Starting phenix.real_space_refine on Fri Nov 15 22:53:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thi_41265/11_2024/8thi_41265.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thi_41265/11_2024/8thi_41265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thi_41265/11_2024/8thi_41265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thi_41265/11_2024/8thi_41265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thi_41265/11_2024/8thi_41265.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8thi_41265/11_2024/8thi_41265.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 66 5.16 5 Na 2 4.78 5 C 6392 2.51 5 N 1464 2.21 5 O 1593 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-5513/modules/chem_data/mon_lib" Total number of atoms: 9519 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4739 Classifications: {'peptide': 613} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 586} Chain: "B" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4719 Classifications: {'peptide': 611} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 584} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {' NA': 1, 'PGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {' NA': 1, 'PGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Time building chain proxies: 7.67, per 1000 atoms: 0.81 Number of scatterers: 9519 At special positions: 0 Unit cell: (73.04, 88.312, 139.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 2 15.00 Na 2 11.00 O 1593 8.00 N 1464 7.00 C 6392 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=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 39 through 63 removed outlier: 3.757A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 removed outlier: 3.735A pdb=" N MET A 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 108 removed outlier: 4.445A pdb=" N PHE A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 126 through 149 removed outlier: 3.881A pdb=" N VAL A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 173 removed outlier: 3.787A pdb=" N PHE A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.733A pdb=" N PHE A 177 " --> pdb=" O PRO A 174 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 178 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 179 " --> pdb=" O TRP A 176 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 180 " --> pdb=" O PHE A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 180' Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 191 through 205 Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.222A pdb=" N PHE A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.763A pdb=" N ALA A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 4.471A pdb=" N VAL A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 260 removed outlier: 4.134A pdb=" N PHE A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 277 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.668A pdb=" N GLY A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 320 removed outlier: 3.592A pdb=" N LEU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.897A pdb=" N LEU A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 354 Processing helix chain 'A' and resid 356 through 387 removed outlier: 4.435A pdb=" N ILE A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 395 through 422 removed outlier: 5.324A pdb=" N TRP A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ALA A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR A 412 " --> pdb=" O TRP A 408 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 426 through 445 Processing helix chain 'A' and resid 450 through 485 removed outlier: 3.969A pdb=" N VAL A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 501 through 517 removed outlier: 3.839A pdb=" N VAL A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 540 removed outlier: 3.786A pdb=" N PHE A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Proline residue: A 531 - end of helix Proline residue: A 535 - end of helix Processing helix chain 'A' and resid 543 through 558 removed outlier: 3.583A pdb=" N GLY A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 561 No H-bonds generated for 'chain 'A' and resid 559 through 561' Processing helix chain 'A' and resid 565 through 576 Processing helix chain 'A' and resid 578 through 587 Processing helix chain 'A' and resid 589 through 603 removed outlier: 4.493A pdb=" N VAL A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 4.599A pdb=" N VAL A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) Proline residue: A 611 - end of helix Processing helix chain 'B' and resid 6 through 32 Processing helix chain 'B' and resid 39 through 63 removed outlier: 3.799A pdb=" N TYR B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 4.048A pdb=" N MET B 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 109 removed outlier: 3.692A pdb=" N PHE B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.975A pdb=" N GLY B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 126 through 149 removed outlier: 3.809A pdb=" N VAL B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 173 removed outlier: 3.767A pdb=" N PHE B 159 " --> pdb=" O PRO B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 removed outlier: 3.725A pdb=" N VAL B 179 " --> pdb=" O TRP B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 191 through 207 removed outlier: 3.596A pdb=" N GLY B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.251A pdb=" N PHE B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 234 through 240 removed outlier: 4.252A pdb=" N VAL B 238 " --> pdb=" O THR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 260 removed outlier: 4.074A pdb=" N PHE B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 277 Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 300 through 308 removed outlier: 3.820A pdb=" N ASP B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 320 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.986A pdb=" N LEU B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 354 Processing helix chain 'B' and resid 356 through 387 removed outlier: 4.360A pdb=" N ILE B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'B' and resid 395 through 423 removed outlier: 5.638A pdb=" N TRP B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ALA B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR B 412 " --> pdb=" O TRP B 408 " (cutoff:3.500A) Proline residue: B 413 - end of helix removed outlier: 3.745A pdb=" N GLY B 423 " --> pdb=" O GLY B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 445 Processing helix chain 'B' and resid 450 through 485 removed outlier: 4.054A pdb=" N VAL B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.533A pdb=" N ARG B 490 " --> pdb=" O GLN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.768A pdb=" N ASP B 500 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 517 removed outlier: 3.630A pdb=" N VAL B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 540 Proline residue: B 531 - end of helix Proline residue: B 535 - end of helix Processing helix chain 'B' and resid 543 through 558 removed outlier: 3.658A pdb=" N GLY B 558 " --> pdb=" O ASN B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 561 No H-bonds generated for 'chain 'B' and resid 559 through 561' Processing helix chain 'B' and resid 565 through 576 removed outlier: 3.520A pdb=" N PHE B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 Processing helix chain 'B' and resid 589 through 603 removed outlier: 4.395A pdb=" N VAL B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 615 removed outlier: 4.450A pdb=" N ILE B 607 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 610 " --> pdb=" O ILE B 606 " (cutoff:3.500A) Proline residue: B 611 - end of helix 699 hydrogen bonds defined for protein. 2061 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: 2.78 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1427 1.32 - 1.44: 2580 1.44 - 1.56: 5611 1.56 - 1.69: 4 1.69 - 1.81: 122 Bond restraints: 9744 Sorted by residual: bond pdb=" N ILE A 4 " pdb=" CA ILE A 4 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.32e+01 bond pdb=" N THR A 280 " pdb=" CA THR A 280 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.19e+00 bond pdb=" N ASN A 5 " pdb=" CA ASN A 5 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.36e-02 5.41e+03 6.43e+00 bond pdb=" N LYS A 178 " pdb=" CA LYS A 178 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.31e-02 5.83e+03 6.36e+00 bond pdb=" N VAL B 498 " pdb=" CA VAL B 498 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.33e-02 5.65e+03 6.35e+00 ... (remaining 9739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 12758 1.14 - 2.28: 366 2.28 - 3.42: 79 3.42 - 4.56: 15 4.56 - 5.70: 20 Bond angle restraints: 13238 Sorted by residual: angle pdb=" N VAL A 498 " pdb=" CA VAL A 498 " pdb=" C VAL A 498 " ideal model delta sigma weight residual 113.10 110.06 3.04 9.70e-01 1.06e+00 9.81e+00 angle pdb=" C GLY A 282 " pdb=" N MET A 283 " pdb=" CA MET A 283 " ideal model delta sigma weight residual 120.31 115.67 4.64 1.52e+00 4.33e-01 9.33e+00 angle pdb=" N ASN A 5 " pdb=" CA ASN A 5 " pdb=" C ASN A 5 " ideal model delta sigma weight residual 114.04 110.50 3.54 1.24e+00 6.50e-01 8.16e+00 angle pdb=" CA ASP B 500 " pdb=" C ASP B 500 " pdb=" O ASP B 500 " ideal model delta sigma weight residual 121.07 117.93 3.14 1.10e+00 8.26e-01 8.14e+00 angle pdb=" N LYS A 178 " pdb=" CA LYS A 178 " pdb=" C LYS A 178 " ideal model delta sigma weight residual 113.18 109.97 3.21 1.21e+00 6.83e-01 7.06e+00 ... (remaining 13233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 5031 16.30 - 32.61: 529 32.61 - 48.91: 120 48.91 - 65.21: 23 65.21 - 81.51: 5 Dihedral angle restraints: 5708 sinusoidal: 2193 harmonic: 3515 Sorted by residual: dihedral pdb=" CB MET B 556 " pdb=" CG MET B 556 " pdb=" SD MET B 556 " pdb=" CE MET B 556 " ideal model delta sinusoidal sigma weight residual 60.00 114.20 -54.20 3 1.50e+01 4.44e-03 9.26e+00 dihedral pdb=" CB LYS B 236 " pdb=" CG LYS B 236 " pdb=" CD LYS B 236 " pdb=" CE LYS B 236 " ideal model delta sinusoidal sigma weight residual -60.00 -114.11 54.11 3 1.50e+01 4.44e-03 9.26e+00 dihedral pdb=" CB MET A 556 " pdb=" CG MET A 556 " pdb=" SD MET A 556 " pdb=" CE MET A 556 " ideal model delta sinusoidal sigma weight residual 60.00 114.10 -54.10 3 1.50e+01 4.44e-03 9.26e+00 ... (remaining 5705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1255 0.046 - 0.091: 299 0.091 - 0.137: 45 0.137 - 0.183: 1 0.183 - 0.229: 3 Chirality restraints: 1603 Sorted by residual: chirality pdb=" CB ILE A 4 " pdb=" CA ILE A 4 " pdb=" CG1 ILE A 4 " pdb=" CG2 ILE A 4 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL B 498 " pdb=" CA VAL B 498 " pdb=" CG1 VAL B 498 " pdb=" CG2 VAL B 498 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL B 498 " pdb=" N VAL B 498 " pdb=" C VAL B 498 " pdb=" CB VAL B 498 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 1600 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 281 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C GLY A 281 " -0.037 2.00e-02 2.50e+03 pdb=" O GLY A 281 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY A 282 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 498 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C VAL B 498 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL B 498 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA B 499 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 426 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 427 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " 0.018 5.00e-02 4.00e+02 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1184 2.75 - 3.29: 9613 3.29 - 3.82: 15789 3.82 - 4.36: 17014 4.36 - 4.90: 31284 Nonbonded interactions: 74884 Sorted by model distance: nonbonded pdb=" O SER A 298 " pdb="NA NA A 702 " model vdw 2.209 2.470 nonbonded pdb=" O VAL B 179 " pdb=" OH TYR B 185 " model vdw 2.209 3.040 nonbonded pdb=" O GLY A 277 " pdb=" OG1 THR A 391 " model vdw 2.234 3.040 nonbonded pdb=" O THR B 450 " pdb=" OG SER B 453 " model vdw 2.281 3.040 nonbonded pdb=" O GLY A 337 " pdb="NA NA A 702 " model vdw 2.303 2.470 ... (remaining 74879 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' and (resid 5 through 615 or (resid 701 and (name C1 or name C11 or na \ me C12 or name C2 or name C3 or name C31 or name C32 or name C33 or name C4 or n \ ame C5 or name C6 or name O11 or name O1P or name O2 or name O2P or name O3 or n \ ame O31 or name O3P or name O4P or name O5 or name O6 or name P )) or resid 702) \ ) 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 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: 5.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.760 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: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 0.045 9744 Z= 0.196 Angle : 0.510 5.699 13238 Z= 0.290 Chirality : 0.038 0.229 1603 Planarity : 0.003 0.033 1597 Dihedral : 13.987 81.514 3444 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.29 % Allowed : 3.05 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.25), residues: 1220 helix: 2.44 (0.17), residues: 954 sheet: None (None), residues: 0 loop : 0.27 (0.41), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 200 HIS 0.002 0.001 HIS B 100 PHE 0.014 0.001 PHE B 98 TYR 0.010 0.001 TYR A 3 ARG 0.002 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 183 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7850 (mtp) cc_final: 0.7553 (mtm) REVERT: A 178 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7069 (mmtt) REVERT: A 198 LEU cc_start: 0.8513 (tp) cc_final: 0.8178 (mp) REVERT: A 264 ILE cc_start: 0.8538 (mt) cc_final: 0.8323 (tp) REVERT: A 508 MET cc_start: 0.8623 (mmt) cc_final: 0.8415 (mmm) REVERT: A 566 MET cc_start: 0.8181 (mmm) cc_final: 0.7977 (mmt) REVERT: B 10 TRP cc_start: 0.8262 (m100) cc_final: 0.7987 (m100) REVERT: B 564 MET cc_start: 0.8459 (tpp) cc_final: 0.7890 (tpp) outliers start: 3 outliers final: 0 residues processed: 185 average time/residue: 0.1667 time to fit residues: 46.9677 Evaluate side-chains 114 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 110 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 ASN A 228 ASN A 486 GLN B 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9744 Z= 0.183 Angle : 0.547 10.715 13238 Z= 0.273 Chirality : 0.039 0.153 1603 Planarity : 0.004 0.033 1597 Dihedral : 5.907 64.822 1340 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.57 % Allowed : 8.64 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.25), residues: 1220 helix: 2.48 (0.17), residues: 958 sheet: None (None), residues: 0 loop : 0.27 (0.42), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 10 HIS 0.003 0.001 HIS A 285 PHE 0.018 0.001 PHE A 158 TYR 0.013 0.001 TYR A 349 ARG 0.003 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.984 Fit side-chains REVERT: A 508 MET cc_start: 0.8629 (mmt) cc_final: 0.8410 (mmm) REVERT: B 204 MET cc_start: 0.8521 (tpp) cc_final: 0.8240 (tpt) REVERT: B 316 MET cc_start: 0.7105 (mtp) cc_final: 0.6885 (mtp) REVERT: B 376 MET cc_start: 0.7193 (mmt) cc_final: 0.6948 (mmt) REVERT: B 378 MET cc_start: 0.8683 (tpp) cc_final: 0.8327 (tpp) REVERT: B 564 MET cc_start: 0.8420 (tpp) cc_final: 0.7915 (tpp) outliers start: 16 outliers final: 6 residues processed: 129 average time/residue: 0.1598 time to fit residues: 32.2195 Evaluate side-chains 113 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 110 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9744 Z= 0.218 Angle : 0.568 8.676 13238 Z= 0.288 Chirality : 0.040 0.149 1603 Planarity : 0.004 0.033 1597 Dihedral : 5.854 65.051 1336 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.06 % Allowed : 10.12 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.25), residues: 1220 helix: 2.29 (0.17), residues: 967 sheet: None (None), residues: 0 loop : 0.32 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 408 HIS 0.004 0.001 HIS B 285 PHE 0.020 0.001 PHE B 20 TYR 0.016 0.001 TYR A 349 ARG 0.005 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.074 Fit side-chains REVERT: A 508 MET cc_start: 0.8670 (mmt) cc_final: 0.8446 (mmm) REVERT: B 10 TRP cc_start: 0.8523 (m100) cc_final: 0.7950 (m100) REVERT: B 378 MET cc_start: 0.8846 (tpp) cc_final: 0.8521 (tpp) REVERT: B 564 MET cc_start: 0.8422 (tpp) cc_final: 0.7940 (tpp) outliers start: 21 outliers final: 13 residues processed: 121 average time/residue: 0.1641 time to fit residues: 31.2064 Evaluate side-chains 114 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 400 CYS Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 74 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 0.0270 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9744 Z= 0.180 Angle : 0.529 7.072 13238 Z= 0.266 Chirality : 0.039 0.151 1603 Planarity : 0.004 0.038 1597 Dihedral : 5.610 66.247 1336 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.77 % Allowed : 11.89 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.25), residues: 1220 helix: 2.33 (0.17), residues: 966 sheet: None (None), residues: 0 loop : 0.34 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 408 HIS 0.002 0.001 HIS A 100 PHE 0.022 0.001 PHE A 251 TYR 0.008 0.001 TYR B 380 ARG 0.005 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.042 Fit side-chains REVERT: A 508 MET cc_start: 0.8678 (mmt) cc_final: 0.8436 (mmm) REVERT: B 10 TRP cc_start: 0.8540 (m100) cc_final: 0.7974 (m100) REVERT: B 378 MET cc_start: 0.8871 (tpp) cc_final: 0.8532 (tpp) REVERT: B 564 MET cc_start: 0.8409 (tpp) cc_final: 0.8127 (tpp) outliers start: 18 outliers final: 11 residues processed: 118 average time/residue: 0.1574 time to fit residues: 29.2834 Evaluate side-chains 108 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.1980 chunk 105 optimal weight: 0.0060 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 278 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9744 Z= 0.225 Angle : 0.564 11.276 13238 Z= 0.283 Chirality : 0.040 0.135 1603 Planarity : 0.004 0.040 1597 Dihedral : 5.389 62.948 1336 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.77 % Allowed : 13.16 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.25), residues: 1220 helix: 2.26 (0.17), residues: 959 sheet: None (None), residues: 0 loop : 0.32 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 408 HIS 0.004 0.001 HIS A 100 PHE 0.020 0.001 PHE B 167 TYR 0.011 0.001 TYR B 221 ARG 0.001 0.000 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.102 Fit side-chains REVERT: A 508 MET cc_start: 0.8706 (mmt) cc_final: 0.8455 (mmm) REVERT: B 10 TRP cc_start: 0.8449 (m100) cc_final: 0.7983 (m100) REVERT: B 185 TYR cc_start: 0.6016 (OUTLIER) cc_final: 0.5112 (m-10) REVERT: B 260 ASN cc_start: 0.8274 (p0) cc_final: 0.7715 (t0) REVERT: B 564 MET cc_start: 0.8406 (tpp) cc_final: 0.8127 (tpp) outliers start: 18 outliers final: 11 residues processed: 112 average time/residue: 0.1702 time to fit residues: 30.0213 Evaluate side-chains 109 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 97 optimal weight: 0.0470 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9744 Z= 0.163 Angle : 0.536 9.814 13238 Z= 0.263 Chirality : 0.038 0.169 1603 Planarity : 0.004 0.044 1597 Dihedral : 5.258 62.142 1336 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.77 % Allowed : 14.24 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.25), residues: 1220 helix: 2.31 (0.17), residues: 963 sheet: None (None), residues: 0 loop : 0.37 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 408 HIS 0.003 0.001 HIS A 100 PHE 0.019 0.001 PHE B 167 TYR 0.009 0.001 TYR B 380 ARG 0.001 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.033 Fit side-chains REVERT: A 508 MET cc_start: 0.8720 (mmt) cc_final: 0.8458 (mmm) REVERT: B 10 TRP cc_start: 0.8417 (m100) cc_final: 0.8000 (m100) REVERT: B 98 PHE cc_start: 0.8952 (t80) cc_final: 0.8517 (t80) REVERT: B 260 ASN cc_start: 0.8192 (p0) cc_final: 0.7603 (t0) REVERT: B 378 MET cc_start: 0.8627 (tpp) cc_final: 0.8260 (tpp) REVERT: B 471 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8349 (mtm) REVERT: B 564 MET cc_start: 0.8382 (tpp) cc_final: 0.8126 (tpp) outliers start: 18 outliers final: 10 residues processed: 109 average time/residue: 0.1629 time to fit residues: 27.9897 Evaluate side-chains 104 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9744 Z= 0.161 Angle : 0.541 9.435 13238 Z= 0.262 Chirality : 0.038 0.150 1603 Planarity : 0.004 0.043 1597 Dihedral : 5.273 60.763 1336 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.67 % Allowed : 14.73 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.25), residues: 1220 helix: 2.42 (0.17), residues: 955 sheet: None (None), residues: 0 loop : 0.35 (0.41), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 408 HIS 0.003 0.001 HIS A 100 PHE 0.023 0.001 PHE B 167 TYR 0.012 0.001 TYR A 321 ARG 0.001 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 1.084 Fit side-chains REVERT: A 508 MET cc_start: 0.8719 (mmt) cc_final: 0.8451 (mmm) REVERT: B 10 TRP cc_start: 0.8355 (m100) cc_final: 0.7983 (m100) REVERT: B 98 PHE cc_start: 0.8943 (t80) cc_final: 0.8499 (t80) REVERT: B 378 MET cc_start: 0.8730 (tpp) cc_final: 0.8253 (tpp) REVERT: B 471 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8286 (mtm) REVERT: B 564 MET cc_start: 0.8390 (tpp) cc_final: 0.8145 (tpp) outliers start: 17 outliers final: 15 residues processed: 110 average time/residue: 0.1677 time to fit residues: 28.9085 Evaluate side-chains 111 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9744 Z= 0.156 Angle : 0.540 9.190 13238 Z= 0.261 Chirality : 0.038 0.146 1603 Planarity : 0.004 0.041 1597 Dihedral : 5.237 61.374 1336 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.57 % Allowed : 15.42 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.25), residues: 1220 helix: 2.42 (0.17), residues: 951 sheet: None (None), residues: 0 loop : 0.35 (0.41), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 408 HIS 0.003 0.001 HIS A 100 PHE 0.023 0.001 PHE B 167 TYR 0.010 0.001 TYR A 321 ARG 0.001 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.041 Fit side-chains REVERT: A 508 MET cc_start: 0.8710 (mmt) cc_final: 0.8448 (mmm) REVERT: B 10 TRP cc_start: 0.8342 (m100) cc_final: 0.7997 (m100) REVERT: B 98 PHE cc_start: 0.8935 (t80) cc_final: 0.8444 (t80) REVERT: B 378 MET cc_start: 0.8728 (tpp) cc_final: 0.8303 (tpp) REVERT: B 471 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8295 (mtm) REVERT: B 564 MET cc_start: 0.8387 (tpp) cc_final: 0.8096 (tpp) outliers start: 16 outliers final: 11 residues processed: 109 average time/residue: 0.1569 time to fit residues: 27.1486 Evaluate side-chains 109 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9744 Z= 0.182 Angle : 0.553 9.246 13238 Z= 0.270 Chirality : 0.039 0.147 1603 Planarity : 0.004 0.037 1597 Dihedral : 5.246 61.388 1336 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.67 % Allowed : 15.42 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.25), residues: 1220 helix: 2.32 (0.17), residues: 960 sheet: None (None), residues: 0 loop : 0.38 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 408 HIS 0.003 0.001 HIS A 100 PHE 0.024 0.001 PHE B 167 TYR 0.010 0.001 TYR A 321 ARG 0.002 0.000 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.175 Fit side-chains REVERT: A 508 MET cc_start: 0.8717 (mmt) cc_final: 0.8461 (mmm) REVERT: B 10 TRP cc_start: 0.8326 (m100) cc_final: 0.8002 (m100) REVERT: B 98 PHE cc_start: 0.8933 (t80) cc_final: 0.8424 (t80) REVERT: B 378 MET cc_start: 0.8778 (tpp) cc_final: 0.8381 (tpp) REVERT: B 467 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7708 (p) REVERT: B 471 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8298 (mtm) REVERT: B 564 MET cc_start: 0.8384 (tpp) cc_final: 0.8143 (tpp) outliers start: 17 outliers final: 13 residues processed: 107 average time/residue: 0.1646 time to fit residues: 27.7056 Evaluate side-chains 113 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9744 Z= 0.184 Angle : 0.577 12.271 13238 Z= 0.278 Chirality : 0.039 0.203 1603 Planarity : 0.004 0.049 1597 Dihedral : 5.275 61.933 1336 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.57 % Allowed : 15.32 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.25), residues: 1220 helix: 2.28 (0.17), residues: 960 sheet: None (None), residues: 0 loop : 0.34 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 408 HIS 0.003 0.001 HIS A 100 PHE 0.027 0.001 PHE B 167 TYR 0.010 0.001 TYR A 321 ARG 0.003 0.000 ARG B 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.895 Fit side-chains REVERT: A 508 MET cc_start: 0.8717 (mmt) cc_final: 0.8463 (mmm) REVERT: B 10 TRP cc_start: 0.8314 (m100) cc_final: 0.7982 (m100) REVERT: B 98 PHE cc_start: 0.8930 (t80) cc_final: 0.8414 (t80) REVERT: B 378 MET cc_start: 0.8754 (tpp) cc_final: 0.8429 (tpp) REVERT: B 467 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7673 (p) REVERT: B 471 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8275 (mtm) REVERT: B 564 MET cc_start: 0.8377 (tpp) cc_final: 0.8090 (tpp) outliers start: 16 outliers final: 14 residues processed: 111 average time/residue: 0.1621 time to fit residues: 28.3195 Evaluate side-chains 116 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 577 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 85 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.096247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.073745 restraints weight = 24062.535| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.10 r_work: 0.3051 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9744 Z= 0.163 Angle : 0.564 10.334 13238 Z= 0.271 Chirality : 0.038 0.199 1603 Planarity : 0.004 0.049 1597 Dihedral : 5.248 62.694 1336 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.38 % Allowed : 15.62 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.25), residues: 1220 helix: 2.27 (0.17), residues: 961 sheet: None (None), residues: 0 loop : 0.38 (0.41), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 408 HIS 0.006 0.001 HIS A 100 PHE 0.024 0.001 PHE B 167 TYR 0.010 0.001 TYR A 321 ARG 0.002 0.000 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.16 seconds wall clock time: 39 minutes 49.64 seconds (2389.64 seconds total)