Starting phenix.real_space_refine on Tue Feb 11 18:42:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7li9_23364/02_2025/7li9_23364.cif Found real_map, /net/cci-nas-00/data/ceres_data/7li9_23364/02_2025/7li9_23364.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/7li9_23364/02_2025/7li9_23364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7li9_23364/02_2025/7li9_23364.map" model { file = "/net/cci-nas-00/data/ceres_data/7li9_23364/02_2025/7li9_23364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7li9_23364/02_2025/7li9_23364.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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 C 4090 2.51 5 N 966 2.21 5 O 1083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6174 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4305 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 23, 'TRANS': 515} 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: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 100 Unusual residues: {' CL': 1, 'D10': 3, 'D12': 2, 'HP6': 2, 'LNK': 1, 'SRO': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Time building chain proxies: 5.16, per 1000 atoms: 0.84 Number of scatterers: 6174 At special positions: 0 Unit cell: (68.929, 74.5395, 122.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 34 16.00 O 1083 8.00 N 966 7.00 C 4090 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: 1.84 Conformation dependent library (CDL) restraints added in 856.0 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: 30 helices and 7 sheets defined 52.4% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 99 through 113 removed outlier: 4.928A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 129 through 144 Processing helix chain 'A' and resid 148 through 153 removed outlier: 3.657A pdb=" N TRP A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 190 removed outlier: 4.148A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.567A pdb=" N SER A 199 " --> pdb=" O PRO A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 252 through 268 removed outlier: 3.770A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 removed outlier: 3.676A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.771A pdb=" N ILE A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.957A pdb=" N LYS A 319 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 320 " --> pdb=" O TRP A 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 316 through 320' Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.738A pdb=" N GLY A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 349 removed outlier: 3.774A pdb=" N ALA A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 391 Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.734A pdb=" N VAL A 397 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 removed outlier: 4.068A pdb=" N ALA A 411 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 451 removed outlier: 3.587A pdb=" N GLY A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 450 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.632A pdb=" N VAL A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 515 removed outlier: 4.036A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 529 Processing helix chain 'A' and resid 534 through 558 removed outlier: 3.514A pdb=" N ARG A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 541 " --> pdb=" O TRP A 537 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 5.287A 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 572 through 585 removed outlier: 3.841A pdb=" N ILE A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 600 removed outlier: 3.551A pdb=" N LEU A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 599 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR A 600 " --> pdb=" O ARG A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 613 removed outlier: 3.583A pdb=" N THR A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 4.092A pdb=" N TYR B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 51' Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.689A pdb=" N SER B 44 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 66 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: 3.696A pdb=" N TYR C 73 " --> pdb=" O ASN C 77 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN C 113 " --> pdb=" O ASN C 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 89 removed outlier: 3.522A pdb=" N SER C 96 " --> pdb=" O SER C 89 " (cutoff:3.500A) 268 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: 1.64 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1817 1.34 - 1.46: 1646 1.46 - 1.58: 2835 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6347 Sorted by residual: bond pdb=" CD1 SRO A 910 " pdb=" NE1 SRO A 910 " ideal model delta sigma weight residual 1.377 1.324 0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" CD1 SRO A 909 " pdb=" NE1 SRO A 909 " ideal model delta sigma weight residual 1.377 1.324 0.053 2.00e-02 2.50e+03 7.01e+00 bond pdb=" CD2 SRO A 909 " pdb=" CE2 SRO A 909 " ideal model delta sigma weight residual 1.419 1.370 0.049 2.00e-02 2.50e+03 6.02e+00 bond pdb=" CD2 SRO A 910 " pdb=" CE2 SRO A 910 " ideal model delta sigma weight residual 1.419 1.370 0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" CB SRO A 910 " pdb=" CG SRO A 910 " ideal model delta sigma weight residual 1.498 1.527 -0.029 2.00e-02 2.50e+03 2.14e+00 ... (remaining 6342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 8270 1.10 - 2.20: 212 2.20 - 3.30: 61 3.30 - 4.40: 51 4.40 - 5.50: 15 Bond angle restraints: 8609 Sorted by residual: angle pdb=" C ALA C 74 " pdb=" N ALA C 75 " pdb=" CA ALA C 75 " ideal model delta sigma weight residual 121.54 126.26 -4.72 1.91e+00 2.74e-01 6.10e+00 angle pdb=" N SER B 122 " pdb=" CA SER B 122 " pdb=" C SER B 122 " ideal model delta sigma weight residual 111.11 113.76 -2.65 1.20e+00 6.94e-01 4.88e+00 angle pdb=" N PHE A 287 " pdb=" CA PHE A 287 " pdb=" C PHE A 287 " ideal model delta sigma weight residual 109.81 114.29 -4.48 2.21e+00 2.05e-01 4.11e+00 angle pdb=" N ILE B 67 " pdb=" CA ILE B 67 " pdb=" C ILE B 67 " ideal model delta sigma weight residual 111.48 109.58 1.90 9.40e-01 1.13e+00 4.09e+00 angle pdb=" N PRO A 403 " pdb=" CA PRO A 403 " pdb=" C PRO A 403 " ideal model delta sigma weight residual 114.68 112.59 2.09 1.04e+00 9.25e-01 4.03e+00 ... (remaining 8604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.59: 3431 20.59 - 41.17: 187 41.17 - 61.76: 19 61.76 - 82.35: 6 82.35 - 102.94: 8 Dihedral angle restraints: 3651 sinusoidal: 1445 harmonic: 2206 Sorted by residual: dihedral pdb=" C1 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sinusoidal sigma weight residual -175.09 -72.15 -102.94 1 3.00e+01 1.11e-03 1.31e+01 dihedral pdb=" C1 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" C4 NAG D 2 " ideal model delta sinusoidal sigma weight residual -52.39 49.80 -102.19 1 3.00e+01 1.11e-03 1.29e+01 dihedral pdb=" N2 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" O3 NAG D 2 " ideal model delta sinusoidal sigma weight residual 62.25 164.33 -102.08 1 3.00e+01 1.11e-03 1.29e+01 ... (remaining 3648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 912 0.087 - 0.175: 30 0.175 - 0.262: 0 0.262 - 0.350: 0 0.350 - 0.437: 1 Chirality restraints: 943 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 -1.96 -0.44 2.00e-02 2.50e+03 4.78e+02 chirality pdb=" CA ILE C 41 " pdb=" N ILE C 41 " pdb=" C ILE C 41 " pdb=" CB ILE C 41 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA VAL C 82 " pdb=" N VAL C 82 " pdb=" C VAL C 82 " pdb=" CB VAL C 82 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 940 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 338 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A 339 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 287 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 288 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 498 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO A 499 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 499 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 499 " 0.016 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1976 2.83 - 3.35: 5574 3.35 - 3.86: 9998 3.86 - 4.38: 11021 4.38 - 4.90: 19411 Nonbonded interactions: 47980 Sorted by model distance: nonbonded pdb=" O SER A 214 " pdb=" OG SER A 214 " model vdw 2.309 3.040 nonbonded pdb=" O SER B 49 " pdb=" OG SER B 49 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR A 110 " pdb=" O ALA A 398 " model vdw 2.321 3.040 nonbonded pdb=" O SER A 190 " pdb=" OG SER A 190 " model vdw 2.330 3.040 nonbonded pdb=" NE2 GLN C 114 " pdb=" O SER C 119 " model vdw 2.345 3.120 ... (remaining 47975 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: 11.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 18.420 Find NCS groups from input model: 0.050 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 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 : 0.003 0.053 6347 Z= 0.172 Angle : 0.559 5.496 8609 Z= 0.269 Chirality : 0.040 0.437 943 Planarity : 0.003 0.037 1049 Dihedral : 13.558 102.936 2242 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: -3.52 (0.26), residues: 761 helix: -1.06 (0.24), residues: 349 sheet: -2.81 (0.55), residues: 76 loop : -3.68 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 317 HIS 0.002 0.000 HIS C 100 PHE 0.007 0.001 PHE A 287 TYR 0.008 0.001 TYR A 175 ARG 0.001 0.000 ARG C 38 *********************** 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 162 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 VAL cc_start: 0.8386 (m) cc_final: 0.8005 (p) REVERT: C 62 GLN cc_start: 0.8423 (tt0) cc_final: 0.8184 (tt0) REVERT: C 114 GLN cc_start: 0.8014 (pp30) cc_final: 0.7472 (pp30) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2035 time to fit residues: 41.9455 Evaluate side-chains 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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: 2.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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** A 194 GLN A 254 GLN A 332 GLN B 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.140748 restraints weight = 8982.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.141946 restraints weight = 6884.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.143532 restraints weight = 5632.737| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6347 Z= 0.242 Angle : 0.611 8.616 8609 Z= 0.306 Chirality : 0.042 0.202 943 Planarity : 0.004 0.039 1049 Dihedral : 8.748 67.518 928 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.33 % Allowed : 13.20 % Favored : 84.47 % 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: -2.36 (0.29), residues: 761 helix: -0.08 (0.27), residues: 350 sheet: -2.60 (0.58), residues: 84 loop : -2.98 (0.30), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 537 HIS 0.002 0.001 HIS A 235 PHE 0.022 0.002 PHE A 531 TYR 0.025 0.002 TYR A 312 ARG 0.004 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 116 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.8662 (mmt-90) cc_final: 0.8285 (mmm-85) REVERT: A 295 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8159 (tt) REVERT: C 114 GLN cc_start: 0.8439 (pp30) cc_final: 0.7831 (pp30) outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 0.1842 time to fit residues: 26.5444 Evaluate side-chains 105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN C 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.148891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126138 restraints weight = 9196.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125817 restraints weight = 7993.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128193 restraints weight = 7417.055| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 6347 Z= 0.311 Angle : 0.611 7.994 8609 Z= 0.308 Chirality : 0.043 0.141 943 Planarity : 0.004 0.040 1049 Dihedral : 6.930 56.540 928 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.42 % Allowed : 16.61 % Favored : 79.97 % 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: -2.13 (0.29), residues: 761 helix: 0.05 (0.27), residues: 349 sheet: -2.52 (0.52), residues: 96 loop : -2.75 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 130 HIS 0.002 0.001 HIS A 235 PHE 0.027 0.002 PHE A 428 TYR 0.012 0.002 TYR A 175 ARG 0.012 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 126 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.572 Fit side-chains REVERT: A 295 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8292 (tt) REVERT: A 410 TYR cc_start: 0.8290 (m-80) cc_final: 0.8079 (m-80) REVERT: A 423 PHE cc_start: 0.7447 (m-80) cc_final: 0.7009 (m-10) REVERT: C 114 GLN cc_start: 0.8978 (pp30) cc_final: 0.8695 (pp30) REVERT: C 116 LYS cc_start: 0.6598 (mttt) cc_final: 0.6109 (mttt) outliers start: 22 outliers final: 15 residues processed: 115 average time/residue: 0.1796 time to fit residues: 27.6940 Evaluate side-chains 108 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 535 TRP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.123986 restraints weight = 9337.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124112 restraints weight = 6964.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125047 restraints weight = 6385.502| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6347 Z= 0.245 Angle : 0.565 7.940 8609 Z= 0.285 Chirality : 0.041 0.143 943 Planarity : 0.004 0.039 1049 Dihedral : 6.245 54.663 928 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.88 % Allowed : 18.17 % Favored : 77.95 % 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: -1.79 (0.30), residues: 761 helix: 0.29 (0.28), residues: 349 sheet: -2.36 (0.53), residues: 94 loop : -2.51 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 130 HIS 0.001 0.001 HIS A 235 PHE 0.029 0.002 PHE A 531 TYR 0.033 0.001 TYR B 46 ARG 0.007 0.001 ARG A 234 *********************** 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 122 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.8644 (ttp) cc_final: 0.8439 (tmm) REVERT: A 295 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8370 (tt) REVERT: C 37 GLN cc_start: 0.8213 (mp10) cc_final: 0.7944 (mp10) REVERT: C 114 GLN cc_start: 0.8951 (pp30) cc_final: 0.8627 (pp30) outliers start: 25 outliers final: 13 residues processed: 113 average time/residue: 0.1652 time to fit residues: 25.5544 Evaluate side-chains 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 55 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.145436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122598 restraints weight = 9199.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121974 restraints weight = 8317.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122910 restraints weight = 8090.989| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6347 Z= 0.233 Angle : 0.565 8.129 8609 Z= 0.284 Chirality : 0.041 0.141 943 Planarity : 0.003 0.039 1049 Dihedral : 5.650 46.251 928 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.42 % Allowed : 20.19 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.30), residues: 761 helix: 0.37 (0.28), residues: 349 sheet: -2.00 (0.57), residues: 85 loop : -2.38 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 130 HIS 0.002 0.001 HIS C 100 PHE 0.024 0.002 PHE A 531 TYR 0.021 0.001 TYR A 142 ARG 0.006 0.000 ARG A 234 *********************** 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 118 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: C 102 MET cc_start: 0.7064 (tmm) cc_final: 0.6703 (ttp) REVERT: C 114 GLN cc_start: 0.9019 (pp30) cc_final: 0.8696 (pp30) outliers start: 22 outliers final: 20 residues processed: 111 average time/residue: 0.1526 time to fit residues: 23.5791 Evaluate side-chains 104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 0.0060 chunk 1 optimal weight: 0.0370 chunk 34 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.147619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.125261 restraints weight = 9102.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.125086 restraints weight = 8333.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127081 restraints weight = 7945.866| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6347 Z= 0.179 Angle : 0.540 8.588 8609 Z= 0.269 Chirality : 0.040 0.143 943 Planarity : 0.003 0.038 1049 Dihedral : 5.135 36.364 928 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.42 % Allowed : 20.81 % Favored : 75.78 % 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: -1.32 (0.31), residues: 761 helix: 0.52 (0.28), residues: 349 sheet: -1.80 (0.58), residues: 85 loop : -2.19 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 130 HIS 0.001 0.001 HIS A 235 PHE 0.022 0.001 PHE A 531 TYR 0.015 0.001 TYR A 142 ARG 0.005 0.000 ARG A 234 *********************** 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 116 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 PHE cc_start: 0.8419 (m-10) cc_final: 0.8165 (m-80) REVERT: A 542 VAL cc_start: 0.8605 (m) cc_final: 0.8395 (p) REVERT: B 100 MET cc_start: 0.8804 (ttt) cc_final: 0.8553 (ttt) REVERT: C 102 MET cc_start: 0.6927 (tmm) cc_final: 0.6655 (ttp) REVERT: C 114 GLN cc_start: 0.8946 (pp30) cc_final: 0.8611 (pp30) outliers start: 22 outliers final: 18 residues processed: 108 average time/residue: 0.1678 time to fit residues: 24.8732 Evaluate side-chains 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 40 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 58 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 40 optimal weight: 0.0770 chunk 52 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.124239 restraints weight = 9113.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123698 restraints weight = 8328.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.125499 restraints weight = 8486.728| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6347 Z= 0.198 Angle : 0.554 9.949 8609 Z= 0.276 Chirality : 0.040 0.151 943 Planarity : 0.003 0.038 1049 Dihedral : 4.882 33.662 928 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.57 % Allowed : 21.58 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.30 (0.31), residues: 761 helix: 0.48 (0.28), residues: 352 sheet: -1.66 (0.58), residues: 85 loop : -2.18 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 326 HIS 0.001 0.001 HIS A 235 PHE 0.019 0.001 PHE A 531 TYR 0.015 0.001 TYR B 46 ARG 0.006 0.000 ARG A 234 *********************** 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 113 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.9062 (tpp) cc_final: 0.8827 (tpp) REVERT: A 295 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8330 (tt) REVERT: A 440 PHE cc_start: 0.8421 (m-10) cc_final: 0.8175 (m-80) REVERT: A 542 VAL cc_start: 0.8662 (m) cc_final: 0.8447 (p) REVERT: B 100 MET cc_start: 0.8821 (ttt) cc_final: 0.8569 (ttt) REVERT: C 37 GLN cc_start: 0.8330 (mm-40) cc_final: 0.7990 (mp10) REVERT: C 102 MET cc_start: 0.6890 (tmm) cc_final: 0.6585 (ttp) outliers start: 23 outliers final: 17 residues processed: 106 average time/residue: 0.1598 time to fit residues: 23.4856 Evaluate side-chains 106 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain C residue 40 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122898 restraints weight = 9062.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.122466 restraints weight = 8103.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124191 restraints weight = 8357.155| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6347 Z= 0.203 Angle : 0.562 9.822 8609 Z= 0.279 Chirality : 0.041 0.139 943 Planarity : 0.003 0.038 1049 Dihedral : 4.776 33.165 928 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.42 % Allowed : 21.43 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.19 (0.31), residues: 761 helix: 0.55 (0.28), residues: 352 sheet: -1.60 (0.58), residues: 85 loop : -2.07 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 326 HIS 0.002 0.001 HIS A 235 PHE 0.018 0.001 PHE A 531 TYR 0.013 0.001 TYR A 142 ARG 0.005 0.000 ARG A 234 *********************** 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 117 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8333 (tt) REVERT: A 542 VAL cc_start: 0.8691 (m) cc_final: 0.8477 (p) REVERT: B 100 MET cc_start: 0.8823 (ttt) cc_final: 0.8569 (ttt) REVERT: C 102 MET cc_start: 0.6828 (tmm) cc_final: 0.6609 (ttp) REVERT: C 103 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7525 (mt-10) outliers start: 22 outliers final: 19 residues processed: 111 average time/residue: 0.1707 time to fit residues: 25.9188 Evaluate side-chains 107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain C residue 40 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.146085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123670 restraints weight = 9132.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123816 restraints weight = 8009.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125516 restraints weight = 7926.190| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6347 Z= 0.182 Angle : 0.578 10.215 8609 Z= 0.287 Chirality : 0.041 0.160 943 Planarity : 0.003 0.038 1049 Dihedral : 4.706 33.132 928 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.80 % Allowed : 21.89 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.63 (0.28), residues: 352 sheet: -1.54 (0.58), residues: 85 loop : -2.03 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 130 HIS 0.002 0.001 HIS A 240 PHE 0.018 0.001 PHE A 531 TYR 0.017 0.001 TYR A 142 ARG 0.010 0.000 ARG A 234 *********************** 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 111 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 542 VAL cc_start: 0.8701 (m) cc_final: 0.8478 (p) REVERT: B 100 MET cc_start: 0.8828 (ttt) cc_final: 0.8589 (ttt) REVERT: B 106 THR cc_start: 0.8849 (t) cc_final: 0.8636 (m) REVERT: C 103 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7564 (mt-10) outliers start: 18 outliers final: 17 residues processed: 106 average time/residue: 0.1525 time to fit residues: 22.5043 Evaluate side-chains 107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain C residue 40 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.0040 chunk 73 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN B 20 GLN C 100 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.145734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122926 restraints weight = 9147.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122247 restraints weight = 7568.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123433 restraints weight = 7403.776| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6347 Z= 0.206 Angle : 0.589 10.169 8609 Z= 0.294 Chirality : 0.041 0.163 943 Planarity : 0.003 0.038 1049 Dihedral : 4.729 32.914 928 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.80 % Allowed : 22.05 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.08 (0.31), residues: 761 helix: 0.60 (0.28), residues: 353 sheet: -1.45 (0.59), residues: 85 loop : -2.01 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 130 HIS 0.002 0.001 HIS A 240 PHE 0.017 0.001 PHE A 531 TYR 0.012 0.001 TYR A 175 ARG 0.009 0.001 ARG A 234 ********************** 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 108 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8284 (tt) REVERT: A 542 VAL cc_start: 0.8753 (m) cc_final: 0.8532 (p) REVERT: B 100 MET cc_start: 0.8839 (ttt) cc_final: 0.8588 (ttt) outliers start: 18 outliers final: 16 residues processed: 104 average time/residue: 0.1591 time to fit residues: 22.9246 Evaluate side-chains 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116906 restraints weight = 9389.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116287 restraints weight = 7670.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117183 restraints weight = 7627.694| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6347 Z= 0.328 Angle : 0.661 9.436 8609 Z= 0.337 Chirality : 0.044 0.185 943 Planarity : 0.004 0.038 1049 Dihedral : 5.406 33.317 928 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 3.26 % Allowed : 22.05 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.31 (0.31), residues: 761 helix: 0.29 (0.27), residues: 357 sheet: -1.45 (0.61), residues: 85 loop : -2.05 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 55 HIS 0.003 0.001 HIS A 235 PHE 0.022 0.002 PHE A 566 TYR 0.015 0.002 TYR B 50 ARG 0.010 0.001 ARG C 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1977.77 seconds wall clock time: 36 minutes 37.85 seconds (2197.85 seconds total)