Starting phenix.real_space_refine on Tue Feb 3 23:24:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9i_65778/02_2026/9w9i_65778_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9i_65778/02_2026/9w9i_65778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w9i_65778/02_2026/9w9i_65778_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9i_65778/02_2026/9w9i_65778_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w9i_65778/02_2026/9w9i_65778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9i_65778/02_2026/9w9i_65778.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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 59 5.16 5 C 4886 2.51 5 N 1329 2.21 5 O 1437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7711 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 588 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 886 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 7, 'TRANS': 106} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 4, 'ASP:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 4342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4342 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 12, 'TRANS': 547} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 2, 'GLN:plan1': 3, 'TYR:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 131 Chain: "D" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1895 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 2, 'TRANS': 262} Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 1.62, per 1000 atoms: 0.21 Number of scatterers: 7711 At special positions: 0 Unit cell: (91, 126.1, 148.2, 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 59 16.00 O 1437 8.00 N 1329 7.00 C 4886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 313.7 milliseconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 2 sheets defined 77.9% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 569 through 598 Processing helix chain 'A' and resid 599 through 609 removed outlier: 3.709A pdb=" N TYR A 609 " --> pdb=" O MET A 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 591 Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 640 through 650 Processing helix chain 'B' and resid 652 through 656 removed outlier: 3.798A pdb=" N TYR B 655 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 656 " --> pdb=" O PRO B 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 652 through 656' Processing helix chain 'C' and resid 139 through 144 removed outlier: 3.884A pdb=" N TYR C 143 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU C 144 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 162 removed outlier: 4.476A pdb=" N ASN C 162 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 172 Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 200 through 206 removed outlier: 3.623A pdb=" N PHE C 204 " --> pdb=" O ILE C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 218 removed outlier: 4.017A pdb=" N LEU C 213 " --> pdb=" O HIS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 245 removed outlier: 3.589A pdb=" N ASN C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'C' and resid 259 through 289 Processing helix chain 'C' and resid 292 through 302 removed outlier: 3.518A pdb=" N LYS C 302 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 312 removed outlier: 4.305A pdb=" N MET C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 332 removed outlier: 3.897A pdb=" N ILE C 332 " --> pdb=" O LYS C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 342 removed outlier: 4.234A pdb=" N GLU C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 removed outlier: 4.195A pdb=" N LYS C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 372 Processing helix chain 'C' and resid 374 through 385 Processing helix chain 'C' and resid 385 through 394 removed outlier: 4.671A pdb=" N LYS C 389 " --> pdb=" O GLY C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 412 Processing helix chain 'C' and resid 413 through 421 removed outlier: 4.027A pdb=" N SER C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET C 419 " --> pdb=" O ARG C 415 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 436 removed outlier: 3.652A pdb=" N LYS C 431 " --> pdb=" O PRO C 427 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS C 436 " --> pdb=" O MET C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 453 removed outlier: 3.629A pdb=" N ILE C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 463 removed outlier: 3.578A pdb=" N LEU C 461 " --> pdb=" O ARG C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 478 removed outlier: 4.527A pdb=" N MET C 470 " --> pdb=" O ASN C 466 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 478 " --> pdb=" O ARG C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 491 removed outlier: 3.632A pdb=" N MET C 484 " --> pdb=" O ASP C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 501 removed outlier: 3.785A pdb=" N ASN C 499 " --> pdb=" O GLY C 495 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 501 " --> pdb=" O THR C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 512 removed outlier: 4.119A pdb=" N GLN C 511 " --> pdb=" O ASP C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 530 Processing helix chain 'C' and resid 538 through 545 Processing helix chain 'C' and resid 547 through 555 removed outlier: 3.541A pdb=" N LEU C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 575 Processing helix chain 'C' and resid 579 through 588 removed outlier: 4.289A pdb=" N ALA C 583 " --> pdb=" O ASP C 579 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU C 584 " --> pdb=" O SER C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 601 removed outlier: 3.823A pdb=" N ALA C 593 " --> pdb=" O GLY C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 620 removed outlier: 4.449A pdb=" N PHE C 620 " --> pdb=" O TYR C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 631 removed outlier: 4.237A pdb=" N VAL C 627 " --> pdb=" O ALA C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 641 removed outlier: 3.823A pdb=" N LEU C 641 " --> pdb=" O TYR C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 664 removed outlier: 3.982A pdb=" N GLU C 662 " --> pdb=" O ASP C 658 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR C 663 " --> pdb=" O ILE C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 removed outlier: 3.539A pdb=" N ALA C 668 " --> pdb=" O ASP C 664 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS C 675 " --> pdb=" O ILE C 671 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TRP C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 688 Processing helix chain 'D' and resid 470 through 485 Processing helix chain 'D' and resid 489 through 508 Processing helix chain 'D' and resid 510 through 519 Processing helix chain 'D' and resid 520 through 530 removed outlier: 3.554A pdb=" N MET D 524 " --> pdb=" O MET D 520 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA D 529 " --> pdb=" O ARG D 525 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D 530 " --> pdb=" O ALA D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 533 No H-bonds generated for 'chain 'D' and resid 531 through 533' Processing helix chain 'D' and resid 535 through 551 Processing helix chain 'D' and resid 554 through 564 Processing helix chain 'D' and resid 565 through 577 removed outlier: 3.654A pdb=" N ALA D 569 " --> pdb=" O GLY D 565 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 575 " --> pdb=" O MET D 571 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 576 " --> pdb=" O GLU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 594 Processing helix chain 'D' and resid 597 through 607 removed outlier: 3.725A pdb=" N LYS D 601 " --> pdb=" O CYS D 597 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 607 " --> pdb=" O ASP D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 615 Processing helix chain 'D' and resid 616 through 618 No H-bonds generated for 'chain 'D' and resid 616 through 618' Processing helix chain 'D' and resid 627 through 645 removed outlier: 4.426A pdb=" N SER D 642 " --> pdb=" O ARG D 638 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU D 643 " --> pdb=" O ASN D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 656 removed outlier: 3.553A pdb=" N ARG D 651 " --> pdb=" O ASN D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 666 removed outlier: 3.653A pdb=" N THR D 662 " --> pdb=" O ASN D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 669 No H-bonds generated for 'chain 'D' and resid 667 through 669' Processing helix chain 'D' and resid 671 through 686 Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.656A pdb=" N GLN D 693 " --> pdb=" O ASN D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 708 removed outlier: 4.217A pdb=" N MET D 704 " --> pdb=" O GLY D 700 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 708 " --> pdb=" O MET D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 729 Processing sheet with id=AA1, first strand: chain 'A' and resid 610 through 613 Processing sheet with id=AA2, first strand: chain 'B' and resid 603 through 606 486 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2053 1.33 - 1.45: 1225 1.45 - 1.58: 4445 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 7821 Sorted by residual: bond pdb=" CB GLN C 622 " pdb=" CG GLN C 622 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.59e+00 bond pdb=" CA ASN C 288 " pdb=" C ASN C 288 " ideal model delta sigma weight residual 1.522 1.542 -0.020 1.38e-02 5.25e+03 2.11e+00 bond pdb=" SD MET C 472 " pdb=" CE MET C 472 " ideal model delta sigma weight residual 1.791 1.761 0.030 2.50e-02 1.60e+03 1.44e+00 bond pdb=" CB MET C 618 " pdb=" CG MET C 618 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" C LEU C 287 " pdb=" N ASN C 288 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.38e-02 5.25e+03 1.21e+00 ... (remaining 7816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.03: 10483 3.03 - 6.06: 91 6.06 - 9.09: 12 9.09 - 12.12: 3 12.12 - 15.16: 2 Bond angle restraints: 10591 Sorted by residual: angle pdb=" CA GLN C 622 " pdb=" CB GLN C 622 " pdb=" CG GLN C 622 " ideal model delta sigma weight residual 114.10 123.45 -9.35 2.00e+00 2.50e-01 2.18e+01 angle pdb=" CA LEU C 287 " pdb=" CB LEU C 287 " pdb=" CG LEU C 287 " ideal model delta sigma weight residual 116.30 131.46 -15.16 3.50e+00 8.16e-02 1.87e+01 angle pdb=" CA LEU A 587 " pdb=" CB LEU A 587 " pdb=" CG LEU A 587 " ideal model delta sigma weight residual 116.30 130.05 -13.75 3.50e+00 8.16e-02 1.54e+01 angle pdb=" CA ARG B 578 " pdb=" CB ARG B 578 " pdb=" CG ARG B 578 " ideal model delta sigma weight residual 114.10 121.81 -7.71 2.00e+00 2.50e-01 1.49e+01 angle pdb=" N ASP B 674 " pdb=" CA ASP B 674 " pdb=" C ASP B 674 " ideal model delta sigma weight residual 107.73 112.38 -4.65 1.34e+00 5.57e-01 1.20e+01 ... (remaining 10586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4164 17.35 - 34.70: 504 34.70 - 52.05: 104 52.05 - 69.39: 23 69.39 - 86.74: 9 Dihedral angle restraints: 4804 sinusoidal: 1820 harmonic: 2984 Sorted by residual: dihedral pdb=" CA GLN C 617 " pdb=" C GLN C 617 " pdb=" N MET C 618 " pdb=" CA MET C 618 " ideal model delta harmonic sigma weight residual -180.00 -155.49 -24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA GLU C 561 " pdb=" C GLU C 561 " pdb=" N ASP C 562 " pdb=" CA ASP C 562 " ideal model delta harmonic sigma weight residual 180.00 -156.86 -23.14 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA LYS C 675 " pdb=" C LYS C 675 " pdb=" N PHE C 676 " pdb=" CA PHE C 676 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 4801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 810 0.036 - 0.073: 355 0.073 - 0.109: 79 0.109 - 0.145: 16 0.145 - 0.182: 2 Chirality restraints: 1262 Sorted by residual: chirality pdb=" CB ILE C 321 " pdb=" CA ILE C 321 " pdb=" CG1 ILE C 321 " pdb=" CG2 ILE C 321 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CB ILE D 653 " pdb=" CA ILE D 653 " pdb=" CG1 ILE D 653 " pdb=" CG2 ILE D 653 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA PHE C 620 " pdb=" N PHE C 620 " pdb=" C PHE C 620 " pdb=" CB PHE C 620 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 1259 not shown) Planarity restraints: 1354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 622 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.40e+00 pdb=" C GLN C 622 " 0.053 2.00e-02 2.50e+03 pdb=" O GLN C 622 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 623 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 353 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO C 354 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 354 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 354 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 426 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO C 427 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 427 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 427 " -0.029 5.00e-02 4.00e+02 ... (remaining 1351 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 4 2.49 - 3.09: 5662 3.09 - 3.69: 12083 3.69 - 4.30: 16987 4.30 - 4.90: 27265 Nonbonded interactions: 62001 Sorted by model distance: nonbonded pdb=" OD2 ASP B 674 " pdb=" CD2 TYR B 675 " model vdw 1.882 3.340 nonbonded pdb=" OD1 ASP C 644 " pdb=" N LYS C 645 " model vdw 2.122 3.120 nonbonded pdb=" OD2 ASP B 674 " pdb=" CE2 TYR B 675 " model vdw 2.243 3.340 nonbonded pdb=" O GLN C 622 " pdb=" OE1 GLN C 622 " model vdw 2.447 3.040 nonbonded pdb=" OD1 ASP C 579 " pdb=" N SER C 580 " model vdw 2.488 3.120 ... (remaining 61996 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 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 : 0.004 0.048 7821 Z= 0.194 Angle : 0.759 15.155 10591 Z= 0.396 Chirality : 0.041 0.182 1262 Planarity : 0.005 0.078 1354 Dihedral : 16.159 86.743 2850 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.30 % Rotamer: Outliers : 0.88 % Allowed : 20.43 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.27), residues: 1001 helix: 0.53 (0.20), residues: 702 sheet: -2.63 (1.24), residues: 12 loop : -1.15 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 578 TYR 0.028 0.002 TYR A 609 PHE 0.023 0.002 PHE C 620 TRP 0.014 0.002 TRP C 237 HIS 0.007 0.001 HIS D 670 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 7821) covalent geometry : angle 0.75905 (10591) hydrogen bonds : bond 0.14032 ( 486) hydrogen bonds : angle 5.95266 ( 1434) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 LEU cc_start: 0.8882 (pp) cc_final: 0.8562 (pp) REVERT: A 591 MET cc_start: 0.8125 (mtp) cc_final: 0.7897 (mtp) REVERT: D 483 MET cc_start: 0.4992 (ptt) cc_final: 0.4253 (ppp) outliers start: 7 outliers final: 3 residues processed: 152 average time/residue: 0.4695 time to fit residues: 75.7041 Evaluate side-chains 136 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 539 GLU Chi-restraints excluded: chain C residue 618 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 ASN C 602 GLN C 622 GLN ** D 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.225357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.191749 restraints weight = 11200.807| |-----------------------------------------------------------------------------| r_work (start): 0.4730 rms_B_bonded: 3.60 r_work: 0.4562 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5426 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7821 Z= 0.136 Angle : 0.649 12.972 10591 Z= 0.327 Chirality : 0.039 0.203 1262 Planarity : 0.005 0.057 1354 Dihedral : 5.109 47.037 1078 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 3.91 % Allowed : 20.93 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.27), residues: 1001 helix: 0.68 (0.19), residues: 733 sheet: None (None), residues: 0 loop : -1.15 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 677 TYR 0.014 0.002 TYR C 613 PHE 0.014 0.001 PHE A 597 TRP 0.008 0.001 TRP C 237 HIS 0.014 0.001 HIS C 229 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7821) covalent geometry : angle 0.64884 (10591) hydrogen bonds : bond 0.04235 ( 486) hydrogen bonds : angle 4.73258 ( 1434) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 ILE cc_start: 0.6191 (mm) cc_final: 0.5986 (mp) REVERT: A 591 MET cc_start: 0.7931 (mtp) cc_final: 0.7721 (mtp) REVERT: C 229 HIS cc_start: 0.6569 (t-170) cc_final: 0.6176 (t-90) REVERT: C 339 ASP cc_start: 0.4738 (m-30) cc_final: 0.4477 (m-30) REVERT: C 340 MET cc_start: 0.5852 (mtt) cc_final: 0.5356 (ttm) REVERT: C 472 MET cc_start: 0.6472 (ttm) cc_final: 0.6171 (ttp) REVERT: C 486 MET cc_start: 0.6451 (ttt) cc_final: 0.6108 (tmm) REVERT: C 604 ASP cc_start: 0.6844 (OUTLIER) cc_final: 0.6585 (m-30) REVERT: D 483 MET cc_start: 0.4498 (ptt) cc_final: 0.4223 (pp-130) REVERT: D 621 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7650 (ttp80) REVERT: D 682 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.6732 (mm) outliers start: 31 outliers final: 9 residues processed: 155 average time/residue: 0.3819 time to fit residues: 63.5684 Evaluate side-chains 147 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 GLN Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 507 ASP Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain D residue 498 TYR Chi-restraints excluded: chain D residue 598 THR Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN C 530 ASN C 621 HIS ** D 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.223310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.189532 restraints weight = 11176.653| |-----------------------------------------------------------------------------| r_work (start): 0.4706 rms_B_bonded: 3.57 r_work: 0.4535 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5473 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7821 Z= 0.151 Angle : 0.671 11.957 10591 Z= 0.332 Chirality : 0.039 0.149 1262 Planarity : 0.004 0.058 1354 Dihedral : 4.663 32.573 1072 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.90 % Favored : 96.00 % Rotamer: Outliers : 4.67 % Allowed : 21.44 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.27), residues: 1001 helix: 0.74 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -1.18 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 673 TYR 0.022 0.002 TYR A 609 PHE 0.018 0.001 PHE A 597 TRP 0.010 0.002 TRP C 237 HIS 0.007 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7821) covalent geometry : angle 0.67069 (10591) hydrogen bonds : bond 0.04005 ( 486) hydrogen bonds : angle 4.58493 ( 1434) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 MET cc_start: 0.7998 (mtp) cc_final: 0.7790 (mtp) REVERT: C 229 HIS cc_start: 0.6709 (t-170) cc_final: 0.6213 (t-90) REVERT: C 340 MET cc_start: 0.5571 (mtt) cc_final: 0.5092 (ttm) REVERT: C 404 MET cc_start: 0.5948 (ptm) cc_final: 0.5516 (ptm) REVERT: C 472 MET cc_start: 0.6348 (ttm) cc_final: 0.6070 (ttp) REVERT: C 486 MET cc_start: 0.6619 (ttt) cc_final: 0.6309 (tmm) REVERT: C 500 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7135 (mm) REVERT: C 543 LYS cc_start: 0.7153 (pttp) cc_final: 0.6903 (pttp) REVERT: C 622 GLN cc_start: 0.6349 (tp40) cc_final: 0.6118 (tp-100) REVERT: D 483 MET cc_start: 0.4467 (ptt) cc_final: 0.4143 (pp-130) REVERT: D 524 MET cc_start: 0.3961 (ptp) cc_final: 0.3753 (ptm) outliers start: 37 outliers final: 14 residues processed: 164 average time/residue: 0.3452 time to fit residues: 61.0307 Evaluate side-chains 151 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 507 ASP Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 596 ASN C 288 ASN C 530 ASN ** D 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.222978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.188796 restraints weight = 11365.087| |-----------------------------------------------------------------------------| r_work (start): 0.4700 rms_B_bonded: 3.61 r_work: 0.4528 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5478 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7821 Z= 0.147 Angle : 0.682 11.471 10591 Z= 0.333 Chirality : 0.040 0.273 1262 Planarity : 0.004 0.057 1354 Dihedral : 4.643 31.845 1072 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.70 % Rotamer: Outliers : 5.30 % Allowed : 21.56 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.27), residues: 1001 helix: 0.69 (0.19), residues: 739 sheet: None (None), residues: 0 loop : -1.32 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 673 TYR 0.021 0.002 TYR A 609 PHE 0.018 0.001 PHE A 597 TRP 0.008 0.001 TRP A 612 HIS 0.006 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7821) covalent geometry : angle 0.68164 (10591) hydrogen bonds : bond 0.03830 ( 486) hydrogen bonds : angle 4.55708 ( 1434) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 MET cc_start: 0.7984 (mtp) cc_final: 0.7744 (mtp) REVERT: C 229 HIS cc_start: 0.6695 (t-170) cc_final: 0.6222 (t-90) REVERT: C 237 TRP cc_start: 0.6380 (m-10) cc_final: 0.6085 (m-90) REVERT: C 340 MET cc_start: 0.5520 (mtt) cc_final: 0.5114 (ttm) REVERT: C 404 MET cc_start: 0.5955 (ptm) cc_final: 0.5552 (ptm) REVERT: C 472 MET cc_start: 0.6297 (ttm) cc_final: 0.6040 (ttp) REVERT: C 500 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7125 (mm) REVERT: C 543 LYS cc_start: 0.7461 (pttp) cc_final: 0.7089 (pttp) REVERT: C 622 GLN cc_start: 0.6300 (tp40) cc_final: 0.6083 (tp-100) REVERT: C 641 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6187 (pp) REVERT: C 642 MET cc_start: 0.6405 (ttm) cc_final: 0.6137 (ttt) REVERT: D 483 MET cc_start: 0.4479 (ptt) cc_final: 0.4126 (pp-130) REVERT: D 524 MET cc_start: 0.4420 (ptp) cc_final: 0.4167 (ptm) outliers start: 42 outliers final: 19 residues processed: 166 average time/residue: 0.3678 time to fit residues: 65.5664 Evaluate side-chains 156 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 507 ASP Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 598 THR Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 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 596 ASN C 530 ASN D 666 HIS ** D 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.222772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.188824 restraints weight = 11197.474| |-----------------------------------------------------------------------------| r_work (start): 0.4700 rms_B_bonded: 3.56 r_work: 0.4531 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.4531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5482 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7821 Z= 0.140 Angle : 0.699 12.227 10591 Z= 0.337 Chirality : 0.040 0.302 1262 Planarity : 0.004 0.058 1354 Dihedral : 4.626 31.663 1072 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.70 % Rotamer: Outliers : 4.41 % Allowed : 23.33 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.27), residues: 1001 helix: 0.76 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -1.32 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 673 TYR 0.018 0.002 TYR A 609 PHE 0.017 0.001 PHE A 597 TRP 0.009 0.001 TRP A 612 HIS 0.005 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7821) covalent geometry : angle 0.69928 (10591) hydrogen bonds : bond 0.03725 ( 486) hydrogen bonds : angle 4.51179 ( 1434) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 MET cc_start: 0.7989 (mtp) cc_final: 0.7746 (mtp) REVERT: C 340 MET cc_start: 0.5496 (mtt) cc_final: 0.5204 (ttm) REVERT: C 404 MET cc_start: 0.5924 (ptm) cc_final: 0.5524 (ptm) REVERT: C 472 MET cc_start: 0.6257 (ttm) cc_final: 0.6028 (ttp) REVERT: C 543 LYS cc_start: 0.7386 (pttp) cc_final: 0.6976 (pttp) REVERT: C 641 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6331 (pp) REVERT: D 483 MET cc_start: 0.4475 (ptt) cc_final: 0.4114 (pp-130) outliers start: 35 outliers final: 19 residues processed: 160 average time/residue: 0.4105 time to fit residues: 70.6843 Evaluate side-chains 156 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 507 ASP Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain D residue 598 THR Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 80 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 68 optimal weight: 0.0670 chunk 40 optimal weight: 1.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 HIS C 530 ASN C 622 GLN ** D 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.223388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.189451 restraints weight = 11137.686| |-----------------------------------------------------------------------------| r_work (start): 0.4706 rms_B_bonded: 3.54 r_work: 0.4542 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5462 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7821 Z= 0.145 Angle : 0.743 12.233 10591 Z= 0.359 Chirality : 0.040 0.218 1262 Planarity : 0.004 0.057 1354 Dihedral : 4.590 32.171 1072 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 5.04 % Allowed : 23.08 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.27), residues: 1001 helix: 0.77 (0.19), residues: 735 sheet: None (None), residues: 0 loop : -1.39 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 161 TYR 0.014 0.001 TYR C 613 PHE 0.017 0.001 PHE A 597 TRP 0.050 0.002 TRP C 237 HIS 0.005 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7821) covalent geometry : angle 0.74286 (10591) hydrogen bonds : bond 0.03729 ( 486) hydrogen bonds : angle 4.58066 ( 1434) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 MET cc_start: 0.8020 (mtp) cc_final: 0.7744 (mtp) REVERT: B 596 LYS cc_start: 0.6231 (tptp) cc_final: 0.5961 (tptp) REVERT: C 340 MET cc_start: 0.5499 (mtt) cc_final: 0.4832 (ttm) REVERT: C 471 LEU cc_start: 0.5534 (OUTLIER) cc_final: 0.4988 (mm) REVERT: C 472 MET cc_start: 0.6287 (ttm) cc_final: 0.6067 (ttp) REVERT: C 486 MET cc_start: 0.6596 (ttt) cc_final: 0.6196 (tmm) REVERT: C 543 LYS cc_start: 0.7398 (pttp) cc_final: 0.6975 (pttp) REVERT: C 605 ASP cc_start: 0.6176 (t0) cc_final: 0.5761 (m-30) REVERT: C 641 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6286 (pp) REVERT: D 483 MET cc_start: 0.4575 (ptt) cc_final: 0.4167 (pp-130) outliers start: 40 outliers final: 19 residues processed: 161 average time/residue: 0.4067 time to fit residues: 70.1730 Evaluate side-chains 156 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 507 ASP Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain D residue 598 THR Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 38 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 530 ASN C 622 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5043 r_free = 0.5043 target = 0.223098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.189409 restraints weight = 11153.631| |-----------------------------------------------------------------------------| r_work (start): 0.4709 rms_B_bonded: 3.51 r_work: 0.4543 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5456 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7821 Z= 0.141 Angle : 0.759 12.406 10591 Z= 0.368 Chirality : 0.041 0.354 1262 Planarity : 0.004 0.055 1354 Dihedral : 4.606 32.377 1072 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 4.67 % Allowed : 24.21 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.27), residues: 1001 helix: 0.80 (0.20), residues: 730 sheet: None (None), residues: 0 loop : -1.43 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 621 TYR 0.021 0.001 TYR D 498 PHE 0.017 0.001 PHE A 597 TRP 0.068 0.002 TRP C 237 HIS 0.007 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7821) covalent geometry : angle 0.75942 (10591) hydrogen bonds : bond 0.03645 ( 486) hydrogen bonds : angle 4.63917 ( 1434) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 MET cc_start: 0.8021 (mtp) cc_final: 0.7740 (mtp) REVERT: B 596 LYS cc_start: 0.6231 (tptp) cc_final: 0.5977 (tptp) REVERT: C 352 MET cc_start: 0.1108 (tmm) cc_final: 0.0755 (tmm) REVERT: C 432 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6965 (mpp) REVERT: C 471 LEU cc_start: 0.5467 (OUTLIER) cc_final: 0.4884 (mm) REVERT: C 472 MET cc_start: 0.6290 (ttm) cc_final: 0.6069 (ttp) REVERT: C 486 MET cc_start: 0.6773 (OUTLIER) cc_final: 0.6382 (tmm) REVERT: C 543 LYS cc_start: 0.7436 (pttp) cc_final: 0.7039 (pttp) REVERT: C 605 ASP cc_start: 0.6169 (t0) cc_final: 0.5699 (m-30) REVERT: C 607 PHE cc_start: 0.4962 (m-10) cc_final: 0.4737 (m-10) REVERT: C 641 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6311 (pp) REVERT: D 483 MET cc_start: 0.4538 (ptt) cc_final: 0.4137 (pp-130) REVERT: D 501 MET cc_start: 0.6323 (pp-130) cc_final: 0.6117 (pp-130) outliers start: 37 outliers final: 20 residues processed: 155 average time/residue: 0.4730 time to fit residues: 78.5925 Evaluate side-chains 158 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 280 ARG Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 507 ASP Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 7 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 ASN C 530 ASN C 622 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.222842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.188984 restraints weight = 11280.429| |-----------------------------------------------------------------------------| r_work (start): 0.4703 rms_B_bonded: 3.56 r_work: 0.4536 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5471 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7821 Z= 0.147 Angle : 0.809 20.355 10591 Z= 0.386 Chirality : 0.041 0.296 1262 Planarity : 0.004 0.056 1354 Dihedral : 4.633 31.881 1072 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 4.41 % Allowed : 24.84 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.27), residues: 1001 helix: 0.76 (0.20), residues: 724 sheet: None (None), residues: 0 loop : -1.41 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 621 TYR 0.034 0.002 TYR D 498 PHE 0.017 0.001 PHE A 597 TRP 0.059 0.002 TRP C 237 HIS 0.005 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 7821) covalent geometry : angle 0.80869 (10591) hydrogen bonds : bond 0.03722 ( 486) hydrogen bonds : angle 4.65647 ( 1434) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 MET cc_start: 0.8023 (mtp) cc_final: 0.7750 (mtp) REVERT: B 596 LYS cc_start: 0.6252 (tptp) cc_final: 0.5985 (tptp) REVERT: C 432 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6985 (mpp) REVERT: C 471 LEU cc_start: 0.5493 (OUTLIER) cc_final: 0.4884 (mm) REVERT: C 486 MET cc_start: 0.6794 (OUTLIER) cc_final: 0.6391 (tmm) REVERT: C 507 ASP cc_start: 0.6620 (OUTLIER) cc_final: 0.6287 (p0) REVERT: C 543 LYS cc_start: 0.7428 (pttp) cc_final: 0.7058 (pttp) REVERT: C 605 ASP cc_start: 0.6156 (t0) cc_final: 0.5727 (m-30) REVERT: C 641 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6118 (pp) REVERT: D 483 MET cc_start: 0.4535 (ptt) cc_final: 0.3742 (ppp) REVERT: D 501 MET cc_start: 0.6368 (pp-130) cc_final: 0.6135 (pp-130) outliers start: 35 outliers final: 20 residues processed: 154 average time/residue: 0.4697 time to fit residues: 77.3890 Evaluate side-chains 157 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 507 ASP Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain D residue 598 THR Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 ASN C 622 GLN D 596 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.221602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.187962 restraints weight = 11193.652| |-----------------------------------------------------------------------------| r_work (start): 0.4691 rms_B_bonded: 3.48 r_work: 0.4523 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5498 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7821 Z= 0.160 Angle : 0.822 17.730 10591 Z= 0.396 Chirality : 0.042 0.295 1262 Planarity : 0.004 0.055 1354 Dihedral : 4.717 31.216 1072 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.50 % Rotamer: Outliers : 4.16 % Allowed : 25.85 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.27), residues: 1001 helix: 0.64 (0.20), residues: 729 sheet: None (None), residues: 0 loop : -1.39 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 621 TYR 0.038 0.002 TYR D 498 PHE 0.022 0.002 PHE C 620 TRP 0.056 0.003 TRP C 237 HIS 0.005 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 7821) covalent geometry : angle 0.82176 (10591) hydrogen bonds : bond 0.03793 ( 486) hydrogen bonds : angle 4.72129 ( 1434) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 MET cc_start: 0.7983 (mtp) cc_final: 0.7720 (mtp) REVERT: B 596 LYS cc_start: 0.6312 (tptp) cc_final: 0.6076 (tptp) REVERT: C 274 LYS cc_start: 0.4356 (tppt) cc_final: 0.4121 (mtpp) REVERT: C 283 LEU cc_start: 0.5760 (mm) cc_final: 0.5274 (mp) REVERT: C 352 MET cc_start: 0.1045 (tmm) cc_final: 0.0690 (tmm) REVERT: C 432 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.7041 (mpp) REVERT: C 443 LEU cc_start: 0.6333 (tm) cc_final: 0.5859 (mp) REVERT: C 471 LEU cc_start: 0.5472 (OUTLIER) cc_final: 0.4903 (mm) REVERT: C 486 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6464 (tmm) REVERT: C 543 LYS cc_start: 0.7428 (pttp) cc_final: 0.7078 (pttp) REVERT: C 605 ASP cc_start: 0.6141 (t0) cc_final: 0.5742 (m-30) REVERT: C 641 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6180 (pp) REVERT: D 483 MET cc_start: 0.4536 (ptt) cc_final: 0.3728 (ppp) REVERT: D 501 MET cc_start: 0.6342 (pp-130) cc_final: 0.6044 (pp-130) REVERT: D 711 SER cc_start: 0.7988 (t) cc_final: 0.7420 (m) outliers start: 33 outliers final: 21 residues processed: 154 average time/residue: 0.4545 time to fit residues: 74.8875 Evaluate side-chains 159 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 639 ILE Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain D residue 598 THR Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 GLN B 615 HIS ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 ASN C 622 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.221656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.187854 restraints weight = 11101.164| |-----------------------------------------------------------------------------| r_work (start): 0.4692 rms_B_bonded: 3.53 r_work: 0.4524 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5488 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 7821 Z= 0.158 Angle : 0.872 16.727 10591 Z= 0.414 Chirality : 0.044 0.408 1262 Planarity : 0.004 0.056 1354 Dihedral : 4.754 31.685 1072 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 3.91 % Allowed : 26.48 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.27), residues: 1001 helix: 0.64 (0.20), residues: 728 sheet: None (None), residues: 0 loop : -1.44 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 621 TYR 0.035 0.002 TYR D 498 PHE 0.020 0.001 PHE A 597 TRP 0.057 0.002 TRP C 237 HIS 0.005 0.001 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 7821) covalent geometry : angle 0.87231 (10591) hydrogen bonds : bond 0.03779 ( 486) hydrogen bonds : angle 4.76072 ( 1434) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 MET cc_start: 0.8015 (mtp) cc_final: 0.7747 (mtp) REVERT: A 618 GLU cc_start: 0.6340 (mt-10) cc_final: 0.6070 (mt-10) REVERT: B 596 LYS cc_start: 0.6227 (tptp) cc_final: 0.5974 (tptp) REVERT: C 307 MET cc_start: 0.5432 (pmm) cc_final: 0.4951 (pp-130) REVERT: C 352 MET cc_start: 0.0963 (tmm) cc_final: 0.0595 (tmm) REVERT: C 432 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.7010 (mpp) REVERT: C 443 LEU cc_start: 0.6353 (tm) cc_final: 0.5883 (mp) REVERT: C 471 LEU cc_start: 0.5558 (OUTLIER) cc_final: 0.4999 (mm) REVERT: C 486 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6416 (tmm) REVERT: C 543 LYS cc_start: 0.7448 (pttp) cc_final: 0.7064 (pttp) REVERT: C 605 ASP cc_start: 0.6112 (t0) cc_final: 0.5803 (m-30) REVERT: C 641 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6230 (pp) REVERT: D 483 MET cc_start: 0.4515 (ptt) cc_final: 0.3704 (ppp) REVERT: D 501 MET cc_start: 0.6606 (pp-130) cc_final: 0.6261 (pp-130) REVERT: D 711 SER cc_start: 0.7957 (t) cc_final: 0.7349 (m) outliers start: 31 outliers final: 22 residues processed: 156 average time/residue: 0.4736 time to fit residues: 79.0759 Evaluate side-chains 158 residues out of total 910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain B residue 667 MET Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 409 HIS Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 497 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain C residue 607 PHE Chi-restraints excluded: chain C residue 624 THR Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 665 GLU Chi-restraints excluded: chain D residue 598 THR Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 668 LYS Chi-restraints excluded: chain D residue 682 LEU Chi-restraints excluded: chain D residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 16 optimal weight: 0.1980 chunk 30 optimal weight: 0.2980 chunk 46 optimal weight: 0.1980 chunk 97 optimal weight: 0.9980 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 615 HIS ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 530 ASN C 622 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.224487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.191217 restraints weight = 11280.506| |-----------------------------------------------------------------------------| r_work (start): 0.4729 rms_B_bonded: 3.57 r_work: 0.4563 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5426 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7821 Z= 0.144 Angle : 0.874 15.007 10591 Z= 0.415 Chirality : 0.043 0.399 1262 Planarity : 0.004 0.057 1354 Dihedral : 4.610 33.595 1072 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 4.04 % Allowed : 27.11 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.28), residues: 1001 helix: 0.71 (0.20), residues: 730 sheet: None (None), residues: 0 loop : -1.30 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 621 TYR 0.032 0.001 TYR D 498 PHE 0.026 0.001 PHE C 620 TRP 0.052 0.002 TRP C 237 HIS 0.005 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7821) covalent geometry : angle 0.87369 (10591) hydrogen bonds : bond 0.03634 ( 486) hydrogen bonds : angle 4.73071 ( 1434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3406.52 seconds wall clock time: 58 minutes 30.65 seconds (3510.65 seconds total)