Starting phenix.real_space_refine on Fri Jan 17 23:42:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zxk_60542/01_2025/8zxk_60542.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zxk_60542/01_2025/8zxk_60542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zxk_60542/01_2025/8zxk_60542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zxk_60542/01_2025/8zxk_60542.map" model { file = "/net/cci-nas-00/data/ceres_data/8zxk_60542/01_2025/8zxk_60542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zxk_60542/01_2025/8zxk_60542.cif" } resolution = 2.76 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= 0.003 sd= 0.047 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 48 5.16 5 C 7844 2.51 5 N 1794 2.21 5 O 1967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11653 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3866 Classifications: {'peptide': 495} Link IDs: {'CIS': 3, 'PTRANS': 17, 'TRANS': 474} Chain: "B" Number of atoms: 3900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3900 Classifications: {'peptide': 499} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 481} Chain: "C" Number of atoms: 3875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3875 Classifications: {'peptide': 496} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 477} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'KEN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'KEN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'KEN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.93, per 1000 atoms: 0.59 Number of scatterers: 11653 At special positions: 0 Unit cell: (111.3, 116.6, 79.5, 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 48 16.00 O 1967 8.00 N 1794 7.00 C 7844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.6 seconds 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2710 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 0 sheets defined 84.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 14 through 35 removed outlier: 5.266A pdb=" N THR A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 74 removed outlier: 3.656A pdb=" N GLY A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) Proline residue: A 44 - end of helix removed outlier: 5.741A pdb=" N TRP A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N PHE A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.717A pdb=" N ARG A 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.645A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.659A pdb=" N MET A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 130 through 147 Processing helix chain 'A' and resid 147 through 167 removed outlier: 3.564A pdb=" N TRP A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 190 through 226 removed outlier: 3.883A pdb=" N ILE A 194 " --> pdb=" O TRP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 249 Processing helix chain 'A' and resid 262 through 279 Processing helix chain 'A' and resid 280 through 298 Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 318 through 340 Proline residue: A 331 - end of helix removed outlier: 3.975A pdb=" N PHE A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 379 removed outlier: 4.350A pdb=" N VAL A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) Proline residue: A 357 - end of helix removed outlier: 3.987A pdb=" N SER A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 removed outlier: 3.542A pdb=" N ALA A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 400 Processing helix chain 'A' and resid 404 through 437 Processing helix chain 'A' and resid 443 through 464 removed outlier: 4.172A pdb=" N ARG A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 503 Proline residue: A 480 - end of helix Processing helix chain 'B' and resid 16 through 35 Processing helix chain 'B' and resid 35 through 74 Proline residue: B 44 - end of helix removed outlier: 5.701A pdb=" N TRP B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N PHE B 57 " --> pdb=" O ASN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 removed outlier: 4.011A pdb=" N ARG B 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 106 through 123 removed outlier: 5.372A pdb=" N ILE B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA B 115 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Proline residue: B 117 - end of helix Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 147 through 167 removed outlier: 3.614A pdb=" N TRP B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 190 through 226 removed outlier: 3.720A pdb=" N ILE B 194 " --> pdb=" O TRP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 251 removed outlier: 3.741A pdb=" N THR B 246 " --> pdb=" O ILE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 279 removed outlier: 3.754A pdb=" N LYS B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 340 Proline residue: B 331 - end of helix removed outlier: 3.874A pdb=" N PHE B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 379 removed outlier: 4.364A pdb=" N VAL B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Proline residue: B 357 - end of helix removed outlier: 3.956A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 404 through 437 Processing helix chain 'B' and resid 443 through 464 removed outlier: 3.942A pdb=" N ARG B 447 " --> pdb=" O PRO B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 503 Proline residue: B 480 - end of helix removed outlier: 4.008A pdb=" N VAL B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 35 removed outlier: 3.535A pdb=" N ILE C 19 " --> pdb=" O PRO C 15 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR C 20 " --> pdb=" O PRO C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 74 removed outlier: 3.580A pdb=" N VAL C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) Proline residue: C 44 - end of helix removed outlier: 5.694A pdb=" N TRP C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N PHE C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.859A pdb=" N ARG C 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 130 through 147 Processing helix chain 'C' and resid 147 through 167 removed outlier: 3.586A pdb=" N TRP C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.526A pdb=" N PHE C 178 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Proline residue: C 180 - end of helix removed outlier: 4.859A pdb=" N GLY C 183 " --> pdb=" O PRO C 180 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU C 184 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE C 186 " --> pdb=" O GLY C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 226 Processing helix chain 'C' and resid 230 through 251 removed outlier: 3.979A pdb=" N SER C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 279 removed outlier: 3.856A pdb=" N ASN C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET C 265 " --> pdb=" O SER C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 298 Processing helix chain 'C' and resid 298 through 304 Processing helix chain 'C' and resid 318 through 340 Proline residue: C 331 - end of helix removed outlier: 4.244A pdb=" N SER C 335 " --> pdb=" O PRO C 331 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 340 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 378 removed outlier: 4.481A pdb=" N VAL C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Proline residue: C 357 - end of helix removed outlier: 3.977A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 390 Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 404 through 437 Processing helix chain 'C' and resid 443 through 464 removed outlier: 3.861A pdb=" N ARG C 447 " --> pdb=" O PRO C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 503 Proline residue: C 480 - end of helix 916 hydrogen bonds defined for protein. 2718 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: 3.51 Time building geometry restraints manager: 3.34 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: 3400 1.34 - 1.46: 2567 1.46 - 1.57: 5950 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 12007 Sorted by residual: bond pdb=" C PRO C 15 " pdb=" N PRO C 16 " ideal model delta sigma weight residual 1.337 1.357 -0.020 1.24e-02 6.50e+03 2.48e+00 bond pdb=" C LEU B 479 " pdb=" N PRO B 480 " ideal model delta sigma weight residual 1.337 1.353 -0.016 1.24e-02 6.50e+03 1.71e+00 bond pdb=" CB ILE A 186 " pdb=" CG1 ILE A 186 " ideal model delta sigma weight residual 1.530 1.556 -0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" NE1 KEN C 601 " pdb=" CC1 KEN C 601 " ideal model delta sigma weight residual 1.445 1.469 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" NE1 KEN A 601 " pdb=" CA1 KEN A 601 " ideal model delta sigma weight residual 1.446 1.470 -0.024 2.00e-02 2.50e+03 1.45e+00 ... (remaining 12002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 16219 2.28 - 4.56: 130 4.56 - 6.84: 28 6.84 - 9.12: 2 9.12 - 11.40: 2 Bond angle restraints: 16381 Sorted by residual: angle pdb=" C GLU A 441 " pdb=" N SER A 442 " pdb=" CA SER A 442 " ideal model delta sigma weight residual 121.70 133.10 -11.40 1.80e+00 3.09e-01 4.01e+01 angle pdb=" C LYS A 255 " pdb=" N GLY A 256 " pdb=" CA GLY A 256 " ideal model delta sigma weight residual 121.70 131.54 -9.84 1.80e+00 3.09e-01 2.99e+01 angle pdb=" CB ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CD1 ILE A 186 " ideal model delta sigma weight residual 113.80 122.02 -8.22 2.10e+00 2.27e-01 1.53e+01 angle pdb=" N ILE B 186 " pdb=" CA ILE B 186 " pdb=" C ILE B 186 " ideal model delta sigma weight residual 106.21 110.27 -4.06 1.07e+00 8.73e-01 1.44e+01 angle pdb=" CA TRP B 329 " pdb=" CB TRP B 329 " pdb=" CG TRP B 329 " ideal model delta sigma weight residual 113.60 120.20 -6.60 1.90e+00 2.77e-01 1.21e+01 ... (remaining 16376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 5795 17.80 - 35.59: 705 35.59 - 53.39: 158 53.39 - 71.18: 24 71.18 - 88.98: 12 Dihedral angle restraints: 6694 sinusoidal: 2464 harmonic: 4230 Sorted by residual: dihedral pdb=" CA THR B 103 " pdb=" C THR B 103 " pdb=" N GLY B 104 " pdb=" CA GLY B 104 " ideal model delta harmonic sigma weight residual 180.00 161.90 18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CB GLU A 37 " pdb=" CG GLU A 37 " pdb=" CD GLU A 37 " pdb=" OE1 GLU A 37 " ideal model delta sinusoidal sigma weight residual 0.00 88.98 -88.98 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA TRP C 323 " pdb=" CB TRP C 323 " pdb=" CG TRP C 323 " pdb=" CD1 TRP C 323 " ideal model delta sinusoidal sigma weight residual 90.00 159.01 -69.01 2 2.00e+01 2.50e-03 1.05e+01 ... (remaining 6691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1270 0.034 - 0.068: 460 0.068 - 0.101: 135 0.101 - 0.135: 20 0.135 - 0.169: 4 Chirality restraints: 1889 Sorted by residual: chirality pdb=" CG LEU C 23 " pdb=" CB LEU C 23 " pdb=" CD1 LEU C 23 " pdb=" CD2 LEU C 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB ILE A 186 " pdb=" CA ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CG2 ILE A 186 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA LEU C 23 " pdb=" N LEU C 23 " pdb=" C LEU C 23 " pdb=" CB LEU C 23 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 1886 not shown) Planarity restraints: 1975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 14 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO A 15 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 15 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 15 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 366 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C ASN A 366 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN A 366 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 367 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 366 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ASN C 366 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN C 366 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL C 367 " 0.011 2.00e-02 2.50e+03 ... (remaining 1972 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 339 2.72 - 3.26: 12099 3.26 - 3.81: 20987 3.81 - 4.35: 24860 4.35 - 4.90: 43652 Nonbonded interactions: 101937 Sorted by model distance: nonbonded pdb=" O SER C 341 " pdb=" OG SER C 341 " model vdw 2.171 3.040 nonbonded pdb=" O PHE A 299 " pdb=" OG SER A 303 " model vdw 2.206 3.040 nonbonded pdb=" O PHE C 299 " pdb=" OG SER C 303 " model vdw 2.220 3.040 nonbonded pdb=" O LEU C 177 " pdb=" OG SER C 491 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLN B 47 " pdb=" OG1 THR B 472 " model vdw 2.246 3.040 ... (remaining 101932 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 10 through 504 or resid 601)) selection = (chain 'C' and (resid 10 through 504 or resid 601)) } 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 individual isotropic 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: 9.050 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: 26.100 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 0.037 12007 Z= 0.188 Angle : 0.543 11.395 16381 Z= 0.299 Chirality : 0.038 0.169 1889 Planarity : 0.004 0.055 1975 Dihedral : 16.405 88.978 3984 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.16 % Allowed : 24.98 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % 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: 2.48 (0.22), residues: 1484 helix: 2.15 (0.15), residues: 1167 sheet: None (None), residues: 0 loop : -0.25 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 329 HIS 0.002 0.001 HIS C 192 PHE 0.022 0.002 PHE B 417 TYR 0.008 0.001 TYR A 295 ARG 0.003 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 1.299 Fit side-chains REVERT: B 19 ILE cc_start: 0.7971 (mm) cc_final: 0.7745 (mp) REVERT: B 105 MET cc_start: 0.2930 (mmm) cc_final: 0.2617 (mpp) REVERT: C 93 LYS cc_start: 0.4598 (pttp) cc_final: 0.4094 (ptpt) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 0.9375 time to fit residues: 154.2053 Evaluate side-chains 139 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 133 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.159587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116064 restraints weight = 12309.784| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.97 r_work: 0.3014 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.0583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12007 Z= 0.203 Angle : 0.520 6.858 16381 Z= 0.284 Chirality : 0.039 0.148 1889 Planarity : 0.004 0.049 1975 Dihedral : 3.993 17.528 1547 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.07 % Allowed : 21.16 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % 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: 2.61 (0.22), residues: 1484 helix: 2.19 (0.15), residues: 1178 sheet: None (None), residues: 0 loop : -0.06 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 329 HIS 0.003 0.001 HIS C 374 PHE 0.024 0.002 PHE C 122 TYR 0.008 0.001 TYR A 295 ARG 0.003 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 145 time to evaluate : 1.191 Fit side-chains REVERT: A 93 LYS cc_start: 0.3870 (OUTLIER) cc_final: 0.3418 (ttpt) REVERT: A 181 PHE cc_start: 0.7710 (m-10) cc_final: 0.7417 (m-10) REVERT: A 184 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6595 (mm-30) REVERT: B 19 ILE cc_start: 0.7083 (mm) cc_final: 0.6696 (mp) REVERT: B 93 LYS cc_start: 0.3492 (OUTLIER) cc_final: 0.3191 (ttpt) REVERT: C 93 LYS cc_start: 0.2484 (pttp) cc_final: 0.2032 (ptpt) REVERT: C 301 ASP cc_start: 0.7874 (t0) cc_final: 0.7554 (t0) outliers start: 50 outliers final: 16 residues processed: 182 average time/residue: 0.7469 time to fit residues: 154.8808 Evaluate side-chains 153 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 84 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 192 HIS ** 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 = 0.3776 r_free = 0.3776 target = 0.159928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116252 restraints weight = 12460.840| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.95 r_work: 0.3020 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12007 Z= 0.192 Angle : 0.517 7.247 16381 Z= 0.280 Chirality : 0.038 0.146 1889 Planarity : 0.004 0.046 1975 Dihedral : 3.978 18.066 1547 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.15 % Allowed : 21.32 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % 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: 2.62 (0.22), residues: 1484 helix: 2.23 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -0.17 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 329 HIS 0.002 0.001 HIS C 374 PHE 0.022 0.002 PHE B 122 TYR 0.008 0.001 TYR A 295 ARG 0.002 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 1.211 Fit side-chains REVERT: A 93 LYS cc_start: 0.3829 (OUTLIER) cc_final: 0.3383 (ttpt) REVERT: A 123 ASN cc_start: 0.8333 (t0) cc_final: 0.8016 (t0) REVERT: A 181 PHE cc_start: 0.7558 (m-10) cc_final: 0.7193 (m-10) REVERT: A 184 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6509 (mm-30) REVERT: A 265 MET cc_start: 0.7642 (mmp) cc_final: 0.5953 (ttp) REVERT: B 19 ILE cc_start: 0.7057 (mm) cc_final: 0.6700 (mp) REVERT: B 93 LYS cc_start: 0.3434 (OUTLIER) cc_final: 0.3127 (ttpt) REVERT: B 502 LYS cc_start: 0.6491 (ttpt) cc_final: 0.5794 (ttpp) REVERT: C 93 LYS cc_start: 0.2498 (pttp) cc_final: 0.2039 (ptpt) REVERT: C 126 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7730 (mtm180) REVERT: C 301 ASP cc_start: 0.7923 (t0) cc_final: 0.7581 (t0) outliers start: 51 outliers final: 23 residues processed: 176 average time/residue: 0.8731 time to fit residues: 173.4202 Evaluate side-chains 163 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 78 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 0.0020 chunk 115 optimal weight: 0.0980 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 192 HIS ** 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 = 0.3774 r_free = 0.3774 target = 0.159738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116022 restraints weight = 12371.454| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.95 r_work: 0.3014 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12007 Z= 0.201 Angle : 0.514 7.317 16381 Z= 0.279 Chirality : 0.039 0.147 1889 Planarity : 0.004 0.045 1975 Dihedral : 3.958 15.834 1547 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.13 % Allowed : 20.59 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % 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: 2.62 (0.22), residues: 1484 helix: 2.23 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -0.15 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 329 HIS 0.002 0.001 HIS C 374 PHE 0.026 0.002 PHE B 417 TYR 0.008 0.001 TYR C 490 ARG 0.002 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 146 time to evaluate : 1.302 Fit side-chains REVERT: A 93 LYS cc_start: 0.3917 (OUTLIER) cc_final: 0.3451 (ttpt) REVERT: A 123 ASN cc_start: 0.8433 (t0) cc_final: 0.8104 (t0) REVERT: A 184 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6515 (mm-30) REVERT: A 265 MET cc_start: 0.7761 (mmp) cc_final: 0.6096 (ttp) REVERT: A 329 TRP cc_start: 0.7154 (OUTLIER) cc_final: 0.6707 (t60) REVERT: B 19 ILE cc_start: 0.7131 (mm) cc_final: 0.6509 (mp) REVERT: B 23 LEU cc_start: 0.7439 (mm) cc_final: 0.7111 (mm) REVERT: B 93 LYS cc_start: 0.3518 (OUTLIER) cc_final: 0.3196 (ttpt) REVERT: B 502 LYS cc_start: 0.6550 (ttpt) cc_final: 0.5821 (ttpp) REVERT: C 23 LEU cc_start: 0.7695 (mm) cc_final: 0.7385 (mm) REVERT: C 93 LYS cc_start: 0.2417 (pttp) cc_final: 0.2028 (ptpt) REVERT: C 126 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7737 (mtm180) outliers start: 63 outliers final: 33 residues processed: 195 average time/residue: 0.8338 time to fit residues: 184.6190 Evaluate side-chains 176 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 329 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 93 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 115 optimal weight: 0.0370 chunk 74 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 GLN C 123 ASN C 140 GLN ** C 192 HIS ** 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 = 0.3767 r_free = 0.3767 target = 0.159007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.114963 restraints weight = 12377.048| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.95 r_work: 0.3010 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12007 Z= 0.225 Angle : 0.537 9.096 16381 Z= 0.288 Chirality : 0.039 0.179 1889 Planarity : 0.004 0.044 1975 Dihedral : 4.017 16.524 1547 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.29 % Allowed : 20.91 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % 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: 2.55 (0.22), residues: 1484 helix: 2.17 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -0.15 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 329 HIS 0.002 0.001 HIS C 374 PHE 0.023 0.002 PHE B 122 TYR 0.009 0.001 TYR C 490 ARG 0.002 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 140 time to evaluate : 1.159 Fit side-chains REVERT: A 93 LYS cc_start: 0.3788 (OUTLIER) cc_final: 0.3321 (ttpt) REVERT: A 123 ASN cc_start: 0.8376 (t0) cc_final: 0.8064 (t0) REVERT: A 265 MET cc_start: 0.7691 (mmp) cc_final: 0.6016 (ttt) REVERT: B 19 ILE cc_start: 0.7067 (mm) cc_final: 0.6406 (mp) REVERT: B 23 LEU cc_start: 0.7407 (mm) cc_final: 0.7027 (mm) REVERT: B 93 LYS cc_start: 0.3438 (OUTLIER) cc_final: 0.3117 (ttpt) REVERT: B 502 LYS cc_start: 0.6540 (ttpt) cc_final: 0.5812 (ttpp) REVERT: C 23 LEU cc_start: 0.7655 (mm) cc_final: 0.7315 (mm) REVERT: C 48 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7894 (tm) REVERT: C 93 LYS cc_start: 0.2293 (pttp) cc_final: 0.1927 (ptpt) REVERT: C 126 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7616 (mtm180) outliers start: 65 outliers final: 36 residues processed: 191 average time/residue: 0.8252 time to fit residues: 178.7867 Evaluate side-chains 175 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 21 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 0.0570 chunk 82 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 105 optimal weight: 0.0010 chunk 91 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 overall best weight: 0.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN C 123 ASN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.160952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.116700 restraints weight = 12456.057| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.99 r_work: 0.3033 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12007 Z= 0.176 Angle : 0.512 9.328 16381 Z= 0.276 Chirality : 0.038 0.151 1889 Planarity : 0.004 0.044 1975 Dihedral : 3.927 16.374 1547 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.80 % Allowed : 21.32 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % 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: 2.73 (0.22), residues: 1484 helix: 2.32 (0.15), residues: 1174 sheet: None (None), residues: 0 loop : -0.18 (0.39), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 329 HIS 0.002 0.001 HIS A 192 PHE 0.025 0.002 PHE B 417 TYR 0.008 0.001 TYR A 295 ARG 0.004 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 144 time to evaluate : 1.314 Fit side-chains REVERT: A 93 LYS cc_start: 0.3867 (OUTLIER) cc_final: 0.3380 (ttpt) REVERT: A 123 ASN cc_start: 0.8388 (t0) cc_final: 0.8059 (t0) REVERT: A 265 MET cc_start: 0.7791 (mmp) cc_final: 0.6135 (ttt) REVERT: A 336 PHE cc_start: 0.7625 (m-80) cc_final: 0.7381 (m-80) REVERT: B 19 ILE cc_start: 0.7137 (mm) cc_final: 0.6524 (mp) REVERT: B 23 LEU cc_start: 0.7491 (mm) cc_final: 0.7173 (mm) REVERT: B 43 PHE cc_start: 0.5832 (m-10) cc_final: 0.5557 (m-10) REVERT: B 105 MET cc_start: 0.2016 (mmt) cc_final: 0.1506 (mmp) REVERT: B 123 ASN cc_start: 0.8466 (t0) cc_final: 0.8145 (t0) REVERT: B 502 LYS cc_start: 0.6566 (ttpt) cc_final: 0.5828 (ttpp) REVERT: C 23 LEU cc_start: 0.7745 (mm) cc_final: 0.7406 (mm) REVERT: C 93 LYS cc_start: 0.2410 (pttp) cc_final: 0.2024 (ptpt) REVERT: C 126 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7730 (mtm180) REVERT: C 258 LYS cc_start: 0.4580 (OUTLIER) cc_final: 0.3734 (mmtt) outliers start: 59 outliers final: 33 residues processed: 187 average time/residue: 0.7924 time to fit residues: 168.3418 Evaluate side-chains 178 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 142 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN ** C 192 HIS ** 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 = 0.3773 r_free = 0.3773 target = 0.159589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.115533 restraints weight = 12503.481| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.01 r_work: 0.2989 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12007 Z= 0.212 Angle : 0.524 10.614 16381 Z= 0.283 Chirality : 0.039 0.145 1889 Planarity : 0.004 0.043 1975 Dihedral : 3.966 15.776 1547 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.21 % Allowed : 21.24 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % 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: 2.63 (0.22), residues: 1484 helix: 2.23 (0.15), residues: 1177 sheet: None (None), residues: 0 loop : -0.15 (0.39), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 329 HIS 0.002 0.001 HIS C 374 PHE 0.023 0.002 PHE B 122 TYR 0.009 0.001 TYR C 490 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 147 time to evaluate : 1.194 Fit side-chains REVERT: A 93 LYS cc_start: 0.3752 (OUTLIER) cc_final: 0.3262 (ttpt) REVERT: A 123 ASN cc_start: 0.8327 (t0) cc_final: 0.8009 (t0) REVERT: A 184 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6478 (mm-30) REVERT: A 265 MET cc_start: 0.7664 (mmp) cc_final: 0.5980 (ttt) REVERT: A 336 PHE cc_start: 0.7646 (m-80) cc_final: 0.7370 (m-80) REVERT: B 19 ILE cc_start: 0.7024 (mm) cc_final: 0.6405 (mp) REVERT: B 23 LEU cc_start: 0.7439 (mm) cc_final: 0.7116 (mm) REVERT: B 93 LYS cc_start: 0.3387 (OUTLIER) cc_final: 0.3083 (ttpt) REVERT: B 502 LYS cc_start: 0.6502 (ttpt) cc_final: 0.5764 (ttpp) REVERT: C 23 LEU cc_start: 0.7665 (mm) cc_final: 0.7302 (mm) REVERT: C 48 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7846 (tm) REVERT: C 93 LYS cc_start: 0.2317 (pttp) cc_final: 0.1948 (ptpt) REVERT: C 126 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7655 (mtm180) REVERT: C 258 LYS cc_start: 0.4517 (OUTLIER) cc_final: 0.3692 (mmtt) outliers start: 64 outliers final: 37 residues processed: 197 average time/residue: 0.8319 time to fit residues: 186.1019 Evaluate side-chains 187 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 258 LYS Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 112 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.0570 chunk 127 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN ** C 192 HIS ** 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 = 0.3783 r_free = 0.3783 target = 0.160500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117212 restraints weight = 12485.575| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.94 r_work: 0.3012 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12007 Z= 0.183 Angle : 0.523 11.284 16381 Z= 0.281 Chirality : 0.038 0.155 1889 Planarity : 0.004 0.043 1975 Dihedral : 3.926 16.008 1547 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.15 % Allowed : 22.70 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % 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: 2.70 (0.22), residues: 1484 helix: 2.28 (0.15), residues: 1177 sheet: None (None), residues: 0 loop : -0.16 (0.39), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 445 HIS 0.002 0.001 HIS C 120 PHE 0.029 0.002 PHE B 417 TYR 0.008 0.001 TYR A 295 ARG 0.002 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 1.349 Fit side-chains REVERT: A 93 LYS cc_start: 0.3788 (OUTLIER) cc_final: 0.3297 (ttpt) REVERT: A 123 ASN cc_start: 0.8331 (t0) cc_final: 0.8023 (t0) REVERT: A 265 MET cc_start: 0.7676 (mmp) cc_final: 0.5990 (ttt) REVERT: A 336 PHE cc_start: 0.7662 (m-80) cc_final: 0.7426 (m-80) REVERT: B 19 ILE cc_start: 0.7064 (mm) cc_final: 0.6479 (mp) REVERT: B 23 LEU cc_start: 0.7463 (mm) cc_final: 0.7201 (mm) REVERT: B 43 PHE cc_start: 0.5736 (m-10) cc_final: 0.5469 (m-10) REVERT: B 93 LYS cc_start: 0.3419 (OUTLIER) cc_final: 0.3105 (ttpt) REVERT: B 123 ASN cc_start: 0.8382 (t0) cc_final: 0.8064 (t0) REVERT: B 502 LYS cc_start: 0.6500 (ttpt) cc_final: 0.5773 (ttpp) REVERT: C 23 LEU cc_start: 0.7664 (mm) cc_final: 0.7300 (mm) REVERT: C 93 LYS cc_start: 0.2272 (pttp) cc_final: 0.1929 (ptpt) REVERT: C 126 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7667 (mtm180) outliers start: 51 outliers final: 38 residues processed: 183 average time/residue: 0.8519 time to fit residues: 175.7816 Evaluate side-chains 183 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 13 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 109 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN ** C 192 HIS ** 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 = 0.3782 r_free = 0.3782 target = 0.160503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.116267 restraints weight = 12509.864| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.99 r_work: 0.3000 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12007 Z= 0.192 Angle : 0.541 12.824 16381 Z= 0.286 Chirality : 0.038 0.143 1889 Planarity : 0.004 0.042 1975 Dihedral : 3.946 16.123 1547 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.91 % Allowed : 23.19 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % 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: 2.69 (0.22), residues: 1484 helix: 2.26 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.11 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 445 HIS 0.002 0.001 HIS C 145 PHE 0.022 0.002 PHE B 122 TYR 0.008 0.001 TYR A 295 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 142 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.3875 (OUTLIER) cc_final: 0.3373 (ttpt) REVERT: A 123 ASN cc_start: 0.8357 (t0) cc_final: 0.8043 (t0) REVERT: A 265 MET cc_start: 0.7669 (mmp) cc_final: 0.5983 (ttt) REVERT: B 19 ILE cc_start: 0.7164 (mm) cc_final: 0.6570 (mp) REVERT: B 23 LEU cc_start: 0.7414 (mm) cc_final: 0.7157 (mm) REVERT: B 93 LYS cc_start: 0.3366 (OUTLIER) cc_final: 0.3054 (ttpt) REVERT: B 123 ASN cc_start: 0.8392 (t0) cc_final: 0.8080 (t0) REVERT: B 502 LYS cc_start: 0.6479 (ttpt) cc_final: 0.5745 (ttpp) REVERT: C 93 LYS cc_start: 0.2242 (pttp) cc_final: 0.1895 (ptpt) REVERT: C 126 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7670 (mtm180) outliers start: 48 outliers final: 38 residues processed: 181 average time/residue: 0.8684 time to fit residues: 176.7269 Evaluate side-chains 183 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN ** C 192 HIS ** 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 = 0.3781 r_free = 0.3781 target = 0.160393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.116204 restraints weight = 12419.220| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.98 r_work: 0.3000 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12007 Z= 0.200 Angle : 0.541 12.259 16381 Z= 0.288 Chirality : 0.039 0.143 1889 Planarity : 0.004 0.042 1975 Dihedral : 3.961 17.815 1547 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.91 % Allowed : 23.43 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % 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: 2.66 (0.22), residues: 1484 helix: 2.24 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.14 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 445 HIS 0.002 0.001 HIS C 374 PHE 0.031 0.002 PHE B 417 TYR 0.008 0.001 TYR C 490 ARG 0.002 0.000 ARG A 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 144 time to evaluate : 1.241 Fit side-chains REVERT: A 93 LYS cc_start: 0.3863 (OUTLIER) cc_final: 0.3341 (ttpt) REVERT: A 123 ASN cc_start: 0.8334 (t0) cc_final: 0.8026 (t0) REVERT: A 265 MET cc_start: 0.7672 (mmp) cc_final: 0.5971 (ttt) REVERT: B 19 ILE cc_start: 0.7147 (mm) cc_final: 0.6551 (mp) REVERT: B 23 LEU cc_start: 0.7463 (mm) cc_final: 0.7205 (mm) REVERT: B 93 LYS cc_start: 0.3345 (OUTLIER) cc_final: 0.3034 (ttpt) REVERT: B 123 ASN cc_start: 0.8374 (t0) cc_final: 0.8066 (t0) REVERT: B 502 LYS cc_start: 0.6472 (ttpt) cc_final: 0.5740 (ttpp) REVERT: C 23 LEU cc_start: 0.7657 (mm) cc_final: 0.7284 (mm) REVERT: C 93 LYS cc_start: 0.2238 (pttp) cc_final: 0.1897 (ptpt) REVERT: C 126 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7649 (mtm180) outliers start: 48 outliers final: 40 residues processed: 183 average time/residue: 0.8438 time to fit residues: 173.5311 Evaluate side-chains 187 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 404 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 323 TRP Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 126 ARG Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 404 PHE Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 85 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 0.0570 chunk 113 optimal weight: 0.1980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 ASN ** C 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.161010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116975 restraints weight = 12384.610| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.97 r_work: 0.3010 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12007 Z= 0.188 Angle : 0.531 11.330 16381 Z= 0.284 Chirality : 0.038 0.142 1889 Planarity : 0.004 0.043 1975 Dihedral : 3.942 17.299 1547 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.42 % Allowed : 24.17 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.28 % 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: 2.72 (0.22), residues: 1484 helix: 2.28 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.10 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 445 HIS 0.002 0.001 HIS C 374 PHE 0.022 0.002 PHE B 122 TYR 0.008 0.001 TYR A 295 ARG 0.002 0.000 ARG A 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7459.22 seconds wall clock time: 135 minutes 41.13 seconds (8141.13 seconds total)