Starting phenix.real_space_refine on Thu Nov 14 23:51:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4e_41028/11_2024/8t4e_41028.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4e_41028/11_2024/8t4e_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4e_41028/11_2024/8t4e_41028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4e_41028/11_2024/8t4e_41028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4e_41028/11_2024/8t4e_41028.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4e_41028/11_2024/8t4e_41028.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLN:plan1': 24, 'ARG:plan': 11, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 16, 'HIS:plan': 7} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} 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: 5.85, per 1000 atoms: 0.76 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: 2.11 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.85 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: 2.46 Time building geometry restraints manager: 2.46 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: 8.670 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.610 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.790 ------------------------------------------------------------------------------- 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= 0.208 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.009 0.001 TRP A 214 HIS 0.003 0.001 HIS B 543 PHE 0.020 0.002 PHE B 157 TYR 0.029 0.001 TYR B 428 ARG 0.011 0.000 ARG A 357 *********************** 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 : 0.885 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: 0.2398 time to fit residues: 40.3246 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 : 0.895 ------------------------------------------------------------------------------- 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 90 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 GLN ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN B 539 HIS ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7839 Z= 0.183 Angle : 0.488 7.839 10680 Z= 0.252 Chirality : 0.037 0.130 1280 Planarity : 0.003 0.042 1395 Dihedral : 3.522 54.982 1155 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.24 % Allowed : 27.36 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.26), residues: 1079 helix: 2.65 (0.18), residues: 724 sheet: -0.54 (0.78), residues: 51 loop : -0.24 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 214 HIS 0.004 0.001 HIS B 584 PHE 0.012 0.001 PHE B 157 TYR 0.011 0.001 TYR B 282 ARG 0.003 0.000 ARG B 333 *********************** 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 127 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 226 ARG cc_start: 0.6169 (OUTLIER) cc_final: 0.5898 (mtp180) REVERT: A 290 GLU cc_start: 0.7107 (pm20) cc_final: 0.6749 (pm20) REVERT: A 347 LYS cc_start: 0.8237 (mttt) cc_final: 0.7767 (pptt) REVERT: A 420 MET cc_start: 0.7130 (mmp) cc_final: 0.6193 (mmm) REVERT: B 195 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6464 (t80) REVERT: B 446 TYR cc_start: 0.5740 (OUTLIER) cc_final: 0.4735 (t80) outliers start: 23 outliers final: 13 residues processed: 117 average time/residue: 0.2588 time to fit residues: 39.0364 Evaluate side-chains 108 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 389 MET 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 54 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 0.0040 chunk 97 optimal weight: 3.9990 chunk 105 optimal weight: 0.0070 chunk 86 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.5610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 ASN B 551 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1420 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= 0.161 Angle : 0.483 10.781 10680 Z= 0.242 Chirality : 0.036 0.125 1280 Planarity : 0.003 0.040 1395 Dihedral : 3.402 54.500 1155 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.37 % Allowed : 25.25 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.26), residues: 1079 helix: 2.79 (0.19), residues: 733 sheet: -0.29 (0.80), residues: 51 loop : -0.12 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.002 0.001 HIS B 543 PHE 0.012 0.001 PHE B 588 TYR 0.015 0.001 TYR B 428 ARG 0.004 0.000 ARG B 252 *********************** 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 123 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.904 Fit side-chains REVERT: A 226 ARG cc_start: 0.6249 (OUTLIER) cc_final: 0.5330 (mtp180) REVERT: A 290 GLU cc_start: 0.7080 (pm20) cc_final: 0.6744 (pm20) REVERT: A 347 LYS cc_start: 0.8276 (mttt) cc_final: 0.7779 (pptt) REVERT: A 420 MET cc_start: 0.7100 (mmp) cc_final: 0.6195 (mmm) REVERT: B 195 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6405 (t80) REVERT: B 446 TYR cc_start: 0.5739 (OUTLIER) cc_final: 0.4697 (t80) outliers start: 31 outliers final: 17 residues processed: 114 average time/residue: 0.2593 time to fit residues: 38.7844 Evaluate side-chains 107 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 325 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.1980 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 518 ASN B 551 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1548 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= 0.187 Angle : 0.480 9.166 10680 Z= 0.242 Chirality : 0.036 0.136 1280 Planarity : 0.003 0.039 1395 Dihedral : 3.405 53.868 1155 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.65 % Allowed : 24.96 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.26), residues: 1079 helix: 2.83 (0.19), residues: 733 sheet: -0.21 (0.81), residues: 51 loop : -0.06 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.002 0.001 HIS B 543 PHE 0.012 0.001 PHE A 207 TYR 0.014 0.001 TYR A 408 ARG 0.003 0.000 ARG B 333 *********************** 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 125 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 226 ARG cc_start: 0.6298 (OUTLIER) cc_final: 0.5389 (mtp180) REVERT: A 290 GLU cc_start: 0.7045 (pm20) cc_final: 0.6726 (pm20) REVERT: A 347 LYS cc_start: 0.8284 (mttt) cc_final: 0.7831 (pptt) REVERT: B 195 PHE cc_start: 0.7088 (OUTLIER) cc_final: 0.6426 (t80) REVERT: B 446 TYR cc_start: 0.5736 (OUTLIER) cc_final: 0.4670 (t80) outliers start: 33 outliers final: 20 residues processed: 115 average time/residue: 0.2429 time to fit residues: 36.2894 Evaluate side-chains 109 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 325 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 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 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 86 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 50.0000 chunk 88 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 518 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1752 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= 0.211 Angle : 0.508 9.559 10680 Z= 0.254 Chirality : 0.037 0.160 1280 Planarity : 0.003 0.040 1395 Dihedral : 3.469 52.869 1155 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.65 % Allowed : 25.39 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.26), residues: 1079 helix: 2.79 (0.19), residues: 734 sheet: -0.18 (0.82), residues: 51 loop : -0.10 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 214 HIS 0.003 0.001 HIS B 543 PHE 0.014 0.001 PHE A 207 TYR 0.013 0.001 TYR B 282 ARG 0.008 0.000 ARG B 252 *********************** 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 122 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.846 Fit side-chains REVERT: A 226 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.5464 (mtp180) REVERT: A 227 ASN cc_start: 0.7710 (m-40) cc_final: 0.7236 (m110) REVERT: A 290 GLU cc_start: 0.7086 (pm20) cc_final: 0.6826 (pm20) REVERT: A 347 LYS cc_start: 0.8361 (mttt) cc_final: 0.7966 (pptt) REVERT: A 420 MET cc_start: 0.7054 (mmp) cc_final: 0.6252 (mmm) REVERT: A 461 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7515 (mp) REVERT: B 195 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: B 333 ARG cc_start: 0.7041 (ttp-110) cc_final: 0.6739 (ttp-110) REVERT: B 446 TYR cc_start: 0.5894 (OUTLIER) cc_final: 0.4779 (t80) outliers start: 33 outliers final: 22 residues processed: 114 average time/residue: 0.2403 time to fit residues: 35.8113 Evaluate side-chains 112 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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 435 THR Chi-restraints excluded: chain A residue 461 LEU 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 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 34 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.1980 chunk 8 optimal weight: 0.3980 chunk 54 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 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 B 518 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.1768 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= 0.163 Angle : 0.490 8.459 10680 Z= 0.243 Chirality : 0.037 0.133 1280 Planarity : 0.003 0.038 1395 Dihedral : 3.405 52.589 1155 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.67 % Allowed : 25.95 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.26), residues: 1079 helix: 2.89 (0.19), residues: 734 sheet: -0.06 (0.81), residues: 51 loop : -0.03 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.002 0.001 HIS B 350 PHE 0.011 0.001 PHE B 588 TYR 0.015 0.001 TYR A 408 ARG 0.008 0.000 ARG B 252 *********************** 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 116 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.890 Fit side-chains REVERT: A 226 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.5380 (mtp180) REVERT: A 290 GLU cc_start: 0.7206 (pm20) cc_final: 0.6985 (pm20) REVERT: A 347 LYS cc_start: 0.8331 (mttt) cc_final: 0.7979 (pptt) REVERT: A 420 MET cc_start: 0.7047 (mmp) cc_final: 0.6199 (mmm) REVERT: B 195 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6773 (m-80) REVERT: B 255 SER cc_start: 0.8698 (t) cc_final: 0.8252 (p) REVERT: B 446 TYR cc_start: 0.5726 (OUTLIER) cc_final: 0.4701 (t80) outliers start: 26 outliers final: 19 residues processed: 110 average time/residue: 0.2407 time to fit residues: 34.6030 Evaluate side-chains 108 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 400 LEU Chi-restraints excluded: chain A residue 414 THR 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7839 Z= 0.240 Angle : 0.535 11.597 10680 Z= 0.265 Chirality : 0.038 0.152 1280 Planarity : 0.003 0.037 1395 Dihedral : 3.512 51.872 1155 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.09 % Allowed : 26.52 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.26), residues: 1079 helix: 2.80 (0.19), residues: 728 sheet: -0.11 (0.80), residues: 51 loop : -0.11 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 214 HIS 0.003 0.001 HIS B 187 PHE 0.016 0.001 PHE A 207 TYR 0.016 0.001 TYR B 446 ARG 0.005 0.000 ARG B 333 *********************** 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 118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.758 Fit side-chains REVERT: A 226 ARG cc_start: 0.6386 (OUTLIER) cc_final: 0.5549 (mtp180) REVERT: A 227 ASN cc_start: 0.7776 (m-40) cc_final: 0.7317 (m110) REVERT: A 290 GLU cc_start: 0.7205 (pm20) cc_final: 0.6973 (pm20) REVERT: A 347 LYS cc_start: 0.8402 (mttt) cc_final: 0.8074 (pptt) REVERT: A 420 MET cc_start: 0.7105 (mmp) cc_final: 0.6244 (mmm) REVERT: B 195 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6827 (m-80) REVERT: B 255 SER cc_start: 0.8727 (t) cc_final: 0.8269 (p) REVERT: B 446 TYR cc_start: 0.6019 (OUTLIER) cc_final: 0.4993 (t80) outliers start: 29 outliers final: 23 residues processed: 109 average time/residue: 0.2401 time to fit residues: 34.0285 Evaluate side-chains 112 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 268 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 426 ILE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 464 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 50 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 518 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.1965 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= 0.174 Angle : 0.506 11.021 10680 Z= 0.249 Chirality : 0.036 0.137 1280 Planarity : 0.003 0.036 1395 Dihedral : 3.413 51.702 1155 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.95 % Allowed : 27.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.26), residues: 1079 helix: 2.94 (0.19), residues: 728 sheet: -0.03 (0.78), residues: 51 loop : -0.05 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.002 0.001 HIS B 543 PHE 0.011 0.001 PHE B 588 TYR 0.015 0.001 TYR A 408 ARG 0.003 0.000 ARG B 333 *********************** 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 122 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 226 ARG cc_start: 0.6317 (OUTLIER) cc_final: 0.5495 (mtp180) REVERT: A 227 ASN cc_start: 0.7737 (m-40) cc_final: 0.7280 (m110) REVERT: A 290 GLU cc_start: 0.7199 (pm20) cc_final: 0.6997 (pm20) REVERT: A 347 LYS cc_start: 0.8395 (mttt) cc_final: 0.8080 (pptt) REVERT: A 420 MET cc_start: 0.7123 (mmp) cc_final: 0.6224 (mmm) REVERT: B 195 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: B 245 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7476 (mmtm) REVERT: B 255 SER cc_start: 0.8729 (t) cc_final: 0.8272 (p) REVERT: B 446 TYR cc_start: 0.5778 (OUTLIER) cc_final: 0.4817 (t80) outliers start: 28 outliers final: 23 residues processed: 115 average time/residue: 0.2504 time to fit residues: 37.3886 Evaluate side-chains 114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 268 VAL Chi-restraints excluded: chain A residue 301 GLU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 98 optimal weight: 0.0040 chunk 57 optimal weight: 0.2980 chunk 41 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 63 optimal weight: 0.1980 chunk 101 optimal weight: 0.8980 overall best weight: 0.3192 ------------------------------------------------------------------------------- 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** B 518 ASN B 551 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7839 Z= 0.135 Angle : 0.491 10.351 10680 Z= 0.242 Chirality : 0.036 0.134 1280 Planarity : 0.003 0.035 1395 Dihedral : 3.305 51.143 1155 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.96 % Allowed : 27.64 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.26), residues: 1079 helix: 3.11 (0.19), residues: 728 sheet: 0.44 (0.88), residues: 39 loop : -0.01 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 214 HIS 0.002 0.001 HIS B 539 PHE 0.012 0.001 PHE B 588 TYR 0.009 0.001 TYR B 282 ARG 0.005 0.000 ARG B 333 *********************** 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 115 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 226 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.5436 (mtp180) REVERT: A 347 LYS cc_start: 0.8378 (mttt) cc_final: 0.8050 (pptt) REVERT: A 420 MET cc_start: 0.7072 (mmp) cc_final: 0.6729 (mmt) REVERT: B 245 LYS cc_start: 0.7788 (mmmt) cc_final: 0.7451 (mmtm) REVERT: B 255 SER cc_start: 0.8739 (t) cc_final: 0.8275 (p) REVERT: B 333 ARG cc_start: 0.6914 (ttp-110) cc_final: 0.6593 (ttp-110) REVERT: B 446 TYR cc_start: 0.5566 (OUTLIER) cc_final: 0.4666 (t80) REVERT: B 528 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7082 (pp) REVERT: B 531 GLU cc_start: 0.8561 (mp0) cc_final: 0.8166 (mp0) REVERT: B 590 GLN cc_start: 0.8040 (tt0) cc_final: 0.7713 (tm-30) outliers start: 21 outliers final: 17 residues processed: 109 average time/residue: 0.2670 time to fit residues: 37.3962 Evaluate side-chains 108 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 301 GLU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 426 ILE 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 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 528 LEU Chi-restraints excluded: chain B residue 552 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 98 optimal weight: 0.0970 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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** B 518 ASN B 551 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7839 Z= 0.154 Angle : 0.508 10.058 10680 Z= 0.250 Chirality : 0.036 0.125 1280 Planarity : 0.003 0.035 1395 Dihedral : 2.941 18.150 1153 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.10 % Allowed : 27.36 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.26), residues: 1079 helix: 3.13 (0.18), residues: 728 sheet: 0.59 (0.88), residues: 39 loop : 0.05 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.002 0.001 HIS B 543 PHE 0.011 0.001 PHE B 588 TYR 0.015 0.001 TYR B 541 ARG 0.004 0.000 ARG B 252 ********************** 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 114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.918 Fit side-chains REVERT: A 290 GLU cc_start: 0.7956 (pm20) cc_final: 0.7560 (pm20) REVERT: A 347 LYS cc_start: 0.8346 (mttt) cc_final: 0.8058 (pptt) REVERT: A 420 MET cc_start: 0.7044 (mmp) cc_final: 0.6702 (mmt) REVERT: B 245 LYS cc_start: 0.7768 (mmmt) cc_final: 0.7436 (mmtm) REVERT: B 255 SER cc_start: 0.8750 (t) cc_final: 0.8287 (p) REVERT: B 333 ARG cc_start: 0.6997 (ttp-110) cc_final: 0.6696 (ttp-110) REVERT: B 446 TYR cc_start: 0.5626 (OUTLIER) cc_final: 0.4684 (t80) REVERT: B 528 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7095 (pp) REVERT: B 531 GLU cc_start: 0.8551 (mp0) cc_final: 0.8154 (mp0) REVERT: B 590 GLN cc_start: 0.8070 (tt0) cc_final: 0.7737 (tm-30) outliers start: 22 outliers final: 17 residues processed: 107 average time/residue: 0.2563 time to fit residues: 35.9416 Evaluate side-chains 109 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 301 GLU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 426 ILE 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 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 528 LEU Chi-restraints excluded: chain B residue 552 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** B 613 GLN ** 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 = 0.4107 r_free = 0.4107 target = 0.169171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140721 restraints weight = 10164.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.140045 restraints weight = 8326.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.140842 restraints weight = 6933.219| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7839 Z= 0.200 Angle : 0.528 9.895 10680 Z= 0.262 Chirality : 0.037 0.147 1280 Planarity : 0.003 0.036 1395 Dihedral : 3.041 18.362 1153 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.24 % Allowed : 27.36 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.26), residues: 1079 helix: 3.00 (0.19), residues: 728 sheet: 0.28 (0.79), residues: 51 loop : -0.00 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 214 HIS 0.002 0.001 HIS B 543 PHE 0.013 0.001 PHE A 207 TYR 0.014 0.001 TYR B 541 ARG 0.003 0.000 ARG B 480 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.22 seconds wall clock time: 33 minutes 4.35 seconds (1984.35 seconds total)