Starting phenix.real_space_refine on Fri Jul 3 00:07:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ppo_13583/07_2026/7ppo_13583.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ppo_13583/07_2026/7ppo_13583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ppo_13583/07_2026/7ppo_13583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ppo_13583/07_2026/7ppo_13583.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ppo_13583/07_2026/7ppo_13583.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ppo_13583/07_2026/7ppo_13583.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ppo_13583/07_2026/7ppo_13583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ppo_13583/07_2026/7ppo_13583.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 1 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 6974 2.51 5 N 1875 2.21 5 O 2103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10990 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4003 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 477} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, '86N:plan-4': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 6099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6099 Classifications: {'peptide': 749} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 31, 'TRANS': 717} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 886 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 13, 'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 4, 'ARG:plan': 5, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 137 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.03, per 1000 atoms: 0.18 Number of scatterers: 10990 At special positions: 0 Unit cell: (139.104, 104.832, 92.736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 35 16.00 P 1 15.00 Mg 1 11.99 O 2103 8.00 N 1875 7.00 C 6974 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: 0.85 Conformation dependent library (CDL) restraints added in 312.9 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 10 sheets defined 54.6% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 278 through 302 removed outlier: 3.834A pdb=" N ARG A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'A' and resid 343 through 365 Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.623A pdb=" N VAL A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 409 removed outlier: 3.675A pdb=" N HIS A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 430 removed outlier: 3.529A pdb=" N PHE A 421 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 452 removed outlier: 3.606A pdb=" N ALA A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 Processing helix chain 'A' and resid 522 through 527 removed outlier: 4.073A pdb=" N ASN A 527 " --> pdb=" O PRO A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.543A pdb=" N TRP A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN A 550 " --> pdb=" O MET A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 removed outlier: 4.151A pdb=" N ALA A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 587 Proline residue: A 582 - end of helix Processing helix chain 'A' and resid 772 through 787 removed outlier: 3.713A pdb=" N GLN A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 808 Processing helix chain 'A' and resid 824 through 831 removed outlier: 3.699A pdb=" N VAL A 828 " --> pdb=" O GLU A 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 158 removed outlier: 4.067A pdb=" N ASN C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.518A pdb=" N ILE C 163 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 182 Processing helix chain 'C' and resid 184 through 206 Proline residue: C 197 - end of helix Processing helix chain 'C' and resid 206 through 218 removed outlier: 3.507A pdb=" N GLU C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 228 removed outlier: 4.379A pdb=" N HIS C 226 " --> pdb=" O TYR C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 246 Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 301 through 311 removed outlier: 3.647A pdb=" N LEU C 305 " --> pdb=" O TYR C 301 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR C 306 " --> pdb=" O HIS C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 391 removed outlier: 3.990A pdb=" N LEU C 378 " --> pdb=" O PRO C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 396 Processing helix chain 'C' and resid 412 through 419 Processing helix chain 'C' and resid 424 through 432 Processing helix chain 'C' and resid 446 through 451 Processing helix chain 'C' and resid 459 through 481 Processing helix chain 'C' and resid 493 through 500 removed outlier: 3.757A pdb=" N GLY C 496 " --> pdb=" O THR C 493 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASP C 498 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 500 " --> pdb=" O GLU C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 552 No H-bonds generated for 'chain 'C' and resid 550 through 552' Processing helix chain 'C' and resid 556 through 563 Processing helix chain 'C' and resid 563 through 569 Processing helix chain 'C' and resid 589 through 622 removed outlier: 3.976A pdb=" N LEU C 593 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLY C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 655 Processing helix chain 'C' and resid 657 through 669 removed outlier: 3.766A pdb=" N ARG C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 682 Processing helix chain 'C' and resid 683 through 688 removed outlier: 4.169A pdb=" N TYR C 686 " --> pdb=" O THR C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 703 removed outlier: 3.667A pdb=" N SER C 700 " --> pdb=" O MET C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 771 removed outlier: 3.664A pdb=" N GLU C 742 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 793 Processing helix chain 'C' and resid 799 through 817 removed outlier: 4.213A pdb=" N LYS C 803 " --> pdb=" O CYS C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 848 removed outlier: 3.648A pdb=" N PHE C 829 " --> pdb=" O TYR C 825 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR C 848 " --> pdb=" O PHE C 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 21 removed outlier: 3.620A pdb=" N GLU B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.804A pdb=" N MET B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 77 Processing helix chain 'B' and resid 82 through 94 removed outlier: 4.010A pdb=" N PHE B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 110 Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 139 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA2, first strand: chain 'A' and resid 468 through 469 removed outlier: 3.724A pdb=" N VAL A 469 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 474 " --> pdb=" O VAL A 469 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 763 through 768 removed outlier: 6.258A pdb=" N ILE A 837 " --> pdb=" O PHE A 893 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE A 895 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU A 839 " --> pdb=" O PHE A 895 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ALA A 897 " --> pdb=" O GLU A 839 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU A 841 " --> pdb=" O ALA A 897 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N LYS A 899 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 818 through 822 Processing sheet with id=AA5, first strand: chain 'C' and resid 105 through 109 Processing sheet with id=AA6, first strand: chain 'C' and resid 121 through 124 removed outlier: 8.116A pdb=" N ALA C 583 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N SER C 585 " --> pdb=" O PRO C 130 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS C 132 " --> pdb=" O SER C 585 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR C 582 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 291 through 292 Processing sheet with id=AA8, first strand: chain 'C' and resid 346 through 350 removed outlier: 6.829A pdb=" N LEU C 355 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE C 349 " --> pdb=" O THR C 353 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N THR C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU C 438 " --> pdb=" O SER C 409 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER C 409 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C 440 " --> pdb=" O GLN C 407 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN C 407 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 442 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 482 through 483 Processing sheet with id=AB1, first strand: chain 'B' and resid 27 through 29 541 hydrogen bonds defined for protein. 1563 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: 1.51 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3615 1.34 - 1.47: 2743 1.47 - 1.60: 4794 1.60 - 1.73: 1 1.73 - 1.87: 68 Bond restraints: 11221 Sorted by residual: bond pdb=" O3P 86N A 860 " pdb=" P 86N A 860 " ideal model delta sigma weight residual 1.494 1.765 -0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" O2P 86N A 860 " pdb=" P 86N A 860 " ideal model delta sigma weight residual 1.490 1.692 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" OE1 86N A 860 " pdb=" P 86N A 860 " ideal model delta sigma weight residual 1.700 1.866 -0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" O5' 86N A 860 " pdb=" P 86N A 860 " ideal model delta sigma weight residual 1.630 1.765 -0.135 2.00e-02 2.50e+03 4.56e+01 bond pdb=" CD 86N A 860 " pdb=" OE1 86N A 860 " ideal model delta sigma weight residual 1.327 1.244 0.083 2.00e-02 2.50e+03 1.70e+01 ... (remaining 11216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.82: 15167 8.82 - 17.65: 3 17.65 - 26.47: 1 26.47 - 35.30: 1 35.30 - 44.12: 1 Bond angle restraints: 15173 Sorted by residual: angle pdb=" CA 86N A 860 " pdb=" CB 86N A 860 " pdb=" CG 86N A 860 " ideal model delta sigma weight residual 112.62 156.74 -44.12 3.00e+00 1.11e-01 2.16e+02 angle pdb=" OE1 86N A 860 " pdb=" P 86N A 860 " pdb=" O5' 86N A 860 " ideal model delta sigma weight residual 96.73 127.40 -30.67 3.00e+00 1.11e-01 1.04e+02 angle pdb=" CB 86N A 860 " pdb=" CG 86N A 860 " pdb=" CD 86N A 860 " ideal model delta sigma weight residual 113.90 132.18 -18.28 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C 86N A 860 " pdb=" CA 86N A 860 " pdb=" CB 86N A 860 " ideal model delta sigma weight residual 110.10 118.16 -8.06 1.90e+00 2.77e-01 1.80e+01 angle pdb=" OE1 86N A 860 " pdb=" P 86N A 860 " pdb=" O2P 86N A 860 " ideal model delta sigma weight residual 105.74 95.13 10.61 3.00e+00 1.11e-01 1.25e+01 ... (remaining 15168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.95: 6526 24.95 - 49.89: 223 49.89 - 74.84: 24 74.84 - 99.78: 3 99.78 - 124.73: 2 Dihedral angle restraints: 6778 sinusoidal: 2732 harmonic: 4046 Sorted by residual: dihedral pdb=" CA SER A 798 " pdb=" C SER A 798 " pdb=" N PRO A 799 " pdb=" CA PRO A 799 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ASP A 796 " pdb=" C ASP A 796 " pdb=" N HIS A 797 " pdb=" CA HIS A 797 " ideal model delta harmonic sigma weight residual -180.00 -156.60 -23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA TYR C 702 " pdb=" C TYR C 702 " pdb=" N SER C 703 " pdb=" CA SER C 703 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 6775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1212 0.045 - 0.091: 381 0.091 - 0.136: 74 0.136 - 0.181: 2 0.181 - 0.227: 1 Chirality restraints: 1670 Sorted by residual: chirality pdb=" CA 86N A 860 " pdb=" N 86N A 860 " pdb=" C 86N A 860 " pdb=" CB 86N A 860 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA THR C 493 " pdb=" N THR C 493 " pdb=" C THR C 493 " pdb=" CB THR C 493 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA ILE C 482 " pdb=" N ILE C 482 " pdb=" C ILE C 482 " pdb=" CB ILE C 482 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 1667 not shown) Planarity restraints: 1965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 66 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 67 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 67 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 67 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 319 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO A 320 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 581 " 0.025 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 582 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " 0.021 5.00e-02 4.00e+02 ... (remaining 1962 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 186 2.65 - 3.22: 10476 3.22 - 3.78: 16991 3.78 - 4.34: 24503 4.34 - 4.90: 39856 Nonbonded interactions: 92012 Sorted by model distance: nonbonded pdb=" OG SER C 220 " pdb=" OD1 ASP C 793 " model vdw 2.092 3.040 nonbonded pdb=" OG SER C 399 " pdb=" OD2 ASP C 473 " model vdw 2.126 3.040 nonbonded pdb=" O GLY A 434 " pdb=" OG1 THR A 438 " model vdw 2.190 3.040 nonbonded pdb=" OD1 ASP A 339 " pdb=" OH TYR A 350 " model vdw 2.200 3.040 nonbonded pdb=" O SER A 771 " pdb=" OG1 THR A 775 " model vdw 2.217 3.040 ... (remaining 92007 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: 1.800 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.340 Find NCS groups from input model: 0.040 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:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.271 11221 Z= 0.314 Angle : 0.775 44.123 15173 Z= 0.369 Chirality : 0.043 0.227 1670 Planarity : 0.004 0.048 1965 Dihedral : 12.738 124.728 4162 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.41 % Allowed : 6.91 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.20), residues: 1364 helix: -1.14 (0.17), residues: 687 sheet: -2.15 (0.46), residues: 91 loop : -2.32 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 660 TYR 0.016 0.002 TYR C 443 PHE 0.015 0.002 PHE C 475 TRP 0.010 0.001 TRP C 526 HIS 0.004 0.001 HIS C 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00693 / 0.31 (11221) covalent geometry : angle 0.77471 / 0.37 (15173) hydrogen bonds : bond 0.13776 / 9.76 ( 541) hydrogen bonds : angle 6.06589 / 4.17 ( 1563) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 310 LYS cc_start: 0.8175 (mptt) cc_final: 0.7483 (pptt) REVERT: A 514 MET cc_start: 0.7505 (ttp) cc_final: 0.6643 (ttp) REVERT: A 518 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8426 (tm-30) REVERT: A 867 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7997 (pt) REVERT: C 403 GLN cc_start: 0.7507 (tt0) cc_final: 0.7303 (tt0) REVERT: C 411 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8235 (mmmt) REVERT: C 459 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.7038 (p0) REVERT: C 489 ASP cc_start: 0.7512 (p0) cc_final: 0.7082 (p0) REVERT: B 73 MET cc_start: 0.7339 (tpp) cc_final: 0.6879 (tpt) outliers start: 40 outliers final: 18 residues processed: 178 average time/residue: 0.5149 time to fit residues: 98.5773 Evaluate side-chains 123 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 845 TRP Chi-restraints excluded: chain B residue 118 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN A 550 ASN A 588 GLN A 818 ASN C 153 GLN C 167 GLN C 454 HIS C 670 ASN C 830 GLN B 42 GLN B 43 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.148577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100429 restraints weight = 14334.953| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.26 r_work: 0.3031 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11221 Z= 0.137 Angle : 0.541 10.135 15173 Z= 0.276 Chirality : 0.040 0.171 1670 Planarity : 0.004 0.045 1965 Dihedral : 7.804 121.135 1541 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.07 % Allowed : 11.51 % Favored : 85.42 % 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: -1.00 (0.22), residues: 1364 helix: 0.30 (0.19), residues: 702 sheet: -1.66 (0.47), residues: 91 loop : -1.68 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 293 TYR 0.013 0.001 TYR C 443 PHE 0.030 0.002 PHE A 309 TRP 0.006 0.001 TRP C 635 HIS 0.005 0.001 HIS C 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11221) covalent geometry : angle 0.54109 / 0.28 (15173) hydrogen bonds : bond 0.04145 / 2.78 ( 541) hydrogen bonds : angle 4.31801 / 2.96 ( 1563) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 514 MET cc_start: 0.8200 (ttp) cc_final: 0.7350 (ttp) REVERT: A 518 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8582 (tm-30) REVERT: A 839 GLU cc_start: 0.7556 (tt0) cc_final: 0.7326 (tt0) REVERT: A 867 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7890 (pt) REVERT: A 885 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7339 (pm20) REVERT: C 123 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8225 (t) REVERT: C 483 MET cc_start: 0.8756 (ptm) cc_final: 0.8473 (ptm) REVERT: C 489 ASP cc_start: 0.7957 (p0) cc_final: 0.7626 (p0) REVERT: B 8 GLU cc_start: 0.7660 (tp30) cc_final: 0.7350 (tp30) outliers start: 36 outliers final: 21 residues processed: 136 average time/residue: 0.5387 time to fit residues: 78.6011 Evaluate side-chains 121 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 425 PHE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 845 TRP Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 94 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 105 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 90 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.147898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100715 restraints weight = 14543.983| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.42 r_work: 0.3005 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11221 Z= 0.189 Angle : 0.564 9.025 15173 Z= 0.286 Chirality : 0.042 0.170 1670 Planarity : 0.004 0.047 1965 Dihedral : 7.603 119.072 1530 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.09 % Allowed : 11.76 % Favored : 84.14 % 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: -0.44 (0.22), residues: 1364 helix: 0.86 (0.19), residues: 691 sheet: -1.30 (0.47), residues: 91 loop : -1.54 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 293 TYR 0.015 0.001 TYR C 443 PHE 0.018 0.002 PHE C 475 TRP 0.008 0.001 TRP A 549 HIS 0.004 0.001 HIS C 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (11221) covalent geometry : angle 0.56403 / 0.29 (15173) hydrogen bonds : bond 0.04386 / 2.93 ( 541) hydrogen bonds : angle 4.20276 / 2.87 ( 1563) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 110 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7914 (ptp) REVERT: A 514 MET cc_start: 0.8247 (ttp) cc_final: 0.7417 (ttp) REVERT: A 518 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8610 (tm-30) REVERT: A 839 GLU cc_start: 0.7630 (tt0) cc_final: 0.7409 (tt0) REVERT: A 867 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7872 (pt) REVERT: A 885 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7052 (pm20) REVERT: C 489 ASP cc_start: 0.8008 (p0) cc_final: 0.7666 (p0) REVERT: C 499 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7465 (mp0) REVERT: B 7 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6917 (tm-30) REVERT: B 52 MET cc_start: 0.7755 (mmm) cc_final: 0.6998 (tpt) outliers start: 48 outliers final: 29 residues processed: 144 average time/residue: 0.4958 time to fit residues: 77.2109 Evaluate side-chains 134 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 557 ASP Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain C residue 845 TRP Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 72 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.149397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098435 restraints weight = 14411.857| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.13 r_work: 0.3051 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11221 Z= 0.125 Angle : 0.508 8.274 15173 Z= 0.261 Chirality : 0.039 0.161 1670 Planarity : 0.004 0.047 1965 Dihedral : 7.318 117.956 1529 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.50 % Allowed : 13.81 % Favored : 82.69 % 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: 0.03 (0.23), residues: 1364 helix: 1.25 (0.19), residues: 699 sheet: -1.02 (0.47), residues: 93 loop : -1.36 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 293 TYR 0.013 0.001 TYR C 443 PHE 0.015 0.001 PHE C 475 TRP 0.012 0.001 TRP A 549 HIS 0.004 0.001 HIS C 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (11221) covalent geometry : angle 0.50777 / 0.26 (15173) hydrogen bonds : bond 0.03808 / 2.54 ( 541) hydrogen bonds : angle 3.95799 / 2.69 ( 1563) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 514 MET cc_start: 0.8239 (ttp) cc_final: 0.7385 (ttp) REVERT: A 518 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8575 (tm-30) REVERT: A 867 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7868 (pt) REVERT: A 885 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: C 483 MET cc_start: 0.8717 (ptm) cc_final: 0.8437 (ptm) REVERT: C 489 ASP cc_start: 0.7979 (p0) cc_final: 0.7561 (p0) REVERT: C 499 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7415 (mp0) REVERT: B 8 GLU cc_start: 0.7599 (tp30) cc_final: 0.7125 (tm-30) REVERT: B 37 MET cc_start: 0.8891 (mmm) cc_final: 0.8648 (mmm) REVERT: B 52 MET cc_start: 0.7742 (mmm) cc_final: 0.7053 (tpt) outliers start: 41 outliers final: 25 residues processed: 133 average time/residue: 0.5201 time to fit residues: 74.5225 Evaluate side-chains 127 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 94 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 ASN C 658 GLN B 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.149129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098589 restraints weight = 14350.123| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.12 r_work: 0.3054 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11221 Z= 0.129 Angle : 0.508 10.101 15173 Z= 0.258 Chirality : 0.040 0.158 1670 Planarity : 0.004 0.047 1965 Dihedral : 7.125 117.482 1525 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.92 % Allowed : 13.98 % Favored : 82.10 % 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: 0.33 (0.23), residues: 1364 helix: 1.48 (0.19), residues: 701 sheet: -0.87 (0.48), residues: 94 loop : -1.21 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 293 TYR 0.012 0.001 TYR C 443 PHE 0.018 0.001 PHE C 425 TRP 0.023 0.001 TRP A 549 HIS 0.003 0.001 HIS C 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11221) covalent geometry : angle 0.50831 / 0.26 (15173) hydrogen bonds : bond 0.03775 / 2.50 ( 541) hydrogen bonds : angle 3.85977 / 2.61 ( 1563) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 106 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 416 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7459 (tm130) REVERT: A 514 MET cc_start: 0.8082 (ttp) cc_final: 0.7065 (ttp) REVERT: A 518 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8540 (tm-30) REVERT: A 885 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7048 (pm20) REVERT: C 127 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7556 (ttm110) REVERT: C 340 GLN cc_start: 0.8200 (pm20) cc_final: 0.7887 (pm20) REVERT: C 483 MET cc_start: 0.8702 (ptm) cc_final: 0.8418 (ptm) REVERT: C 499 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7377 (mp0) REVERT: B 8 GLU cc_start: 0.7638 (tp30) cc_final: 0.7434 (tp30) REVERT: B 52 MET cc_start: 0.7702 (mmm) cc_final: 0.7119 (tpt) REVERT: B 64 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7968 (mp) outliers start: 46 outliers final: 24 residues processed: 133 average time/residue: 0.5661 time to fit residues: 81.2652 Evaluate side-chains 129 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 725 THR Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 64 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 72 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN B 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.148623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098165 restraints weight = 14388.372| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.08 r_work: 0.3048 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11221 Z= 0.160 Angle : 0.528 8.919 15173 Z= 0.269 Chirality : 0.041 0.162 1670 Planarity : 0.004 0.049 1965 Dihedral : 7.070 117.860 1522 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.32 % Allowed : 14.83 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.41 (0.23), residues: 1364 helix: 1.55 (0.20), residues: 694 sheet: -0.72 (0.49), residues: 92 loop : -1.16 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 293 TYR 0.014 0.001 TYR C 443 PHE 0.016 0.001 PHE C 475 TRP 0.027 0.001 TRP A 549 HIS 0.004 0.001 HIS C 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (11221) covalent geometry : angle 0.52791 / 0.27 (15173) hydrogen bonds : bond 0.04013 / 2.67 ( 541) hydrogen bonds : angle 3.90458 / 2.64 ( 1563) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7961 (ptp) REVERT: A 416 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7440 (tm130) REVERT: A 430 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8664 (pt0) REVERT: A 514 MET cc_start: 0.8041 (ttp) cc_final: 0.7095 (ttp) REVERT: A 518 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8534 (tm-30) REVERT: A 885 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7013 (pm20) REVERT: C 127 ARG cc_start: 0.8035 (mtm-85) cc_final: 0.7609 (ttm110) REVERT: C 215 GLU cc_start: 0.8192 (tp30) cc_final: 0.7888 (tt0) REVERT: C 489 ASP cc_start: 0.8025 (p0) cc_final: 0.7752 (p0) REVERT: C 658 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8555 (mm-40) REVERT: B 7 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6766 (tm-30) REVERT: B 37 MET cc_start: 0.8900 (mmm) cc_final: 0.8677 (mmm) REVERT: B 52 MET cc_start: 0.7750 (mmm) cc_final: 0.7229 (tpt) outliers start: 39 outliers final: 24 residues processed: 138 average time/residue: 0.6375 time to fit residues: 94.3431 Evaluate side-chains 132 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 658 GLN Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 725 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 106 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.0060 chunk 62 optimal weight: 0.3980 chunk 48 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 GLN C 658 GLN B 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.151150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103625 restraints weight = 14336.639| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.31 r_work: 0.3070 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11221 Z= 0.105 Angle : 0.508 8.637 15173 Z= 0.260 Chirality : 0.038 0.155 1670 Planarity : 0.004 0.048 1965 Dihedral : 6.883 117.221 1522 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.13 % Allowed : 16.79 % Favored : 81.07 % 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: 0.66 (0.23), residues: 1364 helix: 1.72 (0.20), residues: 702 sheet: -0.54 (0.49), residues: 94 loop : -1.04 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 293 TYR 0.012 0.001 TYR A 347 PHE 0.015 0.001 PHE C 425 TRP 0.028 0.001 TRP A 549 HIS 0.004 0.001 HIS C 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (11221) covalent geometry : angle 0.50845 / 0.26 (15173) hydrogen bonds : bond 0.03507 / 2.32 ( 541) hydrogen bonds : angle 3.73423 / 2.52 ( 1563) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7950 (ptp) REVERT: A 514 MET cc_start: 0.8150 (ttp) cc_final: 0.7229 (ttp) REVERT: A 518 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8506 (tm-30) REVERT: A 885 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: C 127 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7601 (ttm110) REVERT: C 483 MET cc_start: 0.8718 (ptm) cc_final: 0.8442 (ptm) REVERT: C 499 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7291 (mp0) REVERT: B 37 MET cc_start: 0.8819 (mmm) cc_final: 0.8605 (mmm) REVERT: B 52 MET cc_start: 0.7714 (mmm) cc_final: 0.7359 (tpt) outliers start: 25 outliers final: 15 residues processed: 126 average time/residue: 0.6078 time to fit residues: 82.6627 Evaluate side-chains 118 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 725 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 108 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 0.0770 chunk 109 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN B 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.150602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.103771 restraints weight = 14363.215| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.29 r_work: 0.3078 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11221 Z= 0.117 Angle : 0.520 11.262 15173 Z= 0.262 Chirality : 0.039 0.154 1670 Planarity : 0.004 0.047 1965 Dihedral : 6.766 117.876 1520 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.81 % Allowed : 16.20 % Favored : 80.99 % 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: 0.78 (0.23), residues: 1364 helix: 1.80 (0.20), residues: 702 sheet: -0.40 (0.50), residues: 94 loop : -0.98 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 293 TYR 0.012 0.001 TYR A 347 PHE 0.015 0.001 PHE C 475 TRP 0.030 0.001 TRP A 549 HIS 0.003 0.001 HIS C 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (11221) covalent geometry : angle 0.52007 / 0.26 (15173) hydrogen bonds : bond 0.03548 / 2.35 ( 541) hydrogen bonds : angle 3.72486 / 2.52 ( 1563) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 271 MET cc_start: 0.9008 (tpp) cc_final: 0.8723 (tpt) REVERT: A 514 MET cc_start: 0.8135 (ttp) cc_final: 0.7212 (ttp) REVERT: A 518 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8498 (tm-30) REVERT: A 885 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7071 (pm20) REVERT: C 127 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7594 (ttm110) REVERT: C 215 GLU cc_start: 0.8212 (tp30) cc_final: 0.7866 (tt0) REVERT: C 340 GLN cc_start: 0.8032 (pm20) cc_final: 0.7796 (pm20) REVERT: C 403 GLN cc_start: 0.8035 (tt0) cc_final: 0.7500 (mt0) REVERT: C 483 MET cc_start: 0.8734 (ptm) cc_final: 0.8452 (ptm) REVERT: C 499 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7237 (mp0) REVERT: C 768 GLN cc_start: 0.8714 (tp40) cc_final: 0.8461 (tt0) REVERT: B 8 GLU cc_start: 0.7338 (tp30) cc_final: 0.6913 (tm-30) REVERT: B 37 MET cc_start: 0.8840 (mmm) cc_final: 0.8627 (mmm) REVERT: B 52 MET cc_start: 0.7695 (mmm) cc_final: 0.7387 (tpt) outliers start: 33 outliers final: 16 residues processed: 133 average time/residue: 0.6069 time to fit residues: 86.6770 Evaluate side-chains 120 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 725 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 131 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 112 optimal weight: 0.0980 chunk 119 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.149199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.103108 restraints weight = 14234.942| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.26 r_work: 0.3044 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11221 Z= 0.153 Angle : 0.543 10.894 15173 Z= 0.274 Chirality : 0.040 0.159 1670 Planarity : 0.004 0.047 1965 Dihedral : 6.788 118.259 1519 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.22 % Allowed : 17.56 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.69 (0.23), residues: 1364 helix: 1.75 (0.20), residues: 701 sheet: -0.57 (0.49), residues: 94 loop : -1.01 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 293 TYR 0.013 0.001 TYR C 443 PHE 0.016 0.001 PHE C 475 TRP 0.033 0.001 TRP A 549 HIS 0.004 0.001 HIS C 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (11221) covalent geometry : angle 0.54295 / 0.27 (15173) hydrogen bonds : bond 0.03904 / 2.59 ( 541) hydrogen bonds : angle 3.82645 / 2.59 ( 1563) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 885 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: C 127 ARG cc_start: 0.8038 (mtm-85) cc_final: 0.7602 (ttm110) REVERT: C 215 GLU cc_start: 0.8292 (tp30) cc_final: 0.7935 (tt0) REVERT: C 340 GLN cc_start: 0.8152 (pm20) cc_final: 0.7849 (pm20) REVERT: C 416 LEU cc_start: 0.8508 (mm) cc_final: 0.8241 (mm) REVERT: C 499 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7288 (mp0) REVERT: B 7 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6734 (tm-30) REVERT: B 37 MET cc_start: 0.8871 (mmm) cc_final: 0.8656 (mmm) REVERT: B 52 MET cc_start: 0.7679 (mmm) cc_final: 0.7429 (tpt) outliers start: 26 outliers final: 20 residues processed: 122 average time/residue: 0.6253 time to fit residues: 82.3177 Evaluate side-chains 123 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 725 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 128 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.149924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.102624 restraints weight = 14360.859| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.28 r_work: 0.3054 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11221 Z= 0.135 Angle : 0.539 10.945 15173 Z= 0.272 Chirality : 0.040 0.156 1670 Planarity : 0.004 0.047 1965 Dihedral : 6.759 118.236 1519 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.88 % Allowed : 18.07 % Favored : 80.05 % 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: 0.76 (0.23), residues: 1364 helix: 1.78 (0.20), residues: 701 sheet: -0.48 (0.50), residues: 94 loop : -0.97 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 293 TYR 0.012 0.001 TYR C 443 PHE 0.015 0.001 PHE C 475 TRP 0.034 0.001 TRP A 549 HIS 0.004 0.001 HIS C 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (11221) covalent geometry : angle 0.53890 / 0.27 (15173) hydrogen bonds : bond 0.03746 / 2.48 ( 541) hydrogen bonds : angle 3.79051 / 2.57 ( 1563) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 885 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7057 (pm20) REVERT: C 127 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7644 (ttm110) REVERT: C 215 GLU cc_start: 0.8260 (tp30) cc_final: 0.7958 (tt0) REVERT: C 337 PHE cc_start: 0.8570 (t80) cc_final: 0.8342 (t80) REVERT: C 340 GLN cc_start: 0.8239 (pm20) cc_final: 0.7853 (pm20) REVERT: C 403 GLN cc_start: 0.8047 (tt0) cc_final: 0.7503 (mt0) REVERT: C 416 LEU cc_start: 0.8510 (mm) cc_final: 0.8255 (mm) REVERT: C 489 ASP cc_start: 0.8042 (p0) cc_final: 0.7836 (p0) REVERT: C 499 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7270 (mp0) REVERT: B 7 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6706 (tm-30) REVERT: B 37 MET cc_start: 0.8868 (mmm) cc_final: 0.8651 (mmm) REVERT: B 52 MET cc_start: 0.7642 (mmm) cc_final: 0.7396 (tpt) outliers start: 22 outliers final: 20 residues processed: 120 average time/residue: 0.5240 time to fit residues: 68.1702 Evaluate side-chains 122 residues out of total 1225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 885 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 658 GLN Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 725 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 4 optimal weight: 0.1980 chunk 115 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 124 optimal weight: 0.3980 chunk 46 optimal weight: 0.0770 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.151638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.105133 restraints weight = 14304.285| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.32 r_work: 0.3090 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11221 Z= 0.103 Angle : 0.512 10.964 15173 Z= 0.259 Chirality : 0.038 0.150 1670 Planarity : 0.004 0.047 1965 Dihedral : 6.666 118.282 1519 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.62 % Allowed : 18.16 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.97 (0.23), residues: 1364 helix: 1.96 (0.20), residues: 699 sheet: -0.26 (0.50), residues: 93 loop : -0.89 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 293 TYR 0.011 0.001 TYR A 347 PHE 0.015 0.001 PHE C 475 TRP 0.033 0.001 TRP A 549 HIS 0.004 0.001 HIS C 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (11221) covalent geometry : angle 0.51225 / 0.26 (15173) hydrogen bonds : bond 0.03387 / 2.24 ( 541) hydrogen bonds : angle 3.66764 / 2.49 ( 1563) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3882.36 seconds wall clock time: 66 minutes 51.14 seconds (4011.14 seconds total)