Starting phenix.real_space_refine on Thu Jul 2 22:56:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rpk_24617/07_2026/7rpk_24617.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rpk_24617/07_2026/7rpk_24617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rpk_24617/07_2026/7rpk_24617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rpk_24617/07_2026/7rpk_24617.map" model { file = "/net/cci-nas-00/data/ceres_data/7rpk_24617/07_2026/7rpk_24617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rpk_24617/07_2026/7rpk_24617.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rpk_24617/07_2026/7rpk_24617.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rpk_24617/07_2026/7rpk_24617.cif" } resolution = 2.7 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= 0.011 sd= 0.574 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 P 1 5.49 5 S 71 5.16 5 Na 2 4.78 5 C 6659 2.51 5 N 1455 2.21 5 O 1827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 10018 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7606 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 953, 7598 Classifications: {'peptide': 953} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 912} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 953, 7598 Classifications: {'peptide': 953} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 912} Chain breaks: 2 bond proxies already assigned to first conformer: 7793 Chain: "H" Number of atoms: 1215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1215 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "A" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 1147 Unusual residues: {' NA': 2, '6OE': 1, 'AV0': 2, 'NAG': 5, 'Y01': 26} Classifications: {'undetermined': 36} Link IDs: {None: 35} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 8 Unusual residues: {' CA': 2, ' ZN': 1, 'SO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AMET A 557 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 557 " occ=0.50 Time building chain proxies: 3.16, per 1000 atoms: 0.32 Number of scatterers: 10018 At special positions: 0 Unit cell: (91.015, 85.17, 132.765, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 71 16.00 P 1 15.00 Na 2 11.00 O 1827 8.00 N 1455 7.00 C 6659 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 348 " distance=2.02 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 366 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 410 " distance=2.04 Simple disulfide: pdb=" SG CYS A 829 " - pdb=" SG CYS A 849 " distance=2.04 Simple disulfide: pdb=" SG CYS A 863 " - pdb=" SG CYS A 872 " distance=2.02 Simple disulfide: pdb=" SG CYS A 871 " - pdb=" SG CYS A 887 " distance=2.04 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 Links applied NAG-ASN " NAG A2132 " - " ASN A 915 " " NAG A2133 " - " ASN A 475 " " NAG A2134 " - " ASN A 834 " " NAG A2135 " - " ASN A 362 " " NAG A2136 " - " ASN A 390 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 694.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 141 " pdb="ZN ZN H 203 " - pdb=" ND1 HIS H 183 " 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 4 sheets defined 62.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 187 through 209 Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 314 through 329 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 352 through 361 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 390 removed outlier: 4.980A pdb=" N LYS A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N HIS A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 388 " --> pdb=" O CYS A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.762A pdb=" N LYS A 419 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 471 Processing helix chain 'A' and resid 490 through 502 removed outlier: 4.147A pdb=" N GLN A 496 " --> pdb=" O HIS A 492 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASP A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 522 Processing helix chain 'A' and resid 523 through 548 removed outlier: 3.813A pdb=" N LEU A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 560 through 570 removed outlier: 4.514A pdb=" N ALA A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 591 through 620 removed outlier: 5.241A pdb=" N LEU A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N SER A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 624 Processing helix chain 'A' and resid 626 through 649 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 681 through 685 removed outlier: 3.625A pdb=" N VAL A 684 " --> pdb=" O CYS A 681 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 685 " --> pdb=" O TRP A 682 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 681 through 685' Processing helix chain 'A' and resid 688 through 706 Processing helix chain 'A' and resid 706 through 715 removed outlier: 3.563A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 736 Processing helix chain 'A' and resid 746 through 750 Processing helix chain 'A' and resid 757 through 766 Processing helix chain 'A' and resid 770 through 778 removed outlier: 3.645A pdb=" N HIS A 776 " --> pdb=" O PHE A 772 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 833 Processing helix chain 'A' and resid 849 through 860 removed outlier: 3.540A pdb=" N THR A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 Proline residue: A 870 - end of helix Processing helix chain 'A' and resid 880 through 899 removed outlier: 4.225A pdb=" N LYS A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 954 Processing helix chain 'A' and resid 955 through 956 No H-bonds generated for 'chain 'A' and resid 955 through 956' Processing helix chain 'A' and resid 957 through 961 removed outlier: 3.800A pdb=" N SER A 961 " --> pdb=" O GLU A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1001 Processing helix chain 'A' and resid 1003 through 1028 Processing helix chain 'A' and resid 1033 through 1061 removed outlier: 3.650A pdb=" N VAL A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1094 removed outlier: 4.952A pdb=" N SER A1079 " --> pdb=" O SER A1075 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ALA A1080 " --> pdb=" O ARG A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1123 Processing helix chain 'A' and resid 1123 through 1133 Processing helix chain 'H' and resid 71 through 77 Processing helix chain 'H' and resid 94 through 96 No H-bonds generated for 'chain 'H' and resid 94 through 96' Processing helix chain 'H' and resid 100 through 118 Processing helix chain 'H' and resid 139 through 144 Processing helix chain 'H' and resid 155 through 157 No H-bonds generated for 'chain 'H' and resid 155 through 157' Processing helix chain 'H' and resid 158 through 170 Processing sheet with id=AA1, first strand: chain 'A' and resid 450 through 458 removed outlier: 3.938A pdb=" N SER A 300 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 485 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA A 305 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL A 483 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 909 through 912 removed outlier: 4.490A pdb=" N MET A 783 " --> pdb=" O SER A 927 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'H' and resid 85 through 87 removed outlier: 6.518A pdb=" N ILE H 86 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N GLU H 127 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP H 148 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N HIS H 181 " --> pdb=" O GLU H 177 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU H 177 " --> pdb=" O HIS H 181 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1458 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: 1.64 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1493 1.29 - 1.43: 2608 1.43 - 1.56: 5756 1.56 - 1.69: 321 1.69 - 1.82: 106 Bond restraints: 10284 Sorted by residual: bond pdb=" C PHE A 556 " pdb=" N BMET A 557 " ideal model delta sigma weight residual 1.331 1.473 -0.142 1.48e-02 4.57e+03 9.19e+01 bond pdb=" C SER A1037 " pdb=" O SER A1037 " ideal model delta sigma weight residual 1.237 1.161 0.076 1.16e-02 7.43e+03 4.25e+01 bond pdb=" CA ALA H 166 " pdb=" CB ALA H 166 " ideal model delta sigma weight residual 1.529 1.430 0.099 1.55e-02 4.16e+03 4.07e+01 bond pdb=" C ARG A 268 " pdb=" O ARG A 268 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.26e-02 6.30e+03 2.76e+01 bond pdb=" C02 6OE A2131 " pdb=" N01 6OE A2131 " ideal model delta sigma weight residual 1.452 1.537 -0.085 2.00e-02 2.50e+03 1.83e+01 ... (remaining 10279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 11070 2.12 - 4.24: 2750 4.24 - 6.37: 262 6.37 - 8.49: 19 8.49 - 10.61: 6 Bond angle restraints: 14107 Sorted by residual: angle pdb=" N VAL A1034 " pdb=" CA VAL A1034 " pdb=" C VAL A1034 " ideal model delta sigma weight residual 110.53 119.77 -9.24 9.40e-01 1.13e+00 9.67e+01 angle pdb=" O PHE A 556 " pdb=" C PHE A 556 " pdb=" N BMET A 557 " ideal model delta sigma weight residual 122.39 111.78 10.61 1.30e+00 5.92e-01 6.66e+01 angle pdb=" CA PHE A 556 " pdb=" C PHE A 556 " pdb=" N BMET A 557 " ideal model delta sigma weight residual 118.08 126.82 -8.74 1.30e+00 5.92e-01 4.52e+01 angle pdb=" N ARG H 62 " pdb=" CA ARG H 62 " pdb=" C ARG H 62 " ideal model delta sigma weight residual 110.10 119.89 -9.79 1.49e+00 4.50e-01 4.31e+01 angle pdb=" CA ASP H 155 " pdb=" CB ASP H 155 " pdb=" CG ASP H 155 " ideal model delta sigma weight residual 112.60 118.36 -5.76 1.00e+00 1.00e+00 3.32e+01 ... (remaining 14102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.31: 5585 30.31 - 60.63: 139 60.63 - 90.94: 20 90.94 - 121.26: 2 121.26 - 151.57: 3 Dihedral angle restraints: 5749 sinusoidal: 2500 harmonic: 3249 Sorted by residual: dihedral pdb=" CA PRO A 438 " pdb=" C PRO A 438 " pdb=" N LYS A 439 " pdb=" CA LYS A 439 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA TYR A 420 " pdb=" C TYR A 420 " pdb=" N ASN A 421 " pdb=" CA ASN A 421 " ideal model delta harmonic sigma weight residual -180.00 -153.51 -26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA ASP A 396 " pdb=" C ASP A 396 " pdb=" N CYS A 397 " pdb=" CA CYS A 397 " ideal model delta harmonic sigma weight residual 180.00 -154.45 -25.55 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 5746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1242 0.113 - 0.226: 364 0.226 - 0.340: 35 0.340 - 0.453: 3 0.453 - 0.566: 3 Chirality restraints: 1647 Sorted by residual: chirality pdb=" CB THR A1099 " pdb=" CA THR A1099 " pdb=" OG1 THR A1099 " pdb=" CG2 THR A1099 " both_signs ideal model delta sigma weight residual False 2.55 1.99 0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" CA ALA H 166 " pdb=" N ALA H 166 " pdb=" C ALA H 166 " pdb=" CB ALA H 166 " both_signs ideal model delta sigma weight residual False 2.48 1.94 0.54 2.00e-01 2.50e+01 7.43e+00 chirality pdb=" CA THR A1099 " pdb=" N THR A1099 " pdb=" C THR A1099 " pdb=" CB THR A1099 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.47 2.00e-01 2.50e+01 5.56e+00 ... (remaining 1644 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 398 " 0.155 2.00e-02 2.50e+03 7.81e-02 1.52e+02 pdb=" CG TRP A 398 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 398 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 398 " -0.083 2.00e-02 2.50e+03 pdb=" NE1 TRP A 398 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TRP A 398 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP A 398 " -0.107 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 398 " 0.082 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 398 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 398 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 719 " 0.126 2.00e-02 2.50e+03 7.71e-02 1.48e+02 pdb=" CG TRP A 719 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP A 719 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 719 " -0.084 2.00e-02 2.50e+03 pdb=" NE1 TRP A 719 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP A 719 " -0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP A 719 " -0.125 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 719 " 0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 719 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 719 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 362 " -0.099 2.00e-02 2.50e+03 1.03e-01 1.34e+02 pdb=" CG ASN A 362 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN A 362 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 362 " 0.158 2.00e-02 2.50e+03 pdb=" C1 NAG A2135 " -0.125 2.00e-02 2.50e+03 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 14 2.34 - 2.98: 4271 2.98 - 3.62: 14413 3.62 - 4.26: 23786 4.26 - 4.90: 39452 Nonbonded interactions: 81936 Sorted by model distance: nonbonded pdb=" OD1 ASP H 148 " pdb="ZN ZN H 203 " model vdw 1.695 2.230 nonbonded pdb=" OD1 ASP A1049 " pdb="NA NA A2129 " model vdw 2.125 2.470 nonbonded pdb=" OD1 ASP A 571 " pdb="NA NA A2130 " model vdw 2.149 2.470 nonbonded pdb=" O GLY A1045 " pdb="NA NA A2129 " model vdw 2.208 2.470 nonbonded pdb=" O GLY A 567 " pdb="NA NA A2130 " model vdw 2.252 2.470 ... (remaining 81931 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=0.50 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: 1.420 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.016 0.396 10299 Z= 0.877 Angle : 1.759 10.611 14138 Z= 1.135 Chirality : 0.101 0.566 1647 Planarity : 0.014 0.100 1607 Dihedral : 14.279 151.569 3623 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.21 % Allowed : 3.20 % Favored : 96.59 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.22 % 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: 0.02 (0.24), residues: 1099 helix: -0.14 (0.19), residues: 595 sheet: 0.81 (0.96), residues: 26 loop : 0.43 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 341 TYR 0.115 0.021 TYR A 388 PHE 0.064 0.012 PHE A 877 TRP 0.155 0.025 TRP A 398 HIS 0.011 0.003 HIS A 777 Details of bonding type rmsd/Z covalent geometry : bond 0.01526 / 0.86 (10284) covalent geometry : angle 1.75426 / 1.13 (14107) SS BOND : bond 0.00710 / 0.37 ( 8) SS BOND : angle 1.68378 / 0.95 ( 16) hydrogen bonds : bond 0.19055 / 12.44 ( 509) hydrogen bonds : angle 6.97410 / 4.93 ( 1458) metal coordination : bond 0.36440 / 18.45 ( 2) link_NAG-ASN : bond 0.01453 / 0.82 ( 5) link_NAG-ASN : angle 4.46144 / 2.71 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 377 THR cc_start: 0.9077 (m) cc_final: 0.8845 (p) REVERT: A 436 MET cc_start: 0.6797 (mmt) cc_final: 0.6540 (mpt) REVERT: A 449 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7353 (tptt) REVERT: A 701 ARG cc_start: 0.7857 (tmm160) cc_final: 0.7572 (tpm170) REVERT: A 940 GLN cc_start: 0.7646 (tt0) cc_final: 0.7247 (tm-30) REVERT: A 997 MET cc_start: 0.8130 (tpp) cc_final: 0.7880 (tpt) REVERT: A 1066 ARG cc_start: 0.7604 (ptp-170) cc_final: 0.7147 (ptp-170) REVERT: A 1140 GLN cc_start: 0.7519 (tt0) cc_final: 0.7175 (tm-30) REVERT: H 55 LYS cc_start: 0.7669 (ptmt) cc_final: 0.7364 (mmtm) REVERT: H 104 LYS cc_start: 0.7944 (ttpp) cc_final: 0.7726 (ttpp) REVERT: H 122 LYS cc_start: 0.7345 (mttt) cc_final: 0.7144 (mmtp) REVERT: H 165 LEU cc_start: 0.8113 (mt) cc_final: 0.7861 (mt) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.5115 time to fit residues: 87.4031 Evaluate side-chains 94 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 968 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.163234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111925 restraints weight = 22061.181| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.63 r_work: 0.3140 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10299 Z= 0.133 Angle : 0.708 26.394 14138 Z= 0.330 Chirality : 0.056 1.490 1647 Planarity : 0.004 0.045 1607 Dihedral : 11.775 161.090 1586 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.19 % Favored : 98.72 % Rotamer: Outliers : 1.76 % Allowed : 7.85 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.06 (0.26), residues: 1099 helix: 1.95 (0.21), residues: 593 sheet: 0.13 (0.76), residues: 46 loop : 0.89 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 363 TYR 0.015 0.002 TYR A 619 PHE 0.014 0.001 PHE A 585 TRP 0.026 0.002 TRP A 398 HIS 0.012 0.001 HIS A 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (10284) covalent geometry : angle 0.65244 / 0.32 (14107) SS BOND : bond 0.00266 / 0.12 ( 8) SS BOND : angle 1.21424 / 0.73 ( 16) hydrogen bonds : bond 0.05606 / 3.82 ( 509) hydrogen bonds : angle 4.57025 / 3.25 ( 1458) metal coordination : bond 0.00232 / 0.12 ( 2) link_NAG-ASN : bond 0.01818 / 0.96 ( 5) link_NAG-ASN : angle 8.36442 / 4.94 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.310 Fit side-chains REVERT: A 436 MET cc_start: 0.6459 (mmt) cc_final: 0.6117 (mpt) REVERT: A 449 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7702 (tptm) REVERT: A 690 ARG cc_start: 0.6281 (mtt180) cc_final: 0.5999 (ptp-170) REVERT: A 698 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 701 ARG cc_start: 0.8243 (tmm160) cc_final: 0.7603 (tpm170) REVERT: A 813 THR cc_start: 0.8742 (t) cc_final: 0.8483 (t) REVERT: A 940 GLN cc_start: 0.8351 (tt0) cc_final: 0.7952 (tm-30) REVERT: A 997 MET cc_start: 0.8298 (tpp) cc_final: 0.7964 (tpt) REVERT: A 1140 GLN cc_start: 0.7873 (tt0) cc_final: 0.7437 (mt0) REVERT: H 55 LYS cc_start: 0.8251 (ptmt) cc_final: 0.7661 (mmtm) REVERT: H 112 ILE cc_start: 0.7909 (mt) cc_final: 0.7634 (mp) REVERT: H 122 LYS cc_start: 0.7264 (mttt) cc_final: 0.6956 (mptm) REVERT: H 165 LEU cc_start: 0.8276 (mt) cc_final: 0.8054 (mt) outliers start: 16 outliers final: 2 residues processed: 131 average time/residue: 0.4831 time to fit residues: 68.4010 Evaluate side-chains 96 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 416 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 874 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.159716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110452 restraints weight = 16054.594| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.28 r_work: 0.3093 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10299 Z= 0.172 Angle : 0.692 22.192 14138 Z= 0.325 Chirality : 0.046 0.614 1647 Planarity : 0.004 0.042 1607 Dihedral : 11.737 154.685 1586 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.48 % Allowed : 8.47 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.02 (0.26), residues: 1099 helix: 2.07 (0.21), residues: 596 sheet: 0.02 (0.73), residues: 49 loop : 0.64 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 145 TYR 0.018 0.002 TYR A 619 PHE 0.023 0.002 PHE A 608 TRP 0.021 0.002 TRP A 398 HIS 0.010 0.001 HIS A 874 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (10284) covalent geometry : angle 0.65454 / 0.32 (14107) SS BOND : bond 0.00258 / 0.13 ( 8) SS BOND : angle 1.10471 / 0.66 ( 16) hydrogen bonds : bond 0.06176 / 4.20 ( 509) hydrogen bonds : angle 4.46964 / 3.15 ( 1458) metal coordination : bond 0.00143 / 0.07 ( 2) link_NAG-ASN : bond 0.01373 / 0.73 ( 5) link_NAG-ASN : angle 6.87335 / 4.04 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.242 Fit side-chains REVERT: A 223 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: A 387 HIS cc_start: 0.7460 (m-70) cc_final: 0.7259 (m-70) REVERT: A 449 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7649 (tptm) REVERT: A 698 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7203 (mm-30) REVERT: A 701 ARG cc_start: 0.8214 (tmm160) cc_final: 0.7620 (mmp-170) REVERT: A 746 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6377 (pm20) REVERT: A 940 GLN cc_start: 0.8320 (tt0) cc_final: 0.7876 (tm-30) REVERT: A 997 MET cc_start: 0.8359 (tpp) cc_final: 0.8107 (tpt) REVERT: A 1140 GLN cc_start: 0.7888 (tt0) cc_final: 0.7418 (mt0) REVERT: H 55 LYS cc_start: 0.8185 (ptmt) cc_final: 0.7674 (mmtm) REVERT: H 122 LYS cc_start: 0.7272 (mttt) cc_final: 0.6928 (mptm) REVERT: H 165 LEU cc_start: 0.8283 (mt) cc_final: 0.8043 (mt) outliers start: 23 outliers final: 9 residues processed: 115 average time/residue: 0.4720 time to fit residues: 58.4549 Evaluate side-chains 105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain H residue 68 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 104 optimal weight: 0.7980 chunk 67 optimal weight: 0.0870 chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.162984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114357 restraints weight = 15738.537| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.26 r_work: 0.3185 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10299 Z= 0.109 Angle : 0.592 20.702 14138 Z= 0.274 Chirality : 0.041 0.489 1647 Planarity : 0.004 0.040 1607 Dihedral : 11.152 151.089 1586 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.96 % Allowed : 10.33 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.38 (0.26), residues: 1099 helix: 2.40 (0.21), residues: 593 sheet: 0.63 (0.76), residues: 44 loop : 0.69 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 774 TYR 0.012 0.001 TYR A 545 PHE 0.011 0.001 PHE A 495 TRP 0.020 0.001 TRP A 313 HIS 0.009 0.001 HIS A 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (10284) covalent geometry : angle 0.55287 / 0.27 (14107) SS BOND : bond 0.00221 / 0.11 ( 8) SS BOND : angle 0.89267 / 0.54 ( 16) hydrogen bonds : bond 0.04519 / 3.08 ( 509) hydrogen bonds : angle 4.15666 / 2.95 ( 1458) metal coordination : bond 0.00062 / 0.03 ( 2) link_NAG-ASN : bond 0.01167 / 0.62 ( 5) link_NAG-ASN : angle 6.45448 / 3.81 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: A 449 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7520 (tptm) REVERT: A 698 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7166 (mm-30) REVERT: A 701 ARG cc_start: 0.8237 (tmm160) cc_final: 0.7595 (mmm160) REVERT: A 997 MET cc_start: 0.8076 (tpp) cc_final: 0.7834 (tpt) REVERT: A 1140 GLN cc_start: 0.7855 (tt0) cc_final: 0.7410 (mt0) REVERT: H 55 LYS cc_start: 0.8106 (ptmt) cc_final: 0.7568 (mptt) REVERT: H 122 LYS cc_start: 0.7263 (mttt) cc_final: 0.6955 (mptm) REVERT: H 165 LEU cc_start: 0.8200 (mt) cc_final: 0.7920 (mt) outliers start: 18 outliers final: 4 residues processed: 112 average time/residue: 0.4826 time to fit residues: 58.3825 Evaluate side-chains 99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain H residue 68 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.161295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110106 restraints weight = 16305.768| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.42 r_work: 0.3131 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10299 Z= 0.141 Angle : 0.616 20.364 14138 Z= 0.288 Chirality : 0.042 0.459 1647 Planarity : 0.004 0.039 1607 Dihedral : 11.066 143.587 1586 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.38 % Allowed : 10.54 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.35 (0.26), residues: 1099 helix: 2.42 (0.21), residues: 593 sheet: 0.20 (0.75), residues: 49 loop : 0.66 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 145 TYR 0.015 0.001 TYR A 644 PHE 0.016 0.001 PHE A 608 TRP 0.018 0.001 TRP A 650 HIS 0.008 0.001 HIS A 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (10284) covalent geometry : angle 0.58079 / 0.28 (14107) SS BOND : bond 0.00241 / 0.12 ( 8) SS BOND : angle 0.93714 / 0.57 ( 16) hydrogen bonds : bond 0.05289 / 3.61 ( 509) hydrogen bonds : angle 4.22586 / 2.99 ( 1458) metal coordination : bond 0.00114 / 0.06 ( 2) link_NAG-ASN : bond 0.01153 / 0.61 ( 5) link_NAG-ASN : angle 6.31394 / 3.73 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: A 449 LYS cc_start: 0.8077 (ttmt) cc_final: 0.7640 (tptm) REVERT: A 698 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7282 (mm-30) REVERT: A 701 ARG cc_start: 0.8276 (tmm160) cc_final: 0.7752 (mmp-170) REVERT: A 997 MET cc_start: 0.8257 (tpp) cc_final: 0.8012 (tpt) REVERT: A 1140 GLN cc_start: 0.7859 (tt0) cc_final: 0.7408 (mt0) REVERT: H 55 LYS cc_start: 0.8094 (ptmt) cc_final: 0.7582 (mptt) REVERT: H 122 LYS cc_start: 0.7345 (mttt) cc_final: 0.6993 (mptm) REVERT: H 165 LEU cc_start: 0.8337 (mt) cc_final: 0.8043 (mt) outliers start: 22 outliers final: 8 residues processed: 105 average time/residue: 0.4887 time to fit residues: 55.3372 Evaluate side-chains 100 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain H residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 GLN A 643 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.162561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111506 restraints weight = 20890.082| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.58 r_work: 0.3136 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10299 Z= 0.116 Angle : 0.576 19.901 14138 Z= 0.270 Chirality : 0.040 0.434 1647 Planarity : 0.003 0.040 1607 Dihedral : 10.708 139.064 1586 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.55 % Allowed : 11.47 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.41 (0.26), residues: 1099 helix: 2.51 (0.21), residues: 594 sheet: 0.30 (0.76), residues: 49 loop : 0.61 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 774 TYR 0.013 0.001 TYR A 644 PHE 0.011 0.001 PHE A 608 TRP 0.020 0.001 TRP A 313 HIS 0.008 0.001 HIS A 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (10284) covalent geometry : angle 0.54039 / 0.26 (14107) SS BOND : bond 0.00227 / 0.11 ( 8) SS BOND : angle 0.87803 / 0.53 ( 16) hydrogen bonds : bond 0.04716 / 3.22 ( 509) hydrogen bonds : angle 4.11996 / 2.92 ( 1458) metal coordination : bond 0.00078 / 0.04 ( 2) link_NAG-ASN : bond 0.01175 / 0.63 ( 5) link_NAG-ASN : angle 6.13193 / 3.62 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: A 449 LYS cc_start: 0.8039 (ttmt) cc_final: 0.7585 (tptt) REVERT: A 698 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7231 (mm-30) REVERT: A 701 ARG cc_start: 0.8273 (tmm160) cc_final: 0.7705 (mmp-170) REVERT: A 997 MET cc_start: 0.8132 (tpp) cc_final: 0.7887 (tpt) REVERT: A 1008 LEU cc_start: 0.8703 (tp) cc_final: 0.7945 (mm) REVERT: A 1140 GLN cc_start: 0.7869 (tt0) cc_final: 0.7413 (mt0) REVERT: H 55 LYS cc_start: 0.8054 (ptmt) cc_final: 0.7568 (mptt) REVERT: H 122 LYS cc_start: 0.7383 (mttt) cc_final: 0.7034 (mptm) REVERT: H 165 LEU cc_start: 0.8325 (mt) cc_final: 0.8035 (mt) outliers start: 14 outliers final: 7 residues processed: 108 average time/residue: 0.4805 time to fit residues: 56.3312 Evaluate side-chains 102 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 496 GLN A 940 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.162473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111333 restraints weight = 20348.581| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.59 r_work: 0.3131 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10299 Z= 0.117 Angle : 0.580 19.599 14138 Z= 0.272 Chirality : 0.040 0.430 1647 Planarity : 0.003 0.040 1607 Dihedral : 10.542 140.000 1586 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.07 % Allowed : 11.26 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.37 (0.26), residues: 1099 helix: 2.50 (0.21), residues: 596 sheet: 0.33 (0.76), residues: 49 loop : 0.54 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 774 TYR 0.013 0.001 TYR A 644 PHE 0.013 0.001 PHE A 608 TRP 0.017 0.001 TRP A 650 HIS 0.008 0.001 HIS A 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (10284) covalent geometry : angle 0.54321 / 0.26 (14107) SS BOND : bond 0.00199 / 0.10 ( 8) SS BOND : angle 0.87982 / 0.54 ( 16) hydrogen bonds : bond 0.04711 / 3.22 ( 509) hydrogen bonds : angle 4.11340 / 2.92 ( 1458) metal coordination : bond 0.00074 / 0.04 ( 2) link_NAG-ASN : bond 0.01403 / 0.73 ( 5) link_NAG-ASN : angle 6.18739 / 3.64 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: A 449 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7548 (tptt) REVERT: A 698 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7213 (mm-30) REVERT: A 701 ARG cc_start: 0.8257 (tmm160) cc_final: 0.7611 (mmm160) REVERT: A 1008 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.7914 (mm) REVERT: A 1140 GLN cc_start: 0.7864 (tt0) cc_final: 0.7405 (mt0) REVERT: H 55 LYS cc_start: 0.8016 (ptmt) cc_final: 0.7539 (mptt) REVERT: H 122 LYS cc_start: 0.7365 (mttt) cc_final: 0.7014 (mptm) REVERT: H 165 LEU cc_start: 0.8289 (mt) cc_final: 0.7977 (mt) outliers start: 19 outliers final: 8 residues processed: 111 average time/residue: 0.4454 time to fit residues: 53.7949 Evaluate side-chains 108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 10 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 874 HIS A 940 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.162900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111220 restraints weight = 20394.880| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.65 r_work: 0.3143 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10299 Z= 0.112 Angle : 0.569 19.367 14138 Z= 0.267 Chirality : 0.040 0.431 1647 Planarity : 0.003 0.040 1607 Dihedral : 10.400 139.703 1586 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.65 % Allowed : 11.67 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.42 (0.26), residues: 1099 helix: 2.54 (0.21), residues: 596 sheet: 0.64 (0.79), residues: 44 loop : 0.52 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 774 TYR 0.013 0.001 TYR A 545 PHE 0.011 0.001 PHE A 608 TRP 0.018 0.001 TRP A 313 HIS 0.010 0.001 HIS A 874 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (10284) covalent geometry : angle 0.53298 / 0.26 (14107) SS BOND : bond 0.00209 / 0.10 ( 8) SS BOND : angle 0.86351 / 0.52 ( 16) hydrogen bonds : bond 0.04583 / 3.14 ( 509) hydrogen bonds : angle 4.08753 / 2.90 ( 1458) metal coordination : bond 0.00076 / 0.04 ( 2) link_NAG-ASN : bond 0.01270 / 0.67 ( 5) link_NAG-ASN : angle 6.10497 / 3.59 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: A 377 THR cc_start: 0.9061 (m) cc_final: 0.8821 (p) REVERT: A 449 LYS cc_start: 0.7993 (ttmt) cc_final: 0.7527 (tptt) REVERT: A 698 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7197 (mm-30) REVERT: A 701 ARG cc_start: 0.8265 (tmm160) cc_final: 0.7609 (mmm160) REVERT: A 843 GLN cc_start: 0.6749 (tp40) cc_final: 0.6543 (tm-30) REVERT: A 1008 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.7909 (mm) REVERT: A 1140 GLN cc_start: 0.7843 (tt0) cc_final: 0.7376 (mt0) REVERT: H 55 LYS cc_start: 0.7998 (ptmt) cc_final: 0.7530 (mptt) REVERT: H 122 LYS cc_start: 0.7347 (mttt) cc_final: 0.7010 (mptm) REVERT: H 165 LEU cc_start: 0.8255 (mt) cc_final: 0.7965 (mt) outliers start: 15 outliers final: 9 residues processed: 105 average time/residue: 0.4909 time to fit residues: 56.0075 Evaluate side-chains 107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 102 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 ASN A 874 HIS A 940 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.163410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112575 restraints weight = 17778.960| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.39 r_work: 0.3163 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10299 Z= 0.109 Angle : 0.562 18.949 14138 Z= 0.263 Chirality : 0.040 0.432 1647 Planarity : 0.003 0.040 1607 Dihedral : 10.237 139.117 1586 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.55 % Allowed : 11.78 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.46 (0.26), residues: 1099 helix: 2.60 (0.21), residues: 596 sheet: 0.57 (0.80), residues: 44 loop : 0.51 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 774 TYR 0.013 0.001 TYR A 545 PHE 0.011 0.001 PHE A 608 TRP 0.018 0.001 TRP A 313 HIS 0.010 0.001 HIS A 874 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (10284) covalent geometry : angle 0.52644 / 0.25 (14107) SS BOND : bond 0.00204 / 0.10 ( 8) SS BOND : angle 0.83559 / 0.51 ( 16) hydrogen bonds : bond 0.04441 / 3.04 ( 509) hydrogen bonds : angle 4.05289 / 2.87 ( 1458) metal coordination : bond 0.00091 / 0.05 ( 2) link_NAG-ASN : bond 0.01277 / 0.67 ( 5) link_NAG-ASN : angle 5.99468 / 3.52 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: A 449 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7554 (tptt) REVERT: A 698 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7096 (pp20) REVERT: A 701 ARG cc_start: 0.8253 (tmm160) cc_final: 0.7588 (mmm160) REVERT: A 940 GLN cc_start: 0.8080 (tt0) cc_final: 0.7746 (pt0) REVERT: A 1008 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.7918 (mm) REVERT: A 1140 GLN cc_start: 0.7839 (tt0) cc_final: 0.7414 (mt0) REVERT: H 55 LYS cc_start: 0.7900 (ptmt) cc_final: 0.7463 (mptt) REVERT: H 122 LYS cc_start: 0.7369 (mttt) cc_final: 0.7030 (mptm) REVERT: H 165 LEU cc_start: 0.8334 (mt) cc_final: 0.8021 (mt) outliers start: 14 outliers final: 7 residues processed: 105 average time/residue: 0.4807 time to fit residues: 54.7767 Evaluate side-chains 104 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 874 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.163214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.109714 restraints weight = 24729.717| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.78 r_work: 0.3125 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10299 Z= 0.114 Angle : 0.577 18.867 14138 Z= 0.273 Chirality : 0.040 0.436 1647 Planarity : 0.003 0.040 1607 Dihedral : 10.233 139.066 1586 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.45 % Allowed : 12.19 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.43 (0.26), residues: 1099 helix: 2.60 (0.21), residues: 596 sheet: 0.63 (0.83), residues: 41 loop : 0.45 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 774 TYR 0.013 0.001 TYR A 644 PHE 0.010 0.001 PHE A 495 TRP 0.019 0.001 TRP A 313 HIS 0.010 0.001 HIS A 874 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10284) covalent geometry : angle 0.54499 / 0.27 (14107) SS BOND : bond 0.00212 / 0.11 ( 8) SS BOND : angle 0.84761 / 0.52 ( 16) hydrogen bonds : bond 0.04523 / 3.10 ( 509) hydrogen bonds : angle 4.08902 / 2.90 ( 1458) metal coordination : bond 0.00068 / 0.04 ( 2) link_NAG-ASN : bond 0.01383 / 0.71 ( 5) link_NAG-ASN : angle 5.80829 / 3.43 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.359 Fit side-chains REVERT: A 223 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: A 377 THR cc_start: 0.9074 (m) cc_final: 0.8845 (p) REVERT: A 449 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7589 (tptt) REVERT: A 698 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7117 (pp20) REVERT: A 701 ARG cc_start: 0.8296 (tmm160) cc_final: 0.7615 (mmm160) REVERT: A 940 GLN cc_start: 0.8149 (tt0) cc_final: 0.7822 (pt0) REVERT: A 1008 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.7977 (mm) REVERT: A 1140 GLN cc_start: 0.7851 (tt0) cc_final: 0.7423 (mt0) REVERT: H 55 LYS cc_start: 0.7919 (ptmt) cc_final: 0.7484 (mptt) REVERT: H 122 LYS cc_start: 0.7392 (mttt) cc_final: 0.7041 (mptm) REVERT: H 165 LEU cc_start: 0.8329 (mt) cc_final: 0.7998 (mt) outliers start: 13 outliers final: 7 residues processed: 104 average time/residue: 0.5080 time to fit residues: 57.4212 Evaluate side-chains 102 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 106 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 12 optimal weight: 0.0040 chunk 107 optimal weight: 5.9990 chunk 55 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 643 ASN A 874 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.164281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115004 restraints weight = 17638.453| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.34 r_work: 0.3188 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10299 Z= 0.101 Angle : 0.558 18.618 14138 Z= 0.261 Chirality : 0.039 0.431 1647 Planarity : 0.003 0.039 1607 Dihedral : 10.119 139.519 1586 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.93 % Allowed : 12.60 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 2.49 (0.26), residues: 1099 helix: 2.64 (0.21), residues: 597 sheet: 0.67 (0.84), residues: 41 loop : 0.49 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 774 TYR 0.013 0.001 TYR A 545 PHE 0.009 0.001 PHE A 495 TRP 0.018 0.001 TRP A 650 HIS 0.010 0.001 HIS A 874 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (10284) covalent geometry : angle 0.52397 / 0.25 (14107) SS BOND : bond 0.00208 / 0.11 ( 8) SS BOND : angle 0.82389 / 0.49 ( 16) hydrogen bonds : bond 0.04102 / 2.81 ( 509) hydrogen bonds : angle 4.02334 / 2.86 ( 1458) metal coordination : bond 0.00027 / 0.01 ( 2) link_NAG-ASN : bond 0.01164 / 0.62 ( 5) link_NAG-ASN : angle 5.86231 / 3.41 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3099.44 seconds wall clock time: 53 minutes 34.49 seconds (3214.49 seconds total)