fit residues: 31.0312 Evaluate side-chains 134 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 548 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 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 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** ** 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** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.163045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.136567 restraints weight = 8986.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.138946 restraints weight = 6775.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140479 restraints weight = 5579.779| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6349 Z= 0.221 Angle : 0.642 11.344 8596 Z= 0.312 Chirality : 0.042 0.236 942 Planarity : 0.004 0.031 1047 Dihedral : 4.951 57.645 946 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.04 % Allowed : 22.71 % 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 (0.32), residues: 761 helix: 0.68 (0.28), residues: 351 sheet: -1.21 (0.54), residues: 98 loop : -1.71 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 204 HIS 0.003 0.001 HIS A 223 PHE 0.025 0.001 PHE A 586 TYR 0.024 0.002 TYR A 385 ARG 0.005 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 137 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5414 (mmpt) cc_final: 0.4860 (ptmt) REVERT: A 260 MET cc_start: 0.7904 (tmm) cc_final: 0.7683 (tmt) REVERT: A 464 ARG cc_start: 0.7233 (mmp80) cc_final: 0.5216 (tpp-160) REVERT: B 47 ARG cc_start: 0.7182 (mtm180) cc_final: 0.6876 (mtm-85) REVERT: C 71 LEU cc_start: 0.8612 (tp) cc_final: 0.8324 (tt) outliers start: 26 outliers final: 24 residues processed: 129 average time/residue: 0.1972 time to fit residues: 33.4495 Evaluate side-chains 132 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 134 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 GLU 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 53 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 101 GLN C 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.165549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.139045 restraints weight = 8922.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141245 restraints weight = 6705.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.143043 restraints weight = 5542.765| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6349 Z= 0.218 Angle : 0.664 11.638 8596 Z= 0.322 Chirality : 0.042 0.242 942 Planarity : 0.004 0.031 1047 Dihedral : 4.945 58.136 946 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.35 % Allowed : 22.55 % 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: -0.78 (0.31), residues: 761 helix: 0.75 (0.28), residues: 351 sheet: -1.18 (0.56), residues: 87 loop : -1.75 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 204 HIS 0.001 0.000 HIS A 223 PHE 0.021 0.001 PHE A 377 TYR 0.028 0.001 TYR B 120 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 138 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5363 (mmpt) cc_final: 0.4825 (ptmt) REVERT: A 260 MET cc_start: 0.7906 (tmm) cc_final: 0.7692 (tmt) REVERT: A 464 ARG cc_start: 0.7207 (mmp80) cc_final: 0.5223 (tpp-160) REVERT: A 548 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.6234 (t80) REVERT: B 47 ARG cc_start: 0.7174 (mtm180) cc_final: 0.6958 (mtm-85) REVERT: C 71 LEU cc_start: 0.8593 (tp) cc_final: 0.8325 (tt) outliers start: 28 outliers final: 25 residues processed: 129 average time/residue: 0.1844 time to fit residues: 31.2819 Evaluate side-chains 130 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 548 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 134 THR 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: 0.9990 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 101 GLN C 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.165304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.138309 restraints weight = 9062.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.140664 restraints weight = 6825.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142018 restraints weight = 5633.356| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6349 Z= 0.229 Angle : 0.680 12.026 8596 Z= 0.331 Chirality : 0.042 0.243 942 Planarity : 0.004 0.030 1047 Dihedral : 4.982 57.658 946 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.20 % Allowed : 22.55 % 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: -0.75 (0.31), residues: 761 helix: 0.79 (0.28), residues: 346 sheet: -1.21 (0.55), residues: 87 loop : -1.72 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 204 HIS 0.001 0.000 HIS A 143 PHE 0.021 0.001 PHE A 377 TYR 0.025 0.002 TYR A 385 ARG 0.005 0.000 ARG C 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 135 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 LYS cc_start: 0.5433 (mmpt) cc_final: 0.4874 (ptmt) REVERT: A 464 ARG cc_start: 0.7211 (mmp80) cc_final: 0.5224 (tpp-160) REVERT: A 548 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6391 (t80) REVERT: B 47 ARG cc_start: 0.7240 (mtm180) cc_final: 0.7019 (mtm-85) REVERT: C 71 LEU cc_start: 0.8611 (tp) cc_final: 0.8337 (tt) REVERT: C 116 LYS cc_start: 0.5965 (mtmt) cc_final: 0.5259 (ttmt) outliers start: 27 outliers final: 24 residues processed: 126 average time/residue: 0.1844 time to fit residues: 31.1800 Evaluate side-chains 130 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 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 548 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 134 THR Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 104 GLU 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 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- 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 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.164142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.137208 restraints weight = 9171.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.139640 restraints weight = 6896.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140933 restraints weight = 5662.570| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6349 Z= 0.212 Angle : 0.673 11.909 8596 Z= 0.327 Chirality : 0.042 0.248 942 Planarity : 0.004 0.030 1047 Dihedral : 4.942 57.674 946 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.20 % Allowed : 22.08 % Favored : 73.72 % 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: -0.68 (0.31), residues: 761 helix: 0.86 (0.28), residues: 346 sheet: -1.17 (0.55), residues: 87 loop : -1.68 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 204 HIS 0.001 0.000 HIS A 235 PHE 0.021 0.001 PHE A 377 TYR 0.025 0.001 TYR A 385 ARG 0.003 0.000 ARG B 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2248.30 seconds wall clock time: 40 minutes 6.05 seconds (2406.05 seconds total)