Starting phenix.real_space_refine on Fri Jul 19 11:51:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4e_41028/07_2024/8t4e_41028.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4e_41028/07_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_41028/07_2024/8t4e_41028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4e_41028/07_2024/8t4e_41028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4e_41028/07_2024/8t4e_41028.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4e_41028/07_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 Residue "A ASP 297": "OD1" <-> "OD2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.72, per 1000 atoms: 0.74 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 2.7 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: 0.91 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: 2.45 Time building geometry restraints manager: 3.38 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: 99.90 - 106.71: 202 106.71 - 113.52: 4353 113.52 - 120.33: 2815 120.33 - 127.14: 3240 127.14 - 133.95: 70 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 2.520 nonbonded pdb=" O THR A 292 " pdb=" OG SER A 296 " model vdw 2.306 2.440 nonbonded pdb=" NH2 ARG B 561 " pdb=" O CYS B 571 " model vdw 2.346 2.520 nonbonded pdb=" OE1 GLU B 307 " pdb=" OH TYR B 376 " model vdw 2.356 2.440 nonbonded pdb=" OG SER B 296 " pdb=" OE1 GLN B 416 " model vdw 2.357 2.440 ... (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 ========== 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: 0.010 Normalize map: mean=0, sd=1: 4.220 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 26.440 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.950 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 0.961 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: 0.2408 time to fit residues: 40.5495 Evaluate side-chains 96 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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: 0.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 83 optimal weight: 0.0370 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 436 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7839 Z= 0.189 Angle : 0.485 8.313 10680 Z= 0.248 Chirality : 0.037 0.140 1280 Planarity : 0.003 0.042 1395 Dihedral : 3.535 54.961 1155 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: 2.51 (0.26), residues: 1079 helix: 2.59 (0.19), residues: 730 sheet: -0.54 (0.78), residues: 51 loop : -0.32 (0.36), residues: 298 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 A 207 TYR 0.011 0.001 TYR B 282 ARG 0.004 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 130 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 ARG cc_start: 0.6170 (OUTLIER) cc_final: 0.5899 (mtp180) REVERT: A 290 GLU cc_start: 0.6999 (pm20) cc_final: 0.6455 (pm20) REVERT: A 347 LYS cc_start: 0.8248 (mttt) cc_final: 0.7778 (pptt) REVERT: A 420 MET cc_start: 0.7125 (mmp) cc_final: 0.6502 (mmt) REVERT: B 195 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6819 (m-80) REVERT: B 446 TYR cc_start: 0.5749 (OUTLIER) cc_final: 0.4770 (t80) outliers start: 28 outliers final: 15 residues processed: 119 average time/residue: 0.2517 time to fit residues: 39.4682 Evaluate side-chains 112 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 456 GLN 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 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 54 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 0.0010 chunk 86 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** B 436 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: 0.7019 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7839 Z= 0.163 Angle : 0.481 11.132 10680 Z= 0.240 Chirality : 0.036 0.123 1280 Planarity : 0.003 0.040 1395 Dihedral : 3.436 54.512 1155 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.23 % Allowed : 27.22 % Favored : 68.55 % 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: 2.80 (0.26), residues: 1079 helix: 2.79 (0.19), residues: 732 sheet: -0.32 (0.80), residues: 51 loop : -0.20 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.002 0.001 HIS B 539 PHE 0.011 0.001 PHE B 588 TYR 0.012 0.001 TYR B 282 ARG 0.003 0.000 ARG A 467 *********************** 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 121 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 226 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5331 (mtp180) REVERT: A 290 GLU cc_start: 0.7062 (pm20) cc_final: 0.6598 (pm20) REVERT: A 347 LYS cc_start: 0.8275 (mttt) cc_final: 0.7798 (pptt) REVERT: A 420 MET cc_start: 0.7115 (mmp) cc_final: 0.6228 (mmm) REVERT: B 195 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6442 (t80) REVERT: B 319 ARG cc_start: 0.7692 (ptt-90) cc_final: 0.7417 (ptt-90) REVERT: B 446 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.4754 (t80) outliers start: 30 outliers final: 18 residues processed: 112 average time/residue: 0.2234 time to fit residues: 33.1179 Evaluate side-chains 107 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 301 GLU 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: 3.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 51 optimal weight: 30.0000 chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 355 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7839 Z= 0.375 Angle : 0.602 9.725 10680 Z= 0.306 Chirality : 0.040 0.162 1280 Planarity : 0.004 0.040 1395 Dihedral : 3.870 52.732 1155 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 6.21 % Allowed : 25.95 % Favored : 67.84 % 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: 2.18 (0.26), residues: 1079 helix: 2.28 (0.19), residues: 735 sheet: -0.49 (0.81), residues: 51 loop : -0.36 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 348 HIS 0.005 0.001 HIS B 187 PHE 0.022 0.002 PHE B 345 TYR 0.023 0.002 TYR B 446 ARG 0.008 0.001 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 137 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 93 time to evaluate : 0.928 Fit side-chains REVERT: A 226 ARG cc_start: 0.6442 (OUTLIER) cc_final: 0.5613 (mtp180) REVERT: A 290 GLU cc_start: 0.6959 (pm20) cc_final: 0.6518 (pm20) REVERT: A 347 LYS cc_start: 0.8495 (mttt) cc_final: 0.8075 (pptt) REVERT: A 420 MET cc_start: 0.7211 (mmp) cc_final: 0.6593 (mmt) REVERT: A 461 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7557 (mp) REVERT: B 319 ARG cc_start: 0.7726 (ptt-90) cc_final: 0.7503 (ptt-90) REVERT: B 446 TYR cc_start: 0.6376 (OUTLIER) cc_final: 0.5239 (t80) outliers start: 44 outliers final: 28 residues processed: 122 average time/residue: 0.2319 time to fit residues: 38.1010 Evaluate side-chains 116 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 85 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 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 461 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain B residue 132 VAL 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 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 86 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 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 355 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1936 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= 0.196 Angle : 0.498 9.405 10680 Z= 0.249 Chirality : 0.036 0.130 1280 Planarity : 0.003 0.038 1395 Dihedral : 3.237 20.221 1153 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.51 % Allowed : 27.64 % Favored : 67.84 % 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: 2.59 (0.26), residues: 1079 helix: 2.66 (0.19), residues: 728 sheet: -0.43 (0.80), residues: 51 loop : -0.30 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 214 HIS 0.003 0.001 HIS B 350 PHE 0.011 0.001 PHE A 207 TYR 0.014 0.001 TYR A 408 ARG 0.002 0.000 ARG A 270 *********************** 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 124 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 0.836 Fit side-chains REVERT: A 226 ARG cc_start: 0.6372 (OUTLIER) cc_final: 0.5542 (mtp180) REVERT: A 269 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6603 (tp) REVERT: A 290 GLU cc_start: 0.7019 (pm20) cc_final: 0.6580 (pm20) REVERT: A 347 LYS cc_start: 0.8440 (mttt) cc_final: 0.8078 (pptt) REVERT: A 420 MET cc_start: 0.7197 (mmp) cc_final: 0.6565 (mmt) REVERT: A 456 GLN cc_start: 0.6928 (OUTLIER) cc_final: 0.6717 (mp10) REVERT: B 333 ARG cc_start: 0.7112 (ttp-110) cc_final: 0.6747 (ttp-110) REVERT: B 446 TYR cc_start: 0.6054 (OUTLIER) cc_final: 0.4967 (t80) outliers start: 32 outliers final: 23 residues processed: 113 average time/residue: 0.2306 time to fit residues: 34.4823 Evaluate side-chains 113 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 86 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 326 SER 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 456 GLN Chi-restraints excluded: chain A residue 464 ILE 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 535 SER 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: 0.8980 chunk 93 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1977 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= 0.210 Angle : 0.508 8.304 10680 Z= 0.255 Chirality : 0.037 0.165 1280 Planarity : 0.003 0.037 1395 Dihedral : 3.215 20.163 1153 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.22 % Allowed : 27.08 % Favored : 67.70 % 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: 2.64 (0.26), residues: 1079 helix: 2.70 (0.19), residues: 732 sheet: -0.31 (0.79), residues: 51 loop : -0.34 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.003 0.001 HIS B 543 PHE 0.013 0.001 PHE A 207 TYR 0.012 0.001 TYR B 282 ARG 0.003 0.000 ARG A 357 *********************** 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 122 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 85 time to evaluate : 0.885 Fit side-chains REVERT: A 226 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.5500 (mtp180) REVERT: A 227 ASN cc_start: 0.7763 (m110) cc_final: 0.7506 (m110) REVERT: A 269 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6576 (tp) REVERT: A 290 GLU cc_start: 0.7113 (pm20) cc_final: 0.6679 (pm20) REVERT: A 347 LYS cc_start: 0.8460 (mttt) cc_final: 0.8122 (pptt) REVERT: A 420 MET cc_start: 0.7189 (mmp) cc_final: 0.6325 (mmt) REVERT: B 333 ARG cc_start: 0.7044 (ttp-110) cc_final: 0.6677 (ttp-110) REVERT: B 446 TYR cc_start: 0.6047 (OUTLIER) cc_final: 0.4961 (t80) REVERT: B 528 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6818 (pp) outliers start: 37 outliers final: 29 residues processed: 112 average time/residue: 0.2361 time to fit residues: 34.8723 Evaluate side-chains 116 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 83 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 301 GLU Chi-restraints excluded: chain A residue 305 LEU 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 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 528 LEU 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 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 63 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2005 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= 0.201 Angle : 0.506 8.973 10680 Z= 0.253 Chirality : 0.037 0.164 1280 Planarity : 0.003 0.036 1395 Dihedral : 3.193 20.154 1153 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.64 % Allowed : 26.52 % Favored : 67.84 % 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: 2.69 (0.26), residues: 1079 helix: 2.73 (0.19), residues: 732 sheet: -0.26 (0.78), residues: 51 loop : -0.34 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.003 0.001 HIS B 543 PHE 0.012 0.001 PHE A 207 TYR 0.015 0.001 TYR A 408 ARG 0.003 0.000 ARG A 467 *********************** 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 128 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 88 time to evaluate : 0.849 Fit side-chains REVERT: A 226 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.5491 (mtp180) REVERT: A 227 ASN cc_start: 0.7821 (m110) cc_final: 0.7451 (m110) REVERT: A 269 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6575 (tp) REVERT: A 290 GLU cc_start: 0.7085 (pm20) cc_final: 0.6669 (pm20) REVERT: A 347 LYS cc_start: 0.8482 (mttt) cc_final: 0.8169 (pptt) REVERT: A 420 MET cc_start: 0.7191 (mmp) cc_final: 0.6327 (mmt) REVERT: B 255 SER cc_start: 0.8739 (t) cc_final: 0.8287 (p) REVERT: B 446 TYR cc_start: 0.6004 (OUTLIER) cc_final: 0.4927 (t80) REVERT: B 528 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6875 (pp) outliers start: 40 outliers final: 31 residues processed: 117 average time/residue: 0.2171 time to fit residues: 33.7257 Evaluate side-chains 121 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 86 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 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 400 LEU 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 205 LEU Chi-restraints excluded: chain B residue 218 MET 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 528 LEU Chi-restraints excluded: chain B residue 535 SER 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: 0.4980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7839 Z= 0.161 Angle : 0.489 8.329 10680 Z= 0.244 Chirality : 0.036 0.158 1280 Planarity : 0.003 0.036 1395 Dihedral : 3.096 20.701 1153 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.94 % Allowed : 27.08 % Favored : 67.98 % 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: 2.87 (0.26), residues: 1079 helix: 2.88 (0.19), residues: 731 sheet: -0.14 (0.77), residues: 51 loop : -0.29 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.003 0.001 HIS B 350 PHE 0.013 0.001 PHE B 157 TYR 0.011 0.001 TYR B 282 ARG 0.003 0.000 ARG B 480 *********************** 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 125 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 90 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 226 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5398 (mtp180) REVERT: A 269 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6595 (tp) REVERT: A 290 GLU cc_start: 0.7132 (pm20) cc_final: 0.6766 (pm20) REVERT: A 347 LYS cc_start: 0.8449 (mttt) cc_final: 0.8138 (pptt) REVERT: B 255 SER cc_start: 0.8719 (t) cc_final: 0.8256 (p) REVERT: B 446 TYR cc_start: 0.5853 (OUTLIER) cc_final: 0.4807 (t80) REVERT: B 528 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6916 (pp) outliers start: 35 outliers final: 27 residues processed: 118 average time/residue: 0.2230 time to fit residues: 34.6729 Evaluate side-chains 115 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 84 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 301 GLU Chi-restraints excluded: chain A residue 325 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 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 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 528 LEU Chi-restraints excluded: chain B residue 552 GLU Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 57 optimal weight: 0.0270 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 0.2980 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 0.4980 chunk 95 optimal weight: 0.2980 chunk 63 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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** A 402 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7839 Z= 0.142 Angle : 0.500 8.215 10680 Z= 0.247 Chirality : 0.036 0.155 1280 Planarity : 0.003 0.035 1395 Dihedral : 3.010 20.863 1153 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.09 % Allowed : 27.36 % Favored : 68.55 % 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: 3.11 (0.26), residues: 1079 helix: 3.05 (0.19), residues: 732 sheet: 0.32 (0.87), residues: 39 loop : -0.26 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 214 HIS 0.003 0.001 HIS B 350 PHE 0.011 0.001 PHE A 339 TYR 0.015 0.001 TYR A 408 ARG 0.004 0.000 ARG A 467 *********************** 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 123 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 0.970 Fit side-chains REVERT: A 226 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5395 (mtp180) REVERT: A 269 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6504 (tp) REVERT: A 290 GLU cc_start: 0.7135 (pm20) cc_final: 0.6819 (pm20) REVERT: A 347 LYS cc_start: 0.8418 (mttt) cc_final: 0.8116 (pptt) REVERT: A 420 MET cc_start: 0.7045 (mmp) cc_final: 0.6347 (mmm) REVERT: B 255 SER cc_start: 0.8736 (t) cc_final: 0.8260 (p) REVERT: B 446 TYR cc_start: 0.5682 (OUTLIER) cc_final: 0.4604 (t80) REVERT: B 528 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6977 (pp) REVERT: B 531 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8215 (mp0) outliers start: 29 outliers final: 24 residues processed: 115 average time/residue: 0.2459 time to fit residues: 36.8435 Evaluate side-chains 117 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR 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 301 GLU Chi-restraints excluded: chain A residue 325 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 464 ILE 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 528 LEU Chi-restraints excluded: chain B residue 552 GLU Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 98 optimal weight: 0.0970 chunk 84 optimal weight: 0.0870 chunk 8 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- 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** A 402 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2018 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= 0.158 Angle : 0.517 12.254 10680 Z= 0.252 Chirality : 0.036 0.155 1280 Planarity : 0.003 0.035 1395 Dihedral : 3.010 20.655 1153 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.37 % Allowed : 27.22 % Favored : 68.41 % 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: 3.09 (0.26), residues: 1079 helix: 3.03 (0.19), residues: 733 sheet: 0.52 (0.88), residues: 39 loop : -0.27 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.003 0.001 HIS B 350 PHE 0.011 0.001 PHE B 157 TYR 0.016 0.001 TYR B 541 ARG 0.003 0.000 ARG B 480 ********************** 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 121 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 226 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5398 (mtp180) REVERT: A 269 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6522 (tp) REVERT: A 290 GLU cc_start: 0.7104 (pm20) cc_final: 0.6798 (pm20) REVERT: A 347 LYS cc_start: 0.8405 (mttt) cc_final: 0.8112 (pptt) REVERT: A 420 MET cc_start: 0.7089 (mmp) cc_final: 0.6328 (mmm) REVERT: A 421 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7286 (mt) REVERT: B 255 SER cc_start: 0.8732 (t) cc_final: 0.8247 (p) REVERT: B 273 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7267 (ptp-170) REVERT: B 333 ARG cc_start: 0.6878 (ttp-110) cc_final: 0.6550 (ttp-110) REVERT: B 446 TYR cc_start: 0.5761 (OUTLIER) cc_final: 0.4623 (t80) REVERT: B 528 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6989 (pp) REVERT: B 531 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8214 (mp0) outliers start: 31 outliers final: 24 residues processed: 112 average time/residue: 0.2345 time to fit residues: 34.3489 Evaluate side-chains 118 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR 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 301 GLU Chi-restraints excluded: chain A residue 325 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 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 273 ARG 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 528 LEU Chi-restraints excluded: chain B residue 552 GLU Chi-restraints excluded: chain B residue 571 CYS Chi-restraints excluded: chain B residue 598 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.0270 chunk 78 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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** A 402 GLN ** B 436 ASN ** 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 = 0.4108 r_free = 0.4108 target = 0.169189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140984 restraints weight = 10187.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139995 restraints weight = 8090.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140619 restraints weight = 6879.503| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2049 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= 0.177 Angle : 0.523 11.528 10680 Z= 0.255 Chirality : 0.037 0.155 1280 Planarity : 0.003 0.035 1395 Dihedral : 3.053 20.463 1153 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.65 % Allowed : 27.22 % Favored : 68.12 % 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: 3.04 (0.26), residues: 1079 helix: 2.99 (0.19), residues: 733 sheet: 0.24 (0.80), residues: 51 loop : -0.27 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.003 0.001 HIS B 350 PHE 0.011 0.001 PHE A 207 TYR 0.017 0.001 TYR A 408 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: 1730.78 seconds wall clock time: 31 minutes 44.64 seconds (1904.64 seconds total)