Starting phenix.real_space_refine on Sun Dec 29 06:37:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x23_32956/12_2024/7x23_32956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x23_32956/12_2024/7x23_32956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x23_32956/12_2024/7x23_32956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x23_32956/12_2024/7x23_32956.map" model { file = "/net/cci-nas-00/data/ceres_data/7x23_32956/12_2024/7x23_32956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x23_32956/12_2024/7x23_32956.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 50 5.16 5 Na 3 4.78 5 C 6395 2.51 5 N 1650 2.21 5 O 1875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9976 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7666 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 948} Chain: "B" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2255 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 257} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' NA': 3, 'ACP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 6.10, per 1000 atoms: 0.61 Number of scatterers: 9976 At special positions: 0 Unit cell: (122.84, 93.79, 160.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 3 15.00 Na 3 11.00 O 1875 8.00 N 1650 7.00 C 6395 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 277 " distance=2.03 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=1, symmetry=0 Links applied NAG-ASN " NAG B 401 " - " ASN B 158 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 48.5% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 61 through 69 removed outlier: 4.087A pdb=" N GLU A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.594A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 110 Processing helix chain 'A' and resid 113 through 135 removed outlier: 3.575A pdb=" N LEU A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 176 removed outlier: 3.671A pdb=" N MET A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 294 through 325 Processing helix chain 'A' and resid 328 through 344 Processing helix chain 'A' and resid 347 through 366 removed outlier: 3.758A pdb=" N LYS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 381 removed outlier: 3.743A pdb=" N THR A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 441 removed outlier: 3.521A pdb=" N ASN A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 476 Processing helix chain 'A' and resid 478 through 486 Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'A' and resid 543 through 559 Processing helix chain 'A' and resid 610 through 621 Processing helix chain 'A' and resid 632 through 644 Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 706 through 720 Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 751 through 758 Processing helix chain 'A' and resid 767 through 794 removed outlier: 3.639A pdb=" N VAL A 771 " --> pdb=" O PHE A 767 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A 794 " --> pdb=" O TYR A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 809 removed outlier: 3.621A pdb=" N GLU A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) Proline residue: A 801 - end of helix Processing helix chain 'A' and resid 815 through 827 Processing helix chain 'A' and resid 828 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 842 through 846 removed outlier: 4.075A pdb=" N ARG A 846 " --> pdb=" O ILE A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 868 Processing helix chain 'A' and resid 868 through 889 Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 919 through 949 Processing helix chain 'A' and resid 955 through 960 Processing helix chain 'A' and resid 964 through 984 removed outlier: 3.929A pdb=" N TRP A 968 " --> pdb=" O ASN A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1004 through 1025 Processing helix chain 'A' and resid 1028 through 1034 Processing helix chain 'B' and resid 29 through 60 removed outlier: 3.787A pdb=" N LYS B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 removed outlier: 4.253A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.582A pdb=" N TYR B 169 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS B 170 " --> pdb=" O TYR B 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 166 through 170' Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 185 removed outlier: 3.709A pdb=" N VAL A 183 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 206 removed outlier: 4.053A pdb=" N THR A 260 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS A 224 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLY A 264 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY A 222 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA A 266 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER A 220 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY A 268 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL A 218 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A 270 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ARG A 216 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 272 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 206 removed outlier: 4.053A pdb=" N THR A 260 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS A 224 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLY A 264 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY A 222 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA A 266 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER A 220 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY A 268 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL A 218 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A 270 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ARG A 216 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 272 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 5.926A pdb=" N GLY A 743 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU A 762 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA A 745 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 724 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE A 744 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL A 726 " --> pdb=" O ILE A 744 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N MET A 746 " --> pdb=" O VAL A 726 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLY A 728 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 385 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 628 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N SER A 387 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A 625 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N PHE A 702 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N MET A 627 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 675 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ALA A 703 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 677 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 411 removed outlier: 6.194A pdb=" N VAL A 400 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 604 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS A 402 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N PHE A 595 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N TYR A 571 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE A 597 " --> pdb=" O HIS A 569 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N HIS A 569 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A 599 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 567 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 505 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 518 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 503 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 520 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N PHE A 500 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE A 494 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 490 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 411 removed outlier: 6.194A pdb=" N VAL A 400 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 604 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS A 402 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N CYS A 530 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE A 597 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR A 532 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLY A 599 " --> pdb=" O THR A 532 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N MET A 534 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 12.841A pdb=" N LEU A 601 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 910 through 911 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.912A pdb=" N PHE B 90 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 488 hydrogen bonds defined for protein. 1407 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: 3.44 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3174 1.34 - 1.46: 1499 1.46 - 1.58: 5412 1.58 - 1.69: 6 1.69 - 1.81: 81 Bond restraints: 10172 Sorted by residual: bond pdb=" O2B ACP A1101 " pdb=" PB ACP A1101 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" O3A ACP A1101 " pdb=" PB ACP A1101 " ideal model delta sigma weight residual 1.698 1.609 0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C4 ACP A1101 " pdb=" C5 ACP A1101 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" CG PRO A 612 " pdb=" CD PRO A 612 " ideal model delta sigma weight residual 1.503 1.370 0.133 3.40e-02 8.65e+02 1.54e+01 bond pdb=" O3G ACP A1101 " pdb=" PG ACP A1101 " ideal model delta sigma weight residual 1.532 1.610 -0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 10167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 13650 2.39 - 4.78: 125 4.78 - 7.17: 17 7.17 - 9.56: 6 9.56 - 11.95: 3 Bond angle restraints: 13801 Sorted by residual: angle pdb=" N PRO A 612 " pdb=" CD PRO A 612 " pdb=" CG PRO A 612 " ideal model delta sigma weight residual 103.20 93.40 9.80 1.50e+00 4.44e-01 4.27e+01 angle pdb=" C3B ACP A1101 " pdb=" PB ACP A1101 " pdb=" O3A ACP A1101 " ideal model delta sigma weight residual 98.05 110.00 -11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" N ASN B 206 " pdb=" CA ASN B 206 " pdb=" C ASN B 206 " ideal model delta sigma weight residual 109.81 117.62 -7.81 2.21e+00 2.05e-01 1.25e+01 angle pdb=" O1B ACP A1101 " pdb=" PB ACP A1101 " pdb=" O2B ACP A1101 " ideal model delta sigma weight residual 119.60 109.41 10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C LEU A 867 " pdb=" N HIS A 868 " pdb=" CA HIS A 868 " ideal model delta sigma weight residual 122.56 117.50 5.06 1.50e+00 4.44e-01 1.14e+01 ... (remaining 13796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 5533 16.05 - 32.10: 470 32.10 - 48.15: 121 48.15 - 64.21: 25 64.21 - 80.26: 9 Dihedral angle restraints: 6158 sinusoidal: 2499 harmonic: 3659 Sorted by residual: dihedral pdb=" CB CYS B 126 " pdb=" SG CYS B 126 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 148.58 -55.58 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CA TYR B 247 " pdb=" C TYR B 247 " pdb=" N GLY B 248 " pdb=" CA GLY B 248 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TYR A 983 " pdb=" C TYR A 983 " pdb=" N GLY A 984 " pdb=" CA GLY A 984 " ideal model delta harmonic sigma weight residual 180.00 162.76 17.24 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 6155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1256 0.049 - 0.098: 258 0.098 - 0.147: 64 0.147 - 0.196: 2 0.196 - 0.246: 2 Chirality restraints: 1582 Sorted by residual: chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ASN B 206 " pdb=" N ASN B 206 " pdb=" C ASN B 206 " pdb=" CB ASN B 206 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" CB VAL A 110 " pdb=" CA VAL A 110 " pdb=" CG1 VAL A 110 " pdb=" CG2 VAL A 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1579 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 401 " -0.055 2.00e-02 2.50e+03 4.49e-02 2.52e+01 pdb=" C7 NAG B 401 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG B 401 " -0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B 401 " 0.071 2.00e-02 2.50e+03 pdb=" O7 NAG B 401 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 686 " -0.043 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO A 687 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 687 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 687 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 632 " -0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO A 633 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 633 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 633 " -0.029 5.00e-02 4.00e+02 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1650 2.77 - 3.30: 9912 3.30 - 3.83: 16809 3.83 - 4.37: 19518 4.37 - 4.90: 33808 Nonbonded interactions: 81697 Sorted by model distance: nonbonded pdb=" OG1 THR A 793 " pdb="NA NA A1104 " model vdw 2.232 2.470 nonbonded pdb=" OG1 THR A 390 " pdb=" O3G ACP A1101 " model vdw 2.254 3.040 nonbonded pdb=" OE2 GLU A 692 " pdb=" ND2 ASN A 696 " model vdw 2.256 3.120 nonbonded pdb=" OD1 ASP A 782 " pdb=" NH1 ARG A 952 " model vdw 2.261 3.120 nonbonded pdb=" OH TYR A 914 " pdb=" O SER B 62 " model vdw 2.262 3.040 ... (remaining 81692 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: 0.970 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.920 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 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 0.133 10172 Z= 0.257 Angle : 0.589 11.954 13801 Z= 0.296 Chirality : 0.042 0.246 1582 Planarity : 0.004 0.066 1751 Dihedral : 13.252 80.256 3797 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1258 helix: 2.19 (0.23), residues: 543 sheet: 0.28 (0.41), residues: 158 loop : -0.30 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 32 HIS 0.003 0.001 HIS A 632 PHE 0.019 0.001 PHE A 318 TYR 0.014 0.001 TYR A 881 ARG 0.003 0.000 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.1780 (mtt) cc_final: 0.0394 (ptm) REVERT: A 107 LYS cc_start: 0.5045 (tttt) cc_final: 0.4718 (ttmm) REVERT: A 176 MET cc_start: 0.1800 (pmm) cc_final: 0.0525 (ptm) REVERT: A 392 THR cc_start: 0.4596 (m) cc_final: 0.4267 (m) REVERT: A 455 MET cc_start: 0.1475 (ptp) cc_final: 0.1148 (ptm) REVERT: A 613 ASP cc_start: 0.5106 (t70) cc_final: 0.4740 (t70) REVERT: A 746 MET cc_start: 0.5926 (mpp) cc_final: 0.5385 (mmp) REVERT: A 842 ASP cc_start: 0.5850 (t70) cc_final: 0.5535 (t0) REVERT: A 976 ILE cc_start: 0.7888 (mm) cc_final: 0.7466 (mt) REVERT: A 995 MET cc_start: 0.7137 (mtp) cc_final: 0.6895 (mtm) REVERT: A 1017 MET cc_start: 0.6661 (mmp) cc_final: 0.6420 (mmt) REVERT: B 91 ARG cc_start: 0.5144 (ttm-80) cc_final: 0.4833 (ttp-110) REVERT: B 274 ARG cc_start: 0.6115 (mtt180) cc_final: 0.5850 (mtp85) REVERT: B 297 ASP cc_start: 0.7134 (m-30) cc_final: 0.6844 (m-30) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2903 time to fit residues: 79.0762 Evaluate side-chains 118 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 396 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN A 958 GLN B 213 GLN B 263 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10172 Z= 0.189 Angle : 0.552 7.945 13801 Z= 0.289 Chirality : 0.043 0.198 1582 Planarity : 0.004 0.063 1751 Dihedral : 5.390 48.485 1412 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.01 % Allowed : 6.61 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1258 helix: 1.96 (0.22), residues: 558 sheet: 0.18 (0.40), residues: 151 loop : -0.22 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.005 0.001 HIS A 632 PHE 0.014 0.001 PHE A 318 TYR 0.015 0.001 TYR A 881 ARG 0.004 0.000 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.049 Fit side-chains REVERT: A 52 MET cc_start: 0.2024 (mtt) cc_final: 0.0545 (ptm) REVERT: A 176 MET cc_start: 0.1729 (pmm) cc_final: 0.1094 (mtm) REVERT: A 392 THR cc_start: 0.4883 (m) cc_final: 0.4623 (m) REVERT: A 455 MET cc_start: 0.1479 (ptp) cc_final: 0.1224 (ptm) REVERT: A 613 ASP cc_start: 0.5159 (t70) cc_final: 0.4789 (t70) REVERT: A 746 MET cc_start: 0.6149 (mpp) cc_final: 0.5769 (mmp) REVERT: A 842 ASP cc_start: 0.5810 (t70) cc_final: 0.5448 (t0) REVERT: A 906 ASP cc_start: 0.6288 (m-30) cc_final: 0.6014 (m-30) REVERT: A 995 MET cc_start: 0.7149 (mtp) cc_final: 0.6937 (mtm) REVERT: B 39 TYR cc_start: 0.7015 (m-10) cc_final: 0.6662 (m-80) REVERT: B 91 ARG cc_start: 0.5375 (ttm-80) cc_final: 0.5145 (ttp-110) REVERT: B 179 LYS cc_start: 0.8430 (pttt) cc_final: 0.8206 (pttt) outliers start: 11 outliers final: 7 residues processed: 139 average time/residue: 0.2464 time to fit residues: 47.8048 Evaluate side-chains 117 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 267 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 0.0970 chunk 112 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 91 optimal weight: 0.0030 overall best weight: 1.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN A 396 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10172 Z= 0.217 Angle : 0.549 7.642 13801 Z= 0.287 Chirality : 0.043 0.181 1582 Planarity : 0.004 0.062 1751 Dihedral : 5.275 44.949 1412 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.28 % Allowed : 9.36 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.23), residues: 1258 helix: 1.75 (0.22), residues: 564 sheet: -0.06 (0.40), residues: 151 loop : -0.26 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 902 HIS 0.006 0.001 HIS A 632 PHE 0.012 0.002 PHE A 878 TYR 0.018 0.002 TYR A 881 ARG 0.020 0.001 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.2456 (mtt) cc_final: 0.0788 (ptm) REVERT: A 176 MET cc_start: 0.1860 (pmm) cc_final: 0.1308 (mtm) REVERT: A 392 THR cc_start: 0.4898 (m) cc_final: 0.4621 (m) REVERT: A 455 MET cc_start: 0.1594 (ptp) cc_final: 0.1176 (ptm) REVERT: A 641 LYS cc_start: 0.6597 (ttmt) cc_final: 0.5962 (ttmm) REVERT: A 746 MET cc_start: 0.6209 (mpp) cc_final: 0.5841 (mmp) REVERT: A 842 ASP cc_start: 0.6146 (t70) cc_final: 0.5911 (t70) REVERT: A 872 MET cc_start: 0.7764 (mtp) cc_final: 0.7521 (mtp) REVERT: A 906 ASP cc_start: 0.6443 (m-30) cc_final: 0.6107 (m-30) REVERT: B 91 ARG cc_start: 0.5417 (ttm-80) cc_final: 0.5147 (ttp-110) REVERT: B 129 MET cc_start: 0.5195 (mmm) cc_final: 0.4827 (tpt) REVERT: B 179 LYS cc_start: 0.8523 (pttt) cc_final: 0.8223 (pttt) outliers start: 14 outliers final: 13 residues processed: 128 average time/residue: 0.2594 time to fit residues: 46.1632 Evaluate side-chains 128 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 0.0970 chunk 54 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10172 Z= 0.162 Angle : 0.511 8.324 13801 Z= 0.267 Chirality : 0.042 0.187 1582 Planarity : 0.004 0.062 1751 Dihedral : 5.295 46.224 1412 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.47 % Allowed : 10.46 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.23), residues: 1258 helix: 1.85 (0.22), residues: 569 sheet: -0.07 (0.40), residues: 151 loop : -0.26 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 902 HIS 0.005 0.001 HIS A 632 PHE 0.010 0.001 PHE A 935 TYR 0.016 0.001 TYR A 881 ARG 0.007 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.2411 (mtt) cc_final: 0.0660 (ptm) REVERT: A 135 ASN cc_start: 0.5620 (m-40) cc_final: 0.5333 (m110) REVERT: A 176 MET cc_start: 0.1901 (pmm) cc_final: 0.1397 (mtm) REVERT: A 392 THR cc_start: 0.4928 (m) cc_final: 0.4636 (m) REVERT: A 455 MET cc_start: 0.1699 (ptp) cc_final: 0.1159 (ptm) REVERT: A 641 LYS cc_start: 0.6478 (ttmt) cc_final: 0.6269 (ttmt) REVERT: A 746 MET cc_start: 0.6209 (mpp) cc_final: 0.5852 (mmp) REVERT: A 842 ASP cc_start: 0.6153 (t70) cc_final: 0.5934 (t70) REVERT: A 872 MET cc_start: 0.7677 (mtp) cc_final: 0.7421 (mtp) REVERT: B 39 TYR cc_start: 0.6940 (m-10) cc_final: 0.6700 (m-10) REVERT: B 91 ARG cc_start: 0.5342 (ttm-80) cc_final: 0.5140 (ttp-110) REVERT: B 129 MET cc_start: 0.5212 (mmm) cc_final: 0.4807 (tpt) REVERT: B 179 LYS cc_start: 0.8534 (pttt) cc_final: 0.8239 (pttt) outliers start: 16 outliers final: 13 residues processed: 134 average time/residue: 0.2604 time to fit residues: 48.5673 Evaluate side-chains 129 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.0030 chunk 108 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 396 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10172 Z= 0.157 Angle : 0.494 7.513 13801 Z= 0.258 Chirality : 0.041 0.178 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.161 47.912 1412 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.56 % Allowed : 10.64 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1258 helix: 1.95 (0.22), residues: 569 sheet: -0.20 (0.39), residues: 157 loop : -0.20 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.006 0.001 HIS A 632 PHE 0.009 0.001 PHE A 935 TYR 0.016 0.001 TYR A 881 ARG 0.015 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.2025 (pmm) cc_final: 0.1554 (mtm) REVERT: A 340 ILE cc_start: 0.7861 (mm) cc_final: 0.7621 (mp) REVERT: A 392 THR cc_start: 0.4888 (m) cc_final: 0.4581 (m) REVERT: A 455 MET cc_start: 0.1652 (ptp) cc_final: 0.1119 (ptm) REVERT: A 641 LYS cc_start: 0.6498 (ttmt) cc_final: 0.6271 (ttmt) REVERT: A 737 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6898 (mp) REVERT: A 746 MET cc_start: 0.6251 (mpp) cc_final: 0.5878 (mmp) REVERT: A 816 THR cc_start: 0.6683 (OUTLIER) cc_final: 0.6282 (p) REVERT: A 823 ASP cc_start: 0.5893 (t70) cc_final: 0.5575 (t70) REVERT: A 827 ASP cc_start: 0.6023 (m-30) cc_final: 0.5613 (m-30) REVERT: A 842 ASP cc_start: 0.6221 (t70) cc_final: 0.6003 (t70) REVERT: A 906 ASP cc_start: 0.6351 (m-30) cc_final: 0.6070 (m-30) REVERT: B 39 TYR cc_start: 0.6868 (m-10) cc_final: 0.6664 (m-10) REVERT: B 129 MET cc_start: 0.5146 (mmm) cc_final: 0.4820 (tpt) REVERT: B 179 LYS cc_start: 0.8539 (pttt) cc_final: 0.8254 (pttt) outliers start: 17 outliers final: 11 residues processed: 134 average time/residue: 0.2480 time to fit residues: 46.7292 Evaluate side-chains 125 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN A 396 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10172 Z= 0.160 Angle : 0.502 9.693 13801 Z= 0.260 Chirality : 0.041 0.179 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.219 49.806 1412 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.65 % Allowed : 11.10 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1258 helix: 1.98 (0.22), residues: 569 sheet: -0.24 (0.39), residues: 157 loop : -0.21 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.005 0.001 HIS A 632 PHE 0.010 0.001 PHE A 935 TYR 0.016 0.001 TYR A 881 ARG 0.010 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 135 ASN cc_start: 0.5658 (m-40) cc_final: 0.5454 (m110) REVERT: A 176 MET cc_start: 0.2157 (OUTLIER) cc_final: 0.1656 (mtm) REVERT: A 392 THR cc_start: 0.4979 (m) cc_final: 0.4624 (m) REVERT: A 455 MET cc_start: 0.1683 (ptp) cc_final: 0.1141 (ptm) REVERT: A 641 LYS cc_start: 0.6499 (ttmt) cc_final: 0.5894 (ttmm) REVERT: A 737 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6902 (mp) REVERT: A 746 MET cc_start: 0.6274 (mpp) cc_final: 0.6001 (mmm) REVERT: A 823 ASP cc_start: 0.5870 (t70) cc_final: 0.5510 (t70) REVERT: A 827 ASP cc_start: 0.5969 (m-30) cc_final: 0.5517 (m-30) REVERT: A 842 ASP cc_start: 0.6202 (t70) cc_final: 0.5995 (t70) REVERT: A 906 ASP cc_start: 0.6308 (m-30) cc_final: 0.6040 (m-30) REVERT: B 129 MET cc_start: 0.5050 (mmm) cc_final: 0.4786 (tpt) outliers start: 18 outliers final: 13 residues processed: 128 average time/residue: 0.2277 time to fit residues: 41.6624 Evaluate side-chains 129 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 55 optimal weight: 0.0000 chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 396 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10172 Z= 0.154 Angle : 0.495 9.371 13801 Z= 0.257 Chirality : 0.041 0.176 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.207 52.858 1412 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.83 % Allowed : 10.92 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1258 helix: 1.99 (0.22), residues: 569 sheet: -0.29 (0.39), residues: 160 loop : -0.22 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.002 0.000 HIS A 868 PHE 0.009 0.001 PHE A 935 TYR 0.016 0.001 TYR A 881 ARG 0.009 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.2162 (OUTLIER) cc_final: 0.1671 (mtm) REVERT: A 392 THR cc_start: 0.5148 (m) cc_final: 0.4923 (m) REVERT: A 455 MET cc_start: 0.1900 (ptp) cc_final: 0.1129 (mtp) REVERT: A 641 LYS cc_start: 0.6485 (ttmt) cc_final: 0.5885 (ttmm) REVERT: A 737 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6937 (mp) REVERT: A 746 MET cc_start: 0.6158 (mpp) cc_final: 0.5908 (mmm) REVERT: A 823 ASP cc_start: 0.5856 (t70) cc_final: 0.5478 (t70) REVERT: A 827 ASP cc_start: 0.6015 (m-30) cc_final: 0.5479 (m-30) REVERT: A 842 ASP cc_start: 0.6180 (t70) cc_final: 0.5966 (t70) REVERT: A 906 ASP cc_start: 0.6322 (m-30) cc_final: 0.6056 (m-30) REVERT: B 129 MET cc_start: 0.5120 (mmm) cc_final: 0.4843 (tpt) outliers start: 20 outliers final: 15 residues processed: 132 average time/residue: 0.2474 time to fit residues: 45.8728 Evaluate side-chains 132 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN A 396 ASN A 536 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10172 Z= 0.162 Angle : 0.495 7.675 13801 Z= 0.258 Chirality : 0.041 0.177 1582 Planarity : 0.004 0.071 1751 Dihedral : 5.192 52.225 1412 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.93 % Allowed : 11.10 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1258 helix: 1.98 (0.22), residues: 571 sheet: -0.32 (0.38), residues: 161 loop : -0.21 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.003 0.000 HIS A 868 PHE 0.009 0.001 PHE A 935 TYR 0.016 0.001 TYR A 881 ARG 0.014 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.2160 (OUTLIER) cc_final: 0.1637 (mtm) REVERT: A 392 THR cc_start: 0.5183 (m) cc_final: 0.4968 (m) REVERT: A 455 MET cc_start: 0.1822 (ptp) cc_final: 0.0953 (mtp) REVERT: A 641 LYS cc_start: 0.6528 (ttmt) cc_final: 0.5950 (ttmm) REVERT: A 737 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6931 (mp) REVERT: A 746 MET cc_start: 0.6161 (mpp) cc_final: 0.5907 (mmm) REVERT: A 823 ASP cc_start: 0.5838 (t70) cc_final: 0.5434 (t70) REVERT: A 827 ASP cc_start: 0.5957 (m-30) cc_final: 0.5394 (m-30) REVERT: A 842 ASP cc_start: 0.6221 (t70) cc_final: 0.6014 (t70) REVERT: A 906 ASP cc_start: 0.6307 (m-30) cc_final: 0.6045 (m-30) REVERT: B 129 MET cc_start: 0.5114 (mmm) cc_final: 0.4838 (tpt) outliers start: 21 outliers final: 14 residues processed: 137 average time/residue: 0.2427 time to fit residues: 46.6577 Evaluate side-chains 135 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 101 optimal weight: 0.0070 chunk 106 optimal weight: 0.1980 chunk 111 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 168 ASN A 396 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN B 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 10172 Z= 0.151 Angle : 0.488 7.444 13801 Z= 0.256 Chirality : 0.041 0.179 1582 Planarity : 0.004 0.080 1751 Dihedral : 5.139 52.706 1412 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.83 % Allowed : 11.56 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.24), residues: 1258 helix: 2.00 (0.22), residues: 572 sheet: -0.30 (0.38), residues: 160 loop : -0.19 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.002 0.000 HIS A 868 PHE 0.009 0.001 PHE A 105 TYR 0.016 0.001 TYR A 881 ARG 0.016 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.2148 (OUTLIER) cc_final: 0.1642 (mtm) REVERT: A 455 MET cc_start: 0.1816 (ptp) cc_final: 0.0984 (mtp) REVERT: A 641 LYS cc_start: 0.6568 (ttmt) cc_final: 0.5987 (ttmm) REVERT: A 737 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6933 (mp) REVERT: A 746 MET cc_start: 0.6144 (mpp) cc_final: 0.5901 (mmm) REVERT: A 823 ASP cc_start: 0.5792 (t70) cc_final: 0.5386 (t70) REVERT: A 827 ASP cc_start: 0.5907 (m-30) cc_final: 0.5310 (m-30) REVERT: A 842 ASP cc_start: 0.6218 (t70) cc_final: 0.5930 (t0) REVERT: A 906 ASP cc_start: 0.6283 (m-30) cc_final: 0.6037 (m-30) REVERT: B 129 MET cc_start: 0.5168 (mmm) cc_final: 0.4888 (tpt) REVERT: B 208 ASN cc_start: 0.7001 (OUTLIER) cc_final: 0.6159 (m-40) outliers start: 20 outliers final: 15 residues processed: 133 average time/residue: 0.2284 time to fit residues: 43.3788 Evaluate side-chains 135 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 114 optimal weight: 0.0070 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 10172 Z= 0.182 Angle : 0.511 8.630 13801 Z= 0.265 Chirality : 0.042 0.160 1582 Planarity : 0.004 0.062 1751 Dihedral : 5.194 53.469 1412 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.83 % Allowed : 11.65 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1258 helix: 1.93 (0.22), residues: 572 sheet: -0.33 (0.38), residues: 158 loop : -0.20 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.003 0.001 HIS A 868 PHE 0.010 0.001 PHE A 935 TYR 0.016 0.001 TYR A 881 ARG 0.013 0.000 ARG A 704 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.2155 (OUTLIER) cc_final: 0.1670 (mtm) REVERT: A 455 MET cc_start: 0.1819 (ptp) cc_final: 0.1079 (mtp) REVERT: A 641 LYS cc_start: 0.6582 (ttmt) cc_final: 0.5984 (ttmm) REVERT: A 737 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6972 (mp) REVERT: A 842 ASP cc_start: 0.6227 (t70) cc_final: 0.6022 (t70) REVERT: A 906 ASP cc_start: 0.6310 (m-30) cc_final: 0.6056 (m-30) REVERT: B 129 MET cc_start: 0.5209 (mmm) cc_final: 0.4908 (tpt) outliers start: 20 outliers final: 17 residues processed: 134 average time/residue: 0.2445 time to fit residues: 47.0999 Evaluate side-chains 140 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 831 SER Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 283 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.221169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.169503 restraints weight = 12099.746| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.15 r_work: 0.3398 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 10172 Z= 0.179 Angle : 0.511 8.723 13801 Z= 0.265 Chirality : 0.042 0.154 1582 Planarity : 0.004 0.061 1751 Dihedral : 5.256 53.280 1412 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.93 % Allowed : 11.47 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.24), residues: 1258 helix: 1.95 (0.22), residues: 572 sheet: -0.34 (0.39), residues: 158 loop : -0.20 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 902 HIS 0.003 0.001 HIS A 868 PHE 0.010 0.001 PHE A 935 TYR 0.016 0.001 TYR A 881 ARG 0.009 0.000 ARG A 704 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2409.56 seconds wall clock time: 44 minutes 33.47 seconds (2673.47 seconds total)