Starting phenix.real_space_refine on Sat Apr 6 17:02:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/04_2024/8phf_17660_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/04_2024/8phf_17660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/04_2024/8phf_17660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/04_2024/8phf_17660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/04_2024/8phf_17660_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8phf_17660/04_2024/8phf_17660_updated.pdb" } resolution = 3.6 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= 0.004 sd= 0.103 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 P 4 5.49 5 S 44 5.16 5 C 5488 2.51 5 N 1462 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8640 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4267 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 15, 'TRANS': 531} Chain breaks: 1 Chain: "B" Number of atoms: 4267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4267 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 15, 'TRANS': 531} Chain breaks: 1 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.47, per 1000 atoms: 0.75 Number of scatterers: 8640 At special positions: 0 Unit cell: (121.8, 98.28, 76.44, 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) S 44 16.00 P 4 15.00 O 1642 8.00 N 1462 7.00 C 5488 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 - 3.50 Amino acid : False - 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 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 3.1 seconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 6 sheets defined 56.9% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 50 through 53 No H-bonds generated for 'chain 'A' and resid 50 through 53' Processing helix chain 'A' and resid 61 through 80 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.519A pdb=" N ILE A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N MET A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 159 through 171 Proline residue: A 167 - end of helix Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 292 through 302 removed outlier: 3.838A pdb=" N SER A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 325 removed outlier: 4.126A pdb=" N VAL A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR A 325 " --> pdb=" O MET A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 340 through 367 Processing helix chain 'A' and resid 376 through 404 removed outlier: 3.579A pdb=" N ALA A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLY A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 423 removed outlier: 3.915A pdb=" N ARG A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 448 removed outlier: 4.173A pdb=" N TYR A 435 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE A 436 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 438 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N THR A 439 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY A 440 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN A 442 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 446 " --> pdb=" O HIS A 443 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 447 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 448 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 518 removed outlier: 5.195A pdb=" N ASP A 496 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER A 497 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU A 502 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N CYS A 507 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 527 through 556 Processing helix chain 'A' and resid 561 through 586 removed outlier: 3.550A pdb=" N GLN A 585 " --> pdb=" O PHE A 581 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 608 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 61 through 80 Proline residue: B 73 - end of helix Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 95 through 104 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 122 through 134 removed outlier: 3.983A pdb=" N ILE B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N MET B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 159 through 171 Proline residue: B 167 - end of helix Processing helix chain 'B' and resid 292 through 301 Processing helix chain 'B' and resid 306 through 320 removed outlier: 3.601A pdb=" N ALA B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 328 removed outlier: 3.519A pdb=" N CYS B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 340 through 366 removed outlier: 4.127A pdb=" N LYS B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 406 removed outlier: 5.623A pdb=" N GLY B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU B 404 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR B 406 " --> pdb=" O GLY B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 424 removed outlier: 3.610A pdb=" N ARG B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE B 424 " --> pdb=" O ARG B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 448 removed outlier: 3.630A pdb=" N ALA B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 447 " --> pdb=" O HIS B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 519 removed outlier: 5.234A pdb=" N ASP B 496 " --> pdb=" O SER B 493 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE B 519 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 527 through 556 removed outlier: 3.690A pdb=" N LYS B 531 " --> pdb=" O GLN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 584 removed outlier: 3.589A pdb=" N PHE B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 608 Processing sheet with id= A, first strand: chain 'A' and resid 195 through 198 Processing sheet with id= B, first strand: chain 'A' and resid 209 through 211 removed outlier: 3.762A pdb=" N VAL A 273 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 222 through 230 Processing sheet with id= D, first strand: chain 'B' and resid 195 through 198 Processing sheet with id= E, first strand: chain 'B' and resid 209 through 211 Processing sheet with id= F, first strand: chain 'B' and resid 222 through 230 431 hydrogen bonds defined for protein. 1125 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: 2.23 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2141 1.33 - 1.45: 1616 1.45 - 1.57: 4959 1.57 - 1.69: 6 1.69 - 1.81: 70 Bond restraints: 8792 Sorted by residual: bond pdb=" O3P FAD A 701 " pdb=" P FAD A 701 " ideal model delta sigma weight residual 1.660 1.582 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" O3P FAD B 701 " pdb=" P FAD B 701 " ideal model delta sigma weight residual 1.660 1.586 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" O5B FAD B 701 " pdb=" PA FAD B 701 " ideal model delta sigma weight residual 1.634 1.567 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" O5B FAD A 701 " pdb=" PA FAD A 701 " ideal model delta sigma weight residual 1.634 1.570 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O5' FAD B 701 " pdb=" P FAD B 701 " ideal model delta sigma weight residual 1.637 1.574 0.063 2.00e-02 2.50e+03 9.94e+00 ... (remaining 8787 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.30: 182 106.30 - 113.25: 4799 113.25 - 120.20: 3331 120.20 - 127.15: 3489 127.15 - 134.10: 67 Bond angle restraints: 11868 Sorted by residual: angle pdb=" CA GLU A 426 " pdb=" CB GLU A 426 " pdb=" CG GLU A 426 " ideal model delta sigma weight residual 114.10 120.00 -5.90 2.00e+00 2.50e-01 8.70e+00 angle pdb=" N GLY A 186 " pdb=" CA GLY A 186 " pdb=" C GLY A 186 " ideal model delta sigma weight residual 113.18 106.51 6.67 2.37e+00 1.78e-01 7.93e+00 angle pdb=" CB MET B 124 " pdb=" CG MET B 124 " pdb=" SD MET B 124 " ideal model delta sigma weight residual 112.70 104.50 8.20 3.00e+00 1.11e-01 7.47e+00 angle pdb=" P FAD A 701 " pdb=" O3P FAD A 701 " pdb=" PA FAD A 701 " ideal model delta sigma weight residual 130.34 122.41 7.93 3.00e+00 1.11e-01 6.99e+00 angle pdb=" CB MET B 356 " pdb=" CG MET B 356 " pdb=" SD MET B 356 " ideal model delta sigma weight residual 112.70 104.81 7.89 3.00e+00 1.11e-01 6.91e+00 ... (remaining 11863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.99: 5159 32.99 - 65.97: 150 65.97 - 98.96: 33 98.96 - 131.94: 0 131.94 - 164.93: 2 Dihedral angle restraints: 5344 sinusoidal: 2210 harmonic: 3134 Sorted by residual: dihedral pdb=" O5' FAD A 701 " pdb=" O3P FAD A 701 " pdb=" P FAD A 701 " pdb=" PA FAD A 701 " ideal model delta sinusoidal sigma weight residual 298.23 133.30 164.93 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA PHE A 425 " pdb=" C PHE A 425 " pdb=" N GLU A 426 " pdb=" CA GLU A 426 " ideal model delta harmonic sigma weight residual 180.00 -158.52 -21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" O5' FAD B 701 " pdb=" O3P FAD B 701 " pdb=" P FAD B 701 " pdb=" PA FAD B 701 " ideal model delta sinusoidal sigma weight residual 298.23 163.59 134.64 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 5341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 955 0.042 - 0.084: 312 0.084 - 0.125: 67 0.125 - 0.167: 7 0.167 - 0.209: 3 Chirality restraints: 1344 Sorted by residual: chirality pdb=" C2B FAD B 701 " pdb=" C1B FAD B 701 " pdb=" C3B FAD B 701 " pdb=" O2B FAD B 701 " both_signs ideal model delta sigma weight residual False -2.53 -2.74 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ARG B 329 " pdb=" N ARG B 329 " pdb=" C ARG B 329 " pdb=" CB ARG B 329 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PHE A 54 " pdb=" N PHE A 54 " pdb=" C PHE A 54 " pdb=" CB PHE A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.03e-01 ... (remaining 1341 not shown) Planarity restraints: 1506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 182 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 183 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 425 " 0.009 2.00e-02 2.50e+03 1.35e-02 3.19e+00 pdb=" CG PHE A 425 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 425 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 425 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 425 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 425 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 425 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 515 " -0.008 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C LEU A 515 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU A 515 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 516 " -0.009 2.00e-02 2.50e+03 ... (remaining 1503 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 148 2.69 - 3.24: 8829 3.24 - 3.79: 13195 3.79 - 4.35: 17488 4.35 - 4.90: 28739 Nonbonded interactions: 68399 Sorted by model distance: nonbonded pdb=" O LEU A 64 " pdb=" ND2 ASN A 68 " model vdw 2.134 2.520 nonbonded pdb=" OG SER B 60 " pdb=" OE1 GLU B 63 " model vdw 2.143 2.440 nonbonded pdb=" OG SER A 60 " pdb=" OD1 ASP A 62 " model vdw 2.191 2.440 nonbonded pdb=" O3' FAD B 701 " pdb=" O5' FAD B 701 " model vdw 2.260 2.440 nonbonded pdb=" OD2 ASP A 201 " pdb=" NZ LYS A 203 " model vdw 2.261 2.520 ... (remaining 68394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.050 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 32.280 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 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 : 0.004 0.078 8792 Z= 0.294 Angle : 0.651 8.201 11868 Z= 0.327 Chirality : 0.042 0.209 1344 Planarity : 0.004 0.045 1506 Dihedral : 16.415 164.926 3332 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1086 helix: 1.03 (0.21), residues: 596 sheet: -1.02 (0.53), residues: 90 loop : 0.11 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 213 HIS 0.007 0.001 HIS A 204 PHE 0.031 0.002 PHE A 425 TYR 0.021 0.001 TYR B 361 ARG 0.006 0.000 ARG A 609 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.7705 (m-30) cc_final: 0.7184 (m-30) REVERT: A 609 ARG cc_start: 0.6539 (mmt180) cc_final: 0.6175 (tpt170) REVERT: B 619 ARG cc_start: 0.7354 (ttm-80) cc_final: 0.7123 (ttm-80) outliers start: 1 outliers final: 1 residues processed: 124 average time/residue: 0.2466 time to fit residues: 40.9541 Evaluate side-chains 94 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.0010 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN B 122 ASN B 204 HIS B 527 GLN B 585 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8792 Z= 0.162 Angle : 0.533 9.436 11868 Z= 0.273 Chirality : 0.039 0.141 1344 Planarity : 0.004 0.045 1506 Dihedral : 11.059 174.098 1267 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.52 % Allowed : 6.85 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1086 helix: 1.15 (0.21), residues: 598 sheet: -0.46 (0.49), residues: 114 loop : 0.26 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 213 HIS 0.008 0.001 HIS B 204 PHE 0.010 0.001 PHE B 275 TYR 0.018 0.001 TYR B 435 ARG 0.004 0.000 ARG A 609 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.984 Fit side-chains REVERT: B 329 ARG cc_start: 0.5695 (mmm-85) cc_final: 0.5330 (mmm-85) REVERT: B 619 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7119 (ttm-80) outliers start: 14 outliers final: 8 residues processed: 105 average time/residue: 0.2556 time to fit residues: 36.3175 Evaluate side-chains 95 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.0170 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS B 216 ASN ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8792 Z= 0.153 Angle : 0.487 7.712 11868 Z= 0.254 Chirality : 0.038 0.138 1344 Planarity : 0.004 0.043 1506 Dihedral : 9.609 178.440 1267 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.85 % Allowed : 10.65 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1086 helix: 1.22 (0.21), residues: 596 sheet: -0.79 (0.53), residues: 90 loop : 0.25 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 213 HIS 0.002 0.001 HIS B 563 PHE 0.009 0.001 PHE A 178 TYR 0.016 0.001 TYR A 506 ARG 0.005 0.000 ARG A 609 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: B 619 ARG cc_start: 0.7449 (ttm-80) cc_final: 0.7132 (ttm-80) outliers start: 17 outliers final: 10 residues processed: 107 average time/residue: 0.2395 time to fit residues: 34.6888 Evaluate side-chains 99 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 chunk 104 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8792 Z= 0.156 Angle : 0.477 7.508 11868 Z= 0.249 Chirality : 0.038 0.138 1344 Planarity : 0.004 0.042 1506 Dihedral : 9.222 173.382 1266 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.17 % Allowed : 12.93 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1086 helix: 1.18 (0.21), residues: 608 sheet: -0.81 (0.53), residues: 90 loop : 0.25 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 213 HIS 0.007 0.001 HIS B 204 PHE 0.012 0.001 PHE B 44 TYR 0.017 0.001 TYR A 506 ARG 0.002 0.000 ARG B 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.966 Fit side-chains REVERT: A 522 THR cc_start: 0.7424 (OUTLIER) cc_final: 0.7157 (p) REVERT: B 329 ARG cc_start: 0.5679 (mmm-85) cc_final: 0.5452 (mmm-85) REVERT: B 518 ARG cc_start: 0.6269 (tmm-80) cc_final: 0.5870 (ttt180) REVERT: B 619 ARG cc_start: 0.7421 (ttm-80) cc_final: 0.7116 (ttm-80) outliers start: 20 outliers final: 13 residues processed: 108 average time/residue: 0.2404 time to fit residues: 35.1795 Evaluate side-chains 106 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8792 Z= 0.186 Angle : 0.497 6.312 11868 Z= 0.259 Chirality : 0.039 0.138 1344 Planarity : 0.004 0.040 1506 Dihedral : 9.170 172.280 1266 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.72 % Allowed : 13.26 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1086 helix: 1.11 (0.21), residues: 604 sheet: -0.93 (0.52), residues: 90 loop : 0.18 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 213 HIS 0.003 0.001 HIS A 563 PHE 0.013 0.001 PHE B 44 TYR 0.017 0.001 TYR A 506 ARG 0.002 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 1.014 Fit side-chains REVERT: A 321 MET cc_start: 0.6719 (ttp) cc_final: 0.6502 (mtp) REVERT: A 522 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.7245 (p) REVERT: B 619 ARG cc_start: 0.7418 (ttm-80) cc_final: 0.7131 (ttm-80) outliers start: 25 outliers final: 18 residues processed: 110 average time/residue: 0.2705 time to fit residues: 39.3988 Evaluate side-chains 107 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN B 504 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8792 Z= 0.230 Angle : 0.543 7.008 11868 Z= 0.282 Chirality : 0.040 0.139 1344 Planarity : 0.004 0.039 1506 Dihedral : 9.281 172.632 1266 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.72 % Allowed : 14.24 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1086 helix: 0.87 (0.21), residues: 606 sheet: -1.15 (0.54), residues: 84 loop : 0.12 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 213 HIS 0.005 0.001 HIS B 204 PHE 0.016 0.002 PHE B 44 TYR 0.018 0.001 TYR A 506 ARG 0.002 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 1.026 Fit side-chains REVERT: A 321 MET cc_start: 0.6848 (ttp) cc_final: 0.6621 (mtp) REVERT: A 522 THR cc_start: 0.7569 (OUTLIER) cc_final: 0.7289 (p) REVERT: B 304 ARG cc_start: 0.6659 (mtm-85) cc_final: 0.6438 (mtm110) REVERT: B 518 ARG cc_start: 0.6585 (tmm-80) cc_final: 0.6191 (ttt180) REVERT: B 619 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.7174 (ttm-80) outliers start: 25 outliers final: 19 residues processed: 110 average time/residue: 0.2707 time to fit residues: 39.9641 Evaluate side-chains 107 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 64 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN B 204 HIS B 216 ASN B 277 ASN B 301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8792 Z= 0.185 Angle : 0.518 7.333 11868 Z= 0.269 Chirality : 0.039 0.146 1344 Planarity : 0.004 0.037 1506 Dihedral : 9.170 172.044 1266 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.39 % Allowed : 14.89 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1086 helix: 0.96 (0.21), residues: 594 sheet: -1.12 (0.53), residues: 90 loop : 0.17 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 213 HIS 0.005 0.001 HIS B 204 PHE 0.009 0.001 PHE A 178 TYR 0.019 0.001 TYR A 506 ARG 0.002 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.7007 (tpt) cc_final: 0.6696 (tpt) REVERT: A 321 MET cc_start: 0.6822 (ttp) cc_final: 0.6610 (mtp) REVERT: A 522 THR cc_start: 0.7550 (OUTLIER) cc_final: 0.7260 (p) REVERT: B 619 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.7156 (ttm-80) outliers start: 22 outliers final: 20 residues processed: 104 average time/residue: 0.2731 time to fit residues: 37.8336 Evaluate side-chains 107 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN B 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8792 Z= 0.156 Angle : 0.495 6.503 11868 Z= 0.258 Chirality : 0.039 0.140 1344 Planarity : 0.004 0.037 1506 Dihedral : 9.070 171.307 1266 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.96 % Allowed : 15.33 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1086 helix: 1.04 (0.21), residues: 604 sheet: -1.06 (0.53), residues: 90 loop : 0.20 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 391 HIS 0.005 0.001 HIS B 204 PHE 0.010 0.001 PHE B 44 TYR 0.020 0.001 TYR A 506 ARG 0.001 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 522 THR cc_start: 0.7473 (OUTLIER) cc_final: 0.7186 (p) REVERT: B 518 ARG cc_start: 0.6530 (tmm-80) cc_final: 0.6170 (ttt180) REVERT: B 619 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.7176 (ttm-80) outliers start: 18 outliers final: 16 residues processed: 103 average time/residue: 0.2702 time to fit residues: 37.4596 Evaluate side-chains 103 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.0070 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN B 204 HIS B 216 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8792 Z= 0.142 Angle : 0.490 7.101 11868 Z= 0.252 Chirality : 0.038 0.169 1344 Planarity : 0.004 0.036 1506 Dihedral : 8.980 170.589 1266 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.41 % Allowed : 15.98 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1086 helix: 1.22 (0.21), residues: 604 sheet: -0.96 (0.53), residues: 90 loop : 0.22 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 391 HIS 0.005 0.001 HIS B 204 PHE 0.018 0.001 PHE B 44 TYR 0.020 0.001 TYR A 506 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 522 THR cc_start: 0.7429 (OUTLIER) cc_final: 0.7148 (p) REVERT: B 518 ARG cc_start: 0.6607 (tmm-80) cc_final: 0.6227 (ttt180) REVERT: B 619 ARG cc_start: 0.7489 (ttm-80) cc_final: 0.7201 (ttm-80) outliers start: 13 outliers final: 11 residues processed: 100 average time/residue: 0.2645 time to fit residues: 35.1763 Evaluate side-chains 101 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 556 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN B 204 HIS ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8792 Z= 0.230 Angle : 0.554 7.218 11868 Z= 0.285 Chirality : 0.041 0.203 1344 Planarity : 0.004 0.037 1506 Dihedral : 9.110 172.819 1266 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.39 % Allowed : 15.43 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1086 helix: 0.94 (0.21), residues: 604 sheet: -1.15 (0.53), residues: 90 loop : 0.18 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 213 HIS 0.005 0.001 HIS B 204 PHE 0.018 0.001 PHE B 44 TYR 0.019 0.002 TYR A 506 ARG 0.002 0.000 ARG A 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.951 Fit side-chains REVERT: A 124 MET cc_start: 0.7058 (tpt) cc_final: 0.6701 (tpt) REVERT: A 522 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.7255 (p) REVERT: B 142 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6999 (mp) REVERT: B 518 ARG cc_start: 0.6638 (tmm-80) cc_final: 0.6291 (ttt180) REVERT: B 619 ARG cc_start: 0.7498 (ttm-80) cc_final: 0.7200 (ttm-80) outliers start: 22 outliers final: 18 residues processed: 104 average time/residue: 0.2560 time to fit residues: 35.5447 Evaluate side-chains 105 residues out of total 920 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.2980 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN B 204 HIS B 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.218547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.191695 restraints weight = 8530.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.194965 restraints weight = 6311.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.197512 restraints weight = 5059.603| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8792 Z= 0.161 Angle : 0.525 13.286 11868 Z= 0.267 Chirality : 0.039 0.173 1344 Planarity : 0.004 0.036 1506 Dihedral : 8.981 172.685 1266 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.74 % Allowed : 16.20 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1086 helix: 1.11 (0.21), residues: 594 sheet: -1.07 (0.54), residues: 90 loop : 0.24 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 391 HIS 0.004 0.001 HIS B 204 PHE 0.015 0.001 PHE B 44 TYR 0.020 0.001 TYR A 506 ARG 0.001 0.000 ARG B 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1741.58 seconds wall clock time: 32 minutes 37.79 seconds (1957.79 seconds total)