Starting phenix.real_space_refine on Fri Aug 22 20:41:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t4e_41028/08_2025/8t4e_41028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t4e_41028/08_2025/8t4e_41028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t4e_41028/08_2025/8t4e_41028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t4e_41028/08_2025/8t4e_41028.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t4e_41028/08_2025/8t4e_41028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t4e_41028/08_2025/8t4e_41028.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 4886 2.51 5 N 1356 2.21 5 O 1441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7714 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3417 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 18, 'TRANS': 510} Chain breaks: 2 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 881 Unresolved non-hydrogen dihedrals: 545 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'HIS:plan': 7, 'GLU:plan': 16, 'GLN:plan1': 24, 'PHE:plan': 6, 'ASP:plan': 9, 'TYR:plan': 9, 'ASN:plan1': 5, 'ARG:plan': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 400 Chain: "B" Number of atoms: 4227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4227 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 20, 'TRANS': 530} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 4, 'TRP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 70 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Time building chain proxies: 2.22, per 1000 atoms: 0.29 Number of scatterers: 7714 At special positions: 0 Unit cell: (73.832, 104.875, 134.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1441 8.00 N 1356 7.00 C 4886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 480.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2008 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 71.9% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.993A pdb=" N MET A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 4.007A pdb=" N PHE A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 270 removed outlier: 3.587A pdb=" N HIS A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 324 Processing helix chain 'A' and resid 324 through 373 removed outlier: 3.504A pdb=" N THR A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Proline residue: A 336 - end of helix removed outlier: 5.569A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Proline residue: A 342 - end of helix removed outlier: 3.831A pdb=" N LYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 382 through 437 removed outlier: 4.266A pdb=" N THR A 399 " --> pdb=" O GLN A 395 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 476 removed outlier: 3.905A pdb=" N MET A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 539 through 542 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 573 through 581 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 628 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.563A pdb=" N THR A 634 " --> pdb=" O GLY A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 644 through 658 Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 688 through 694 removed outlier: 3.537A pdb=" N ARG A 691 " --> pdb=" O SER A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 708 removed outlier: 3.873A pdb=" N VAL A 706 " --> pdb=" O HIS A 702 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 707 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 702 through 708' Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 734 through 742 Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 148 through 182 Proline residue: B 170 - end of helix removed outlier: 3.837A pdb=" N ILE B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 234 Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.662A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 removed outlier: 3.688A pdb=" N LEU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 removed outlier: 3.746A pdb=" N MET B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'B' and resid 266 through 289 Processing helix chain 'B' and resid 289 through 338 removed outlier: 4.189A pdb=" N LEU B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.652A pdb=" N VAL B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 347 through 400 removed outlier: 3.612A pdb=" N LEU B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 448 removed outlier: 3.684A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.715A pdb=" N ALA B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.566A pdb=" N VAL B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 592 removed outlier: 3.831A pdb=" N GLU B 591 " --> pdb=" O ASP B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 598 removed outlier: 3.737A pdb=" N THR B 598 " --> pdb=" O GLY B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 622 Processing helix chain 'B' and resid 638 through 646 Processing helix chain 'B' and resid 647 through 652 removed outlier: 6.691A pdb=" N SER B 650 " --> pdb=" O ASP B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 668 Processing sheet with id=AA1, first strand: chain 'A' and resid 527 through 528 removed outlier: 3.819A pdb=" N VAL A 503 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 511 removed outlier: 7.274A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 534 through 537 removed outlier: 6.463A pdb=" N PHE A 714 " --> pdb=" O ARG A 721 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 663 through 664 Processing sheet with id=AA5, first strand: chain 'B' and resid 489 through 493 removed outlier: 4.763A pdb=" N LEU B 489 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 491 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B 468 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N PHE B 470 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU B 528 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ASP B 472 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN B 526 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 546 through 549 removed outlier: 6.486A pdb=" N VAL B 498 " --> pdb=" O GLN B 671 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU B 673 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU B 675 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 502 " --> pdb=" O LEU B 675 " (cutoff:3.500A) 599 hydrogen bonds defined for protein. 1740 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2612 1.34 - 1.46: 1673 1.46 - 1.58: 3501 1.58 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 7839 Sorted by residual: bond pdb=" CA GLN B 471 " pdb=" C GLN B 471 " ideal model delta sigma weight residual 1.526 1.496 0.030 1.30e-02 5.92e+03 5.32e+00 bond pdb=" CA SER B 474 " pdb=" C SER B 474 " ideal model delta sigma weight residual 1.520 1.494 0.026 1.20e-02 6.94e+03 4.57e+00 bond pdb=" N VAL B 473 " pdb=" CA VAL B 473 " ideal model delta sigma weight residual 1.457 1.438 0.019 1.19e-02 7.06e+03 2.57e+00 bond pdb=" CA VAL B 473 " pdb=" C VAL B 473 " ideal model delta sigma weight residual 1.522 1.501 0.021 1.35e-02 5.49e+03 2.43e+00 bond pdb=" CA LYS B 469 " pdb=" C LYS B 469 " ideal model delta sigma weight residual 1.521 1.502 0.018 1.24e-02 6.50e+03 2.21e+00 ... (remaining 7834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 10486 1.99 - 3.99: 145 3.99 - 5.98: 32 5.98 - 7.98: 12 7.98 - 9.97: 5 Bond angle restraints: 10680 Sorted by residual: angle pdb=" CA TRP A 348 " pdb=" CB TRP A 348 " pdb=" CG TRP A 348 " ideal model delta sigma weight residual 113.60 120.43 -6.83 1.90e+00 2.77e-01 1.29e+01 angle pdb=" CA LYS C 3 " pdb=" CB LYS C 3 " pdb=" CG LYS C 3 " ideal model delta sigma weight residual 114.10 120.86 -6.76 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CG ARG A 357 " pdb=" CD ARG A 357 " pdb=" NE ARG A 357 " ideal model delta sigma weight residual 112.00 119.28 -7.28 2.20e+00 2.07e-01 1.10e+01 angle pdb=" CB MET A 420 " pdb=" CG MET A 420 " pdb=" SD MET A 420 " ideal model delta sigma weight residual 112.70 122.52 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" C ASP B 472 " pdb=" N VAL B 473 " pdb=" CA VAL B 473 " ideal model delta sigma weight residual 120.50 116.13 4.37 1.34e+00 5.57e-01 1.06e+01 ... (remaining 10675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4135 17.98 - 35.97: 406 35.97 - 53.95: 113 53.95 - 71.94: 17 71.94 - 89.92: 9 Dihedral angle restraints: 4680 sinusoidal: 1563 harmonic: 3117 Sorted by residual: dihedral pdb=" CA ILE A 397 " pdb=" C ILE A 397 " pdb=" N LYS A 398 " pdb=" CA LYS A 398 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CB GLU B 227 " pdb=" CG GLU B 227 " pdb=" CD GLU B 227 " pdb=" OE1 GLU B 227 " ideal model delta sinusoidal sigma weight residual 0.00 -89.92 89.92 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU B 166 " pdb=" CG GLU B 166 " pdb=" CD GLU B 166 " pdb=" OE1 GLU B 166 " ideal model delta sinusoidal sigma weight residual 0.00 89.38 -89.38 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 788 0.028 - 0.056: 294 0.056 - 0.084: 118 0.084 - 0.111: 60 0.111 - 0.139: 20 Chirality restraints: 1280 Sorted by residual: chirality pdb=" CA MET B 300 " pdb=" N MET B 300 " pdb=" C MET B 300 " pdb=" CB MET B 300 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA MET B 592 " pdb=" N MET B 592 " pdb=" C MET B 592 " pdb=" CB MET B 592 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA PHE B 470 " pdb=" N PHE B 470 " pdb=" C PHE B 470 " pdb=" CB PHE B 470 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1277 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 341 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO A 342 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 342 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 342 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 428 " 0.008 2.00e-02 2.50e+03 1.22e-02 2.97e+00 pdb=" CG TYR B 428 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 428 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 428 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 428 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 428 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 428 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 428 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 460 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO B 461 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 461 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 461 " 0.021 5.00e-02 4.00e+02 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2159 2.81 - 3.33: 7661 3.33 - 3.85: 12709 3.85 - 4.38: 12757 4.38 - 4.90: 23342 Nonbonded interactions: 58628 Sorted by model distance: nonbonded pdb=" OE1 GLU A 353 " pdb=" NE ARG A 357 " model vdw 2.286 3.120 nonbonded pdb=" O THR A 292 " pdb=" OG SER A 296 " model vdw 2.306 3.040 nonbonded pdb=" NH2 ARG B 561 " pdb=" O CYS B 571 " model vdw 2.346 3.120 nonbonded pdb=" OE1 GLU B 307 " pdb=" OH TYR B 376 " model vdw 2.356 3.040 nonbonded pdb=" OG SER B 296 " pdb=" OE1 GLN B 416 " model vdw 2.357 3.040 ... (remaining 58623 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.580 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7839 Z= 0.172 Angle : 0.655 9.970 10680 Z= 0.342 Chirality : 0.040 0.139 1280 Planarity : 0.004 0.047 1395 Dihedral : 16.232 89.924 2672 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.28 % Allowed : 26.38 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.25), residues: 1079 helix: 2.04 (0.18), residues: 720 sheet: -0.73 (0.74), residues: 51 loop : -0.45 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 357 TYR 0.029 0.001 TYR B 428 PHE 0.020 0.002 PHE B 157 TRP 0.009 0.001 TRP A 214 HIS 0.003 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7839) covalent geometry : angle 0.65494 (10680) hydrogen bonds : bond 0.10657 ( 599) hydrogen bonds : angle 4.46183 ( 1740) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.320 Fit side-chains REVERT: A 290 GLU cc_start: 0.6812 (pm20) cc_final: 0.6589 (pm20) REVERT: A 329 MET cc_start: 0.6811 (tpt) cc_final: 0.6551 (mmt) REVERT: A 347 LYS cc_start: 0.8261 (mttt) cc_final: 0.7753 (pptt) REVERT: A 420 MET cc_start: 0.7087 (mmp) cc_final: 0.6474 (mmt) REVERT: B 195 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.6109 (t80) REVERT: B 227 GLU cc_start: 0.6870 (tp30) cc_final: 0.6667 (tt0) REVERT: B 245 LYS cc_start: 0.7823 (mmmt) cc_final: 0.7539 (mmtm) REVERT: B 256 ASP cc_start: 0.8068 (t0) cc_final: 0.7656 (m-30) outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.1142 time to fit residues: 19.0880 Evaluate side-chains 96 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN A 402 GLN ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.169581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.141461 restraints weight = 10095.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140136 restraints weight = 8660.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.140953 restraints weight = 7017.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.141545 restraints weight = 6137.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.141897 restraints weight = 5689.855| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7839 Z= 0.165 Angle : 0.522 8.577 10680 Z= 0.270 Chirality : 0.038 0.146 1280 Planarity : 0.004 0.043 1395 Dihedral : 3.605 54.673 1155 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.09 % Allowed : 26.66 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.26), residues: 1079 helix: 2.49 (0.19), residues: 726 sheet: -0.66 (0.78), residues: 51 loop : -0.33 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 333 TYR 0.013 0.001 TYR B 282 PHE 0.016 0.002 PHE A 207 TRP 0.014 0.001 TRP A 214 HIS 0.004 0.001 HIS B 584 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 7839) covalent geometry : angle 0.52219 (10680) hydrogen bonds : bond 0.05011 ( 599) hydrogen bonds : angle 3.69592 ( 1740) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.7035 (mtp180) REVERT: A 420 MET cc_start: 0.7004 (mmp) cc_final: 0.6594 (mmt) REVERT: B 146 ARG cc_start: 0.7581 (tpp-160) cc_final: 0.7371 (tpp-160) REVERT: B 195 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: B 256 ASP cc_start: 0.7631 (t0) cc_final: 0.7421 (m-30) REVERT: B 446 TYR cc_start: 0.6063 (OUTLIER) cc_final: 0.4991 (t80) REVERT: B 597 TYR cc_start: 0.7069 (m-80) cc_final: 0.6808 (m-80) outliers start: 29 outliers final: 17 residues processed: 122 average time/residue: 0.1212 time to fit residues: 19.0153 Evaluate side-chains 110 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 552 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 267 ASN B 539 HIS ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.170254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.142336 restraints weight = 10102.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140661 restraints weight = 8885.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.142193 restraints weight = 7135.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.142405 restraints weight = 5812.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.142677 restraints weight = 5419.664| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7839 Z= 0.132 Angle : 0.503 11.387 10680 Z= 0.254 Chirality : 0.037 0.123 1280 Planarity : 0.003 0.040 1395 Dihedral : 3.466 54.229 1155 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.80 % Allowed : 26.09 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.26), residues: 1079 helix: 2.68 (0.19), residues: 732 sheet: -0.44 (0.80), residues: 51 loop : -0.17 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 252 TYR 0.012 0.001 TYR B 282 PHE 0.011 0.001 PHE B 588 TRP 0.012 0.001 TRP A 214 HIS 0.003 0.001 HIS B 539 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7839) covalent geometry : angle 0.50339 (10680) hydrogen bonds : bond 0.04715 ( 599) hydrogen bonds : angle 3.55852 ( 1740) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.322 Fit side-chains REVERT: A 226 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6884 (mtp180) REVERT: A 269 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7598 (tp) REVERT: A 420 MET cc_start: 0.7059 (mmp) cc_final: 0.6622 (mmt) REVERT: B 146 ARG cc_start: 0.7506 (tpp-160) cc_final: 0.7275 (tpp-160) REVERT: B 195 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: B 446 TYR cc_start: 0.5931 (OUTLIER) cc_final: 0.4893 (t80) outliers start: 34 outliers final: 20 residues processed: 119 average time/residue: 0.1108 time to fit residues: 17.3134 Evaluate side-chains 109 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 552 GLU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 3 optimal weight: 4.9990 chunk 73 optimal weight: 0.0870 chunk 45 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.168899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139473 restraints weight = 10330.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139132 restraints weight = 8029.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.139349 restraints weight = 6821.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.139605 restraints weight = 6449.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.140672 restraints weight = 5674.637| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7839 Z= 0.147 Angle : 0.508 9.812 10680 Z= 0.257 Chirality : 0.037 0.142 1280 Planarity : 0.003 0.039 1395 Dihedral : 3.509 53.438 1155 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.50 % Allowed : 25.53 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.26), residues: 1079 helix: 2.66 (0.19), residues: 733 sheet: -0.36 (0.81), residues: 51 loop : -0.11 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 333 TYR 0.014 0.001 TYR A 408 PHE 0.014 0.001 PHE A 207 TRP 0.010 0.001 TRP A 214 HIS 0.003 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7839) covalent geometry : angle 0.50848 (10680) hydrogen bonds : bond 0.04864 ( 599) hydrogen bonds : angle 3.56058 ( 1740) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 226 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6832 (mtp180) REVERT: A 269 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7563 (tp) REVERT: A 290 GLU cc_start: 0.6738 (pm20) cc_final: 0.6518 (pm20) REVERT: A 420 MET cc_start: 0.7125 (mmp) cc_final: 0.6662 (mmt) REVERT: A 461 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8140 (mp) REVERT: B 146 ARG cc_start: 0.7515 (tpp-160) cc_final: 0.7306 (tpp-160) REVERT: B 195 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: B 446 TYR cc_start: 0.6126 (OUTLIER) cc_final: 0.4981 (t80) outliers start: 39 outliers final: 27 residues processed: 115 average time/residue: 0.1096 time to fit residues: 16.4926 Evaluate side-chains 118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 552 GLU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 84 optimal weight: 0.0670 chunk 17 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.170454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.142256 restraints weight = 10163.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.141616 restraints weight = 7955.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142360 restraints weight = 6831.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.142669 restraints weight = 6086.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.142960 restraints weight = 5436.790| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7839 Z= 0.128 Angle : 0.490 9.945 10680 Z= 0.247 Chirality : 0.037 0.140 1280 Planarity : 0.003 0.038 1395 Dihedral : 3.452 52.834 1155 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.22 % Allowed : 25.11 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.83 (0.26), residues: 1079 helix: 2.78 (0.19), residues: 732 sheet: -0.31 (0.81), residues: 51 loop : -0.06 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 333 TYR 0.012 0.001 TYR B 282 PHE 0.011 0.001 PHE B 588 TRP 0.011 0.001 TRP A 214 HIS 0.002 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7839) covalent geometry : angle 0.49047 (10680) hydrogen bonds : bond 0.04652 ( 599) hydrogen bonds : angle 3.46942 ( 1740) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.327 Fit side-chains REVERT: A 226 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6779 (mtp180) REVERT: A 269 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7577 (tp) REVERT: B 146 ARG cc_start: 0.7441 (tpp-160) cc_final: 0.7222 (tpp-160) REVERT: B 195 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: B 446 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.5034 (t80) outliers start: 37 outliers final: 23 residues processed: 115 average time/residue: 0.1150 time to fit residues: 17.1607 Evaluate side-chains 110 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 552 GLU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 100 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.168197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.139672 restraints weight = 10208.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138452 restraints weight = 8798.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139602 restraints weight = 6799.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139889 restraints weight = 5877.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.140309 restraints weight = 5544.071| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7839 Z= 0.156 Angle : 0.529 8.524 10680 Z= 0.266 Chirality : 0.038 0.140 1280 Planarity : 0.003 0.038 1395 Dihedral : 3.521 52.223 1155 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.92 % Allowed : 25.39 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.26), residues: 1079 helix: 2.69 (0.19), residues: 733 sheet: -0.31 (0.80), residues: 51 loop : -0.15 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.015 0.001 TYR A 408 PHE 0.015 0.001 PHE A 207 TRP 0.010 0.001 TRP A 214 HIS 0.003 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7839) covalent geometry : angle 0.52941 (10680) hydrogen bonds : bond 0.04968 ( 599) hydrogen bonds : angle 3.54021 ( 1740) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.311 Fit side-chains REVERT: A 226 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6871 (mtp180) REVERT: A 269 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7587 (tp) REVERT: B 146 ARG cc_start: 0.7479 (tpp-160) cc_final: 0.7269 (tpp-160) REVERT: B 195 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: B 446 TYR cc_start: 0.6172 (OUTLIER) cc_final: 0.5151 (t80) outliers start: 42 outliers final: 33 residues processed: 116 average time/residue: 0.1111 time to fit residues: 16.8789 Evaluate side-chains 120 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 552 GLU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 101 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 chunk 38 optimal weight: 0.0470 chunk 69 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.170936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143400 restraints weight = 10062.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.142082 restraints weight = 8075.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.143378 restraints weight = 6587.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.143640 restraints weight = 5555.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.144032 restraints weight = 5157.345| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7839 Z= 0.113 Angle : 0.491 9.129 10680 Z= 0.245 Chirality : 0.036 0.127 1280 Planarity : 0.003 0.036 1395 Dihedral : 3.404 52.623 1155 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.37 % Allowed : 26.66 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.96 (0.26), residues: 1079 helix: 2.89 (0.19), residues: 733 sheet: -0.10 (0.79), residues: 51 loop : -0.08 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.011 0.001 TYR B 282 PHE 0.011 0.001 PHE B 588 TRP 0.011 0.001 TRP A 214 HIS 0.002 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 7839) covalent geometry : angle 0.49084 (10680) hydrogen bonds : bond 0.04459 ( 599) hydrogen bonds : angle 3.40590 ( 1740) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.352 Fit side-chains REVERT: A 226 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6724 (mtp180) REVERT: A 269 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7543 (tp) REVERT: B 146 ARG cc_start: 0.7410 (tpp-160) cc_final: 0.7175 (tpp-160) REVERT: B 195 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7862 (m-80) REVERT: B 446 TYR cc_start: 0.5844 (OUTLIER) cc_final: 0.4926 (t80) outliers start: 31 outliers final: 21 residues processed: 113 average time/residue: 0.1137 time to fit residues: 16.8586 Evaluate side-chains 108 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 552 GLU Chi-restraints excluded: chain B residue 571 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.169028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.140560 restraints weight = 10182.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.139186 restraints weight = 8900.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140749 restraints weight = 7193.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141112 restraints weight = 5963.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.141357 restraints weight = 5431.549| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7839 Z= 0.139 Angle : 0.526 11.763 10680 Z= 0.260 Chirality : 0.037 0.139 1280 Planarity : 0.003 0.037 1395 Dihedral : 3.453 51.831 1155 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.94 % Allowed : 26.09 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.89 (0.26), residues: 1079 helix: 2.85 (0.19), residues: 728 sheet: -0.07 (0.79), residues: 51 loop : -0.11 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 333 TYR 0.012 0.001 TYR B 446 PHE 0.013 0.001 PHE A 207 TRP 0.010 0.001 TRP A 214 HIS 0.002 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7839) covalent geometry : angle 0.52643 (10680) hydrogen bonds : bond 0.04727 ( 599) hydrogen bonds : angle 3.46334 ( 1740) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 226 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6725 (mtp180) REVERT: A 269 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7541 (tp) REVERT: B 146 ARG cc_start: 0.7415 (tpp-160) cc_final: 0.7195 (tpp-160) REVERT: B 195 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: B 446 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.5053 (t80) outliers start: 35 outliers final: 28 residues processed: 110 average time/residue: 0.1057 time to fit residues: 15.1731 Evaluate side-chains 115 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 552 GLU Chi-restraints excluded: chain B residue 571 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 78 optimal weight: 0.3980 chunk 61 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.169527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.141209 restraints weight = 10206.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.139655 restraints weight = 8651.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.141105 restraints weight = 7055.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141230 restraints weight = 5835.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143520 restraints weight = 5349.233| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7839 Z= 0.120 Angle : 0.523 11.235 10680 Z= 0.255 Chirality : 0.036 0.128 1280 Planarity : 0.003 0.036 1395 Dihedral : 3.419 51.438 1155 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.80 % Allowed : 25.95 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.26), residues: 1079 helix: 2.95 (0.19), residues: 727 sheet: 0.10 (0.78), residues: 51 loop : -0.07 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 333 TYR 0.015 0.001 TYR A 408 PHE 0.011 0.001 PHE B 588 TRP 0.010 0.001 TRP A 214 HIS 0.002 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7839) covalent geometry : angle 0.52255 (10680) hydrogen bonds : bond 0.04508 ( 599) hydrogen bonds : angle 3.38936 ( 1740) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 87 time to evaluate : 0.281 Fit side-chains REVERT: A 226 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6694 (mtp180) REVERT: A 269 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7519 (tp) REVERT: A 421 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8049 (tp) REVERT: B 146 ARG cc_start: 0.7381 (tpp-160) cc_final: 0.7154 (tpp-160) REVERT: B 195 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: B 446 TYR cc_start: 0.5878 (OUTLIER) cc_final: 0.4920 (t80) outliers start: 34 outliers final: 27 residues processed: 111 average time/residue: 0.1137 time to fit residues: 16.4445 Evaluate side-chains 114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 552 GLU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 58 optimal weight: 0.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.179438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.145538 restraints weight = 10660.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.149554 restraints weight = 6181.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.152220 restraints weight = 4358.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.153564 restraints weight = 3456.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.154926 restraints weight = 3004.731| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7839 Z= 0.156 Angle : 0.557 11.125 10680 Z= 0.276 Chirality : 0.038 0.144 1280 Planarity : 0.003 0.037 1395 Dihedral : 3.531 50.813 1155 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.80 % Allowed : 25.95 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.26), residues: 1079 helix: 2.77 (0.19), residues: 728 sheet: 0.01 (0.78), residues: 51 loop : -0.17 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 333 TYR 0.016 0.001 TYR B 446 PHE 0.015 0.001 PHE A 207 TRP 0.009 0.001 TRP A 214 HIS 0.003 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7839) covalent geometry : angle 0.55660 (10680) hydrogen bonds : bond 0.04966 ( 599) hydrogen bonds : angle 3.52165 ( 1740) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 226 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6759 (mtp180) REVERT: A 269 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7488 (tp) REVERT: B 146 ARG cc_start: 0.7476 (tpp-160) cc_final: 0.7264 (tpp-160) REVERT: B 446 TYR cc_start: 0.6204 (OUTLIER) cc_final: 0.5150 (t80) outliers start: 34 outliers final: 31 residues processed: 110 average time/residue: 0.1179 time to fit residues: 16.7036 Evaluate side-chains 118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 446 TYR Chi-restraints excluded: chain B residue 447 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 552 GLU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 571 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 98 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.183938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.150688 restraints weight = 10581.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.154706 restraints weight = 6119.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.157330 restraints weight = 4295.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.158792 restraints weight = 3400.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.160038 restraints weight = 2926.754| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7839 Z= 0.130 Angle : 0.536 10.977 10680 Z= 0.265 Chirality : 0.037 0.128 1280 Planarity : 0.003 0.036 1395 Dihedral : 3.117 17.293 1153 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.94 % Allowed : 25.95 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.26), residues: 1079 helix: 2.88 (0.19), residues: 727 sheet: 0.16 (0.78), residues: 51 loop : -0.14 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.014 0.001 TYR A 408 PHE 0.011 0.001 PHE B 157 TRP 0.010 0.001 TRP A 214 HIS 0.002 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7839) covalent geometry : angle 0.53628 (10680) hydrogen bonds : bond 0.04680 ( 599) hydrogen bonds : angle 3.44625 ( 1740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1373.29 seconds wall clock time: 24 minutes 26.45 seconds (1466.45 seconds total)