Starting phenix.real_space_refine on Mon Sep 30 07:29:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz2_41731/09_2024/8tz2_41731_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz2_41731/09_2024/8tz2_41731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz2_41731/09_2024/8tz2_41731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz2_41731/09_2024/8tz2_41731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz2_41731/09_2024/8tz2_41731_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tz2_41731/09_2024/8tz2_41731_trim.cif" } resolution = 2.8 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= 0.002 sd= 0.089 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 S 87 5.16 5 Na 6 4.78 5 C 8256 2.51 5 N 1926 2.21 5 O 2145 1.98 5 H 12165 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24591 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 66 Unusual residues: {' NA': 2, 'LBN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 40 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B Time building chain proxies: 22.61, per 1000 atoms: 0.92 Number of scatterers: 24591 At special positions: 0 Unit cell: (130.68, 127.44, 75.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 87 16.00 P 6 15.00 Na 6 11.00 O 2145 8.00 N 1926 7.00 C 8256 6.00 H 12165 1.00 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: 6.53 Conformation dependent library (CDL) restraints added in 1.9 seconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 3 sheets defined 89.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 103 through 130 Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 157 through 198 Proline residue: A 167 - end of helix removed outlier: 4.698A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.716A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.126A pdb=" N VAL A 230 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 4.610A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 272 through 282 removed outlier: 4.392A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 294 through 312 Processing helix chain 'A' and resid 312 through 330 removed outlier: 3.527A pdb=" N TRP A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 349 through 361 Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.502A pdb=" N TYR A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.258A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 437 through 479 removed outlier: 3.503A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.607A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.116A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.709A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 574 through 586 Processing helix chain 'A' and resid 589 through 619 removed outlier: 3.558A pdb=" N ALA A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 157 through 198 Proline residue: C 167 - end of helix removed outlier: 4.698A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.717A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 removed outlier: 4.126A pdb=" N VAL C 230 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 251 removed outlier: 4.610A pdb=" N VAL C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 270 Processing helix chain 'C' and resid 272 through 282 removed outlier: 4.392A pdb=" N GLY C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 312 through 330 removed outlier: 3.527A pdb=" N TRP C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 349 through 361 Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 375 Processing helix chain 'C' and resid 381 through 389 removed outlier: 3.502A pdb=" N TYR C 385 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 removed outlier: 4.259A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 479 removed outlier: 3.504A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.607A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 4.116A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 515 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.708A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 574 through 586 Processing helix chain 'C' and resid 589 through 619 removed outlier: 3.558A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 103 Processing helix chain 'B' and resid 103 through 130 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 157 through 198 Proline residue: B 167 - end of helix removed outlier: 4.698A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.717A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 4.127A pdb=" N VAL B 230 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 251 removed outlier: 4.610A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 270 Processing helix chain 'B' and resid 272 through 282 removed outlier: 4.391A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 294 through 312 Processing helix chain 'B' and resid 312 through 330 removed outlier: 3.526A pdb=" N TRP B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 349 through 361 Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 362 through 375 Processing helix chain 'B' and resid 381 through 389 removed outlier: 3.502A pdb=" N TYR B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 removed outlier: 4.258A pdb=" N ALA B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 437 through 479 removed outlier: 3.503A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 482 No H-bonds generated for 'chain 'B' and resid 480 through 482' Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.607A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.116A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.709A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 589 through 619 removed outlier: 3.558A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA2, first strand: chain 'C' and resid 546 through 547 Processing sheet with id=AA3, first strand: chain 'B' and resid 546 through 547 979 hydrogen bonds defined for protein. 2874 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: 9.43 Time building geometry restraints manager: 7.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12147 1.03 - 1.22: 30 1.22 - 1.42: 5373 1.42 - 1.61: 7191 1.61 - 1.81: 168 Bond restraints: 24909 Sorted by residual: bond pdb=" O4 LBN A 804 " pdb=" P1 LBN A 804 " ideal model delta sigma weight residual 1.497 1.646 -0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" O4 LBN B 804 " pdb=" P1 LBN B 804 " ideal model delta sigma weight residual 1.497 1.646 -0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" O4 LBN A 803 " pdb=" P1 LBN A 803 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" O4 LBN B 803 " pdb=" P1 LBN B 803 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" O4 LBN C 804 " pdb=" P1 LBN C 804 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.46e+01 ... (remaining 24904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 44676 3.21 - 6.42: 132 6.42 - 9.64: 15 9.64 - 12.85: 6 12.85 - 16.06: 6 Bond angle restraints: 44835 Sorted by residual: angle pdb=" O1 LBN C 803 " pdb=" P1 LBN C 803 " pdb=" O2 LBN C 803 " ideal model delta sigma weight residual 93.45 109.51 -16.06 3.00e+00 1.11e-01 2.87e+01 angle pdb=" O1 LBN A 803 " pdb=" P1 LBN A 803 " pdb=" O2 LBN A 803 " ideal model delta sigma weight residual 93.45 109.49 -16.04 3.00e+00 1.11e-01 2.86e+01 angle pdb=" O1 LBN A 804 " pdb=" P1 LBN A 804 " pdb=" O2 LBN A 804 " ideal model delta sigma weight residual 93.45 109.45 -16.00 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O1 LBN B 803 " pdb=" P1 LBN B 803 " pdb=" O2 LBN B 803 " ideal model delta sigma weight residual 93.45 109.45 -16.00 3.00e+00 1.11e-01 2.84e+01 angle pdb=" O1 LBN B 804 " pdb=" P1 LBN B 804 " pdb=" O2 LBN B 804 " ideal model delta sigma weight residual 93.45 109.45 -16.00 3.00e+00 1.11e-01 2.84e+01 ... (remaining 44830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.57: 11442 32.57 - 65.14: 411 65.14 - 97.71: 9 97.71 - 130.28: 6 130.28 - 162.85: 6 Dihedral angle restraints: 11874 sinusoidal: 6144 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN C 804 " pdb=" C2 LBN C 804 " pdb=" C3 LBN C 804 " pdb=" O7 LBN C 804 " ideal model delta sinusoidal sigma weight residual 62.67 -100.18 162.85 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" O5 LBN A 804 " pdb=" C2 LBN A 804 " pdb=" C3 LBN A 804 " pdb=" O7 LBN A 804 " ideal model delta sinusoidal sigma weight residual 62.67 -100.13 162.80 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" O5 LBN B 804 " pdb=" C2 LBN B 804 " pdb=" C3 LBN B 804 " pdb=" O7 LBN B 804 " ideal model delta sinusoidal sigma weight residual 62.67 -100.10 162.77 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 11871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1390 0.038 - 0.075: 437 0.075 - 0.113: 153 0.113 - 0.150: 3 0.150 - 0.188: 6 Chirality restraints: 1989 Sorted by residual: chirality pdb=" C2 LBN C 804 " pdb=" C1 LBN C 804 " pdb=" C3 LBN C 804 " pdb=" O7 LBN C 804 " both_signs ideal model delta sigma weight residual False -2.36 -2.55 0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" C2 LBN A 804 " pdb=" C1 LBN A 804 " pdb=" C3 LBN A 804 " pdb=" O7 LBN A 804 " both_signs ideal model delta sigma weight residual False -2.36 -2.55 0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" C2 LBN B 804 " pdb=" C1 LBN B 804 " pdb=" C3 LBN B 804 " pdb=" O7 LBN B 804 " both_signs ideal model delta sigma weight residual False -2.36 -2.55 0.18 2.00e-01 2.50e+01 8.53e-01 ... (remaining 1986 not shown) Planarity restraints: 3639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 195 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C LEU B 195 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU B 195 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 196 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 195 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C LEU A 195 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU A 195 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A 196 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 195 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C LEU C 195 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU C 195 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL C 196 " -0.014 2.00e-02 2.50e+03 ... (remaining 3636 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 956 2.18 - 2.79: 47350 2.79 - 3.39: 68133 3.39 - 4.00: 88119 4.00 - 4.60: 139696 Nonbonded interactions: 344254 Sorted by model distance: nonbonded pdb=" OE1 GLN C 206 " pdb=" H GLN C 206 " model vdw 1.581 2.450 nonbonded pdb=" OE1 GLN A 206 " pdb=" H GLN A 206 " model vdw 1.582 2.450 nonbonded pdb=" OE1 GLN B 206 " pdb=" H GLN B 206 " model vdw 1.582 2.450 nonbonded pdb=" OE1 GLU B 525 " pdb=" H GLU B 525 " model vdw 1.642 2.450 nonbonded pdb=" OE1 GLU C 525 " pdb=" H GLU C 525 " model vdw 1.642 2.450 ... (remaining 344249 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 5.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.740 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 62.400 Find NCS groups from input model: 0.560 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:19.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 0.007 0.149 12744 Z= 0.480 Angle : 0.753 16.062 17313 Z= 0.343 Chirality : 0.041 0.188 1989 Planarity : 0.004 0.036 2097 Dihedral : 15.024 162.847 4380 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.21), residues: 1593 helix: 2.46 (0.14), residues: 1326 sheet: None (None), residues: 0 loop : -0.12 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 316 HIS 0.003 0.001 HIS A 367 PHE 0.015 0.001 PHE B 413 TYR 0.009 0.001 TYR B 231 ARG 0.002 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7618 (mmt180) REVERT: C 222 LEU cc_start: 0.7957 (tp) cc_final: 0.7687 (mt) REVERT: B 222 LEU cc_start: 0.8096 (tp) cc_final: 0.7841 (mt) REVERT: B 430 MET cc_start: 0.7923 (mtt) cc_final: 0.7649 (mtt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 1.9681 time to fit residues: 531.9098 Evaluate side-chains 156 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12744 Z= 0.160 Angle : 0.473 5.947 17313 Z= 0.252 Chirality : 0.036 0.118 1989 Planarity : 0.004 0.041 2097 Dihedral : 12.530 127.102 1830 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.87 % Allowed : 9.26 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.21), residues: 1593 helix: 2.89 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : 0.25 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 316 HIS 0.003 0.001 HIS B 367 PHE 0.010 0.001 PHE C 279 TYR 0.009 0.001 TYR B 231 ARG 0.002 0.000 ARG C 589 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 436 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7525 (mmt180) REVERT: C 201 LYS cc_start: 0.7187 (mptt) cc_final: 0.6476 (tttt) REVERT: C 222 LEU cc_start: 0.8065 (tp) cc_final: 0.7529 (mt) REVERT: C 305 MET cc_start: 0.7849 (mmm) cc_final: 0.7597 (mmp) REVERT: C 370 MET cc_start: 0.8406 (mtm) cc_final: 0.8031 (mtp) REVERT: C 430 MET cc_start: 0.7897 (mtt) cc_final: 0.7441 (mtt) REVERT: B 222 LEU cc_start: 0.7818 (tp) cc_final: 0.7602 (mt) REVERT: B 440 GLU cc_start: 0.7778 (tt0) cc_final: 0.7573 (tt0) outliers start: 11 outliers final: 4 residues processed: 162 average time/residue: 1.7955 time to fit residues: 330.8953 Evaluate side-chains 151 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 147 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain B residue 350 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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: 0.7906 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12744 Z= 0.300 Angle : 0.532 6.664 17313 Z= 0.284 Chirality : 0.039 0.125 1989 Planarity : 0.004 0.048 2097 Dihedral : 12.047 132.544 1830 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.43 % Allowed : 9.82 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.21), residues: 1593 helix: 2.64 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : -0.12 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 316 HIS 0.005 0.001 HIS B 367 PHE 0.016 0.001 PHE A 279 TYR 0.007 0.002 TYR C 285 ARG 0.002 0.000 ARG C 589 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7090 (mptt) cc_final: 0.6520 (tttt) REVERT: C 201 LYS cc_start: 0.7392 (mptt) cc_final: 0.6734 (tttt) REVERT: C 222 LEU cc_start: 0.8148 (tp) cc_final: 0.7613 (mt) REVERT: C 305 MET cc_start: 0.7897 (mmm) cc_final: 0.7652 (mmp) REVERT: C 355 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7806 (ttt-90) REVERT: C 430 MET cc_start: 0.8174 (mtt) cc_final: 0.7589 (mtt) REVERT: C 592 ASP cc_start: 0.7377 (m-30) cc_final: 0.7162 (m-30) REVERT: B 222 LEU cc_start: 0.7924 (tp) cc_final: 0.7622 (mt) outliers start: 18 outliers final: 11 residues processed: 170 average time/residue: 1.9938 time to fit residues: 381.5831 Evaluate side-chains 165 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12744 Z= 0.170 Angle : 0.455 5.413 17313 Z= 0.240 Chirality : 0.036 0.120 1989 Planarity : 0.003 0.041 2097 Dihedral : 10.894 131.231 1830 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.19 % Allowed : 11.24 % Favored : 87.57 % 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: 3.56 (0.21), residues: 1593 helix: 2.86 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.18 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 316 HIS 0.002 0.001 HIS C 288 PHE 0.011 0.001 PHE C 279 TYR 0.008 0.001 TYR C 231 ARG 0.001 0.000 ARG C 557 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7210 (mptt) cc_final: 0.6651 (tttt) REVERT: C 201 LYS cc_start: 0.7422 (mptt) cc_final: 0.6776 (tttt) REVERT: C 222 LEU cc_start: 0.8022 (tp) cc_final: 0.7447 (mt) REVERT: C 305 MET cc_start: 0.7897 (mmm) cc_final: 0.7642 (mmp) REVERT: C 355 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7751 (ttt-90) REVERT: C 430 MET cc_start: 0.8193 (mtt) cc_final: 0.7646 (mtt) REVERT: B 222 LEU cc_start: 0.7919 (tp) cc_final: 0.7549 (mt) REVERT: B 242 GLN cc_start: 0.8556 (mt0) cc_final: 0.8309 (mt0) REVERT: B 440 GLU cc_start: 0.7679 (tt0) cc_final: 0.7475 (tt0) outliers start: 15 outliers final: 10 residues processed: 168 average time/residue: 1.8838 time to fit residues: 356.3948 Evaluate side-chains 158 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.7918 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12744 Z= 0.291 Angle : 0.522 6.423 17313 Z= 0.278 Chirality : 0.038 0.124 1989 Planarity : 0.004 0.047 2097 Dihedral : 10.640 128.130 1830 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.82 % Allowed : 11.56 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.21), residues: 1593 helix: 2.62 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.34 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.003 0.001 HIS C 288 PHE 0.015 0.001 PHE A 279 TYR 0.009 0.001 TYR C 231 ARG 0.002 0.000 ARG C 436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7315 (mptt) cc_final: 0.6736 (tttt) REVERT: C 222 LEU cc_start: 0.8059 (tp) cc_final: 0.7503 (mt) REVERT: C 355 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7834 (ttt-90) REVERT: C 430 MET cc_start: 0.8254 (mtt) cc_final: 0.7645 (mtt) REVERT: C 592 ASP cc_start: 0.7444 (m-30) cc_final: 0.7218 (m-30) REVERT: B 222 LEU cc_start: 0.7951 (tp) cc_final: 0.7531 (mt) REVERT: B 267 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: B 440 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7478 (tt0) outliers start: 23 outliers final: 17 residues processed: 179 average time/residue: 2.0148 time to fit residues: 404.6109 Evaluate side-chains 174 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 80 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12744 Z= 0.175 Angle : 0.456 5.782 17313 Z= 0.241 Chirality : 0.036 0.119 1989 Planarity : 0.003 0.042 2097 Dihedral : 10.204 125.048 1830 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.98 % Allowed : 11.80 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.21), residues: 1593 helix: 2.87 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.29 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.002 0.001 HIS C 288 PHE 0.011 0.001 PHE C 279 TYR 0.007 0.001 TYR C 231 ARG 0.001 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7245 (mptt) cc_final: 0.6664 (tttt) REVERT: A 242 GLN cc_start: 0.8535 (mt0) cc_final: 0.8297 (mt0) REVERT: C 201 LYS cc_start: 0.7750 (mmtt) cc_final: 0.7092 (tmmt) REVERT: C 222 LEU cc_start: 0.8025 (tp) cc_final: 0.7444 (mt) REVERT: C 355 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7791 (ttt-90) REVERT: C 430 MET cc_start: 0.8229 (mtt) cc_final: 0.7649 (mtt) REVERT: C 489 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6291 (mp0) REVERT: C 592 ASP cc_start: 0.7461 (m-30) cc_final: 0.7200 (m-30) REVERT: B 242 GLN cc_start: 0.8549 (mt0) cc_final: 0.8279 (mt0) REVERT: B 267 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: B 305 MET cc_start: 0.7867 (mmp) cc_final: 0.7479 (mmt) REVERT: B 440 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7459 (tt0) outliers start: 25 outliers final: 13 residues processed: 171 average time/residue: 1.9426 time to fit residues: 373.8481 Evaluate side-chains 166 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7872 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12744 Z= 0.169 Angle : 0.452 5.676 17313 Z= 0.237 Chirality : 0.035 0.118 1989 Planarity : 0.003 0.040 2097 Dihedral : 10.019 122.099 1830 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.66 % Allowed : 12.51 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.21), residues: 1593 helix: 2.96 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.29 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 316 HIS 0.002 0.001 HIS C 288 PHE 0.011 0.001 PHE C 279 TYR 0.007 0.001 TYR C 231 ARG 0.001 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7247 (mptt) cc_final: 0.6659 (tttt) REVERT: A 242 GLN cc_start: 0.8526 (mt0) cc_final: 0.8283 (mt0) REVERT: C 201 LYS cc_start: 0.7577 (mmtt) cc_final: 0.6908 (tttt) REVERT: C 222 LEU cc_start: 0.8018 (tp) cc_final: 0.7420 (mt) REVERT: C 355 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7774 (ttt-90) REVERT: C 430 MET cc_start: 0.8238 (mtt) cc_final: 0.7663 (mtt) REVERT: C 489 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6283 (mp0) REVERT: C 592 ASP cc_start: 0.7387 (m-30) cc_final: 0.7164 (m-30) REVERT: B 201 LYS cc_start: 0.7253 (mptt) cc_final: 0.6682 (tttt) REVERT: B 222 LEU cc_start: 0.8115 (tt) cc_final: 0.7774 (mt) REVERT: B 242 GLN cc_start: 0.8539 (mt0) cc_final: 0.8224 (mt0) REVERT: B 305 MET cc_start: 0.7838 (mmp) cc_final: 0.7436 (mmt) REVERT: B 440 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7467 (tt0) outliers start: 21 outliers final: 14 residues processed: 169 average time/residue: 1.9560 time to fit residues: 370.7304 Evaluate side-chains 167 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.7883 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12744 Z= 0.192 Angle : 0.464 5.852 17313 Z= 0.244 Chirality : 0.036 0.119 1989 Planarity : 0.003 0.041 2097 Dihedral : 9.981 116.998 1830 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.90 % Allowed : 12.43 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.21), residues: 1593 helix: 2.93 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.30 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 316 HIS 0.003 0.001 HIS C 288 PHE 0.014 0.001 PHE C 146 TYR 0.007 0.001 TYR C 231 ARG 0.001 0.000 ARG C 436 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7273 (mptt) cc_final: 0.6677 (tttt) REVERT: A 242 GLN cc_start: 0.8553 (mt0) cc_final: 0.8313 (mt0) REVERT: C 201 LYS cc_start: 0.7537 (mmtt) cc_final: 0.6852 (tmtt) REVERT: C 222 LEU cc_start: 0.8027 (tp) cc_final: 0.7431 (mt) REVERT: C 242 GLN cc_start: 0.8669 (mt0) cc_final: 0.8239 (mt0) REVERT: C 355 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7778 (ttt-90) REVERT: C 430 MET cc_start: 0.8251 (mtt) cc_final: 0.7669 (mtt) REVERT: C 489 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: C 592 ASP cc_start: 0.7401 (m-30) cc_final: 0.7165 (m-30) REVERT: B 201 LYS cc_start: 0.7281 (mptt) cc_final: 0.6703 (tttt) REVERT: B 222 LEU cc_start: 0.8109 (tt) cc_final: 0.7739 (mt) REVERT: B 242 GLN cc_start: 0.8552 (mt0) cc_final: 0.8226 (mt0) REVERT: B 267 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: B 313 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7935 (mt) REVERT: B 440 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7486 (tt0) outliers start: 24 outliers final: 15 residues processed: 172 average time/residue: 1.9501 time to fit residues: 376.1559 Evaluate side-chains 171 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12744 Z= 0.208 Angle : 0.472 5.934 17313 Z= 0.248 Chirality : 0.036 0.120 1989 Planarity : 0.003 0.042 2097 Dihedral : 9.855 106.239 1830 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.90 % Allowed : 12.59 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.21), residues: 1593 helix: 2.91 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.32 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.003 0.001 HIS C 288 PHE 0.012 0.001 PHE A 279 TYR 0.007 0.001 TYR C 231 ARG 0.002 0.000 ARG C 436 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6724 (mmt) cc_final: 0.6347 (mmm) REVERT: A 201 LYS cc_start: 0.7302 (mptt) cc_final: 0.6691 (tttt) REVERT: A 242 GLN cc_start: 0.8575 (mt0) cc_final: 0.8330 (mt0) REVERT: C 201 LYS cc_start: 0.7628 (mmtt) cc_final: 0.6891 (tmtt) REVERT: C 222 LEU cc_start: 0.8031 (tp) cc_final: 0.7436 (mt) REVERT: C 242 GLN cc_start: 0.8718 (mt0) cc_final: 0.8265 (mt0) REVERT: C 355 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7792 (ttt-90) REVERT: C 430 MET cc_start: 0.8247 (mtt) cc_final: 0.7656 (mtt) REVERT: C 489 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: C 592 ASP cc_start: 0.7449 (m-30) cc_final: 0.7189 (m-30) REVERT: B 201 LYS cc_start: 0.7295 (mptt) cc_final: 0.6714 (tttt) REVERT: B 222 LEU cc_start: 0.8135 (tt) cc_final: 0.7762 (mt) REVERT: B 267 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: B 313 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7960 (mt) REVERT: B 440 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7485 (tt0) outliers start: 24 outliers final: 16 residues processed: 169 average time/residue: 1.9455 time to fit residues: 369.4680 Evaluate side-chains 172 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12744 Z= 0.191 Angle : 0.461 5.759 17313 Z= 0.242 Chirality : 0.036 0.119 1989 Planarity : 0.003 0.041 2097 Dihedral : 9.586 101.765 1830 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.82 % Allowed : 12.59 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.21), residues: 1593 helix: 2.96 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.28 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.002 0.001 HIS C 288 PHE 0.015 0.001 PHE C 146 TYR 0.007 0.001 TYR C 231 ARG 0.001 0.000 ARG C 436 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6738 (mmt) cc_final: 0.6364 (mmm) REVERT: A 201 LYS cc_start: 0.7339 (mptt) cc_final: 0.6775 (tttt) REVERT: A 242 GLN cc_start: 0.8552 (mt0) cc_final: 0.8310 (mt0) REVERT: C 201 LYS cc_start: 0.7638 (mmtt) cc_final: 0.6910 (tmtt) REVERT: C 222 LEU cc_start: 0.8020 (tp) cc_final: 0.7422 (mt) REVERT: C 242 GLN cc_start: 0.8675 (mt0) cc_final: 0.8243 (mt0) REVERT: C 355 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7784 (ttt-90) REVERT: C 430 MET cc_start: 0.8246 (mtt) cc_final: 0.7657 (mtt) REVERT: C 489 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6331 (mp0) REVERT: C 592 ASP cc_start: 0.7417 (m-30) cc_final: 0.7170 (m-30) REVERT: B 201 LYS cc_start: 0.7296 (mptt) cc_final: 0.6717 (tttt) REVERT: B 222 LEU cc_start: 0.8145 (tt) cc_final: 0.7752 (mt) REVERT: B 242 GLN cc_start: 0.8611 (mt0) cc_final: 0.8292 (mt0) REVERT: B 313 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7993 (mt) REVERT: B 440 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7490 (tt0) outliers start: 23 outliers final: 16 residues processed: 170 average time/residue: 1.9048 time to fit residues: 363.3093 Evaluate side-chains 170 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.141139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.097735 restraints weight = 36220.696| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.28 r_work: 0.2920 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12744 Z= 0.238 Angle : 0.489 6.008 17313 Z= 0.258 Chirality : 0.037 0.121 1989 Planarity : 0.004 0.043 2097 Dihedral : 9.661 99.348 1830 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.74 % Allowed : 12.83 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.21), residues: 1593 helix: 2.85 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.32 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 316 HIS 0.003 0.001 HIS C 288 PHE 0.014 0.001 PHE A 279 TYR 0.007 0.001 TYR B 553 ARG 0.002 0.000 ARG C 436 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7441.28 seconds wall clock time: 129 minutes 21.58 seconds (7761.58 seconds total)