Starting phenix.real_space_refine on Sun Dec 29 14:58:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rpk_24617/12_2024/7rpk_24617.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rpk_24617/12_2024/7rpk_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_24617/12_2024/7rpk_24617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rpk_24617/12_2024/7rpk_24617.map" model { file = "/net/cci-nas-00/data/ceres_data/7rpk_24617/12_2024/7rpk_24617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rpk_24617/12_2024/7rpk_24617.cif" } resolution = 2.7 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= 0.011 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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 dihedrals: 15 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: 9.82, per 1000 atoms: 0.98 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: 2.82 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.11 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: 2.79 Time building geometry restraints manager: 3.13 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: 7326 30.31 - 60.63: 208 60.63 - 90.94: 30 90.94 - 121.26: 15 121.26 - 151.57: 5 Dihedral angle restraints: 7584 sinusoidal: 4335 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 7581 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: 1.050 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 32.130 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 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 : 0.015 0.142 10284 Z= 0.946 Angle : 1.754 10.611 14107 Z= 1.134 Chirality : 0.101 0.566 1647 Planarity : 0.014 0.100 1607 Dihedral : 14.856 151.569 5458 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 (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: 0.02 (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 TRP 0.155 0.025 TRP A 398 HIS 0.011 0.003 HIS A 777 PHE 0.064 0.012 PHE A 877 TYR 0.115 0.021 TYR A 388 ARG 0.007 0.001 ARG A 341 *********************** 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 : 1.099 Fit side-chains revert: symmetry clash REVERT: A 377 THR cc_start: 0.9077 (m) cc_final: 0.8846 (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: 0.7148 (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: 0.7896 (mt) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 1.3364 time to fit residues: 227.5726 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 : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.0010 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 HIS A 968 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10284 Z= 0.174 Angle : 0.663 11.384 14107 Z= 0.322 Chirality : 0.058 1.543 1647 Planarity : 0.004 0.046 1607 Dihedral : 12.126 171.141 3421 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.19 % Favored : 98.72 % Rotamer: Outliers : 1.65 % Allowed : 7.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.26), residues: 1099 helix: 1.93 (0.21), residues: 593 sheet: 0.12 (0.76), residues: 46 loop : 0.88 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 398 HIS 0.012 0.001 HIS A 777 PHE 0.014 0.001 PHE A 585 TYR 0.015 0.002 TYR A 619 ARG 0.003 0.000 ARG A 774 *********************** 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 141 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.057 Fit side-chains REVERT: A 436 MET cc_start: 0.6465 (mmt) cc_final: 0.6148 (mpt) REVERT: A 449 LYS cc_start: 0.7851 (ttmt) cc_final: 0.7369 (tptm) REVERT: A 531 MET cc_start: 0.8281 (tpt) cc_final: 0.8005 (tpp) REVERT: A 647 MET cc_start: 0.8435 (mmt) cc_final: 0.8194 (mmp) REVERT: A 698 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6811 (mm-30) REVERT: A 701 ARG cc_start: 0.7941 (tmm160) cc_final: 0.7425 (tpm170) REVERT: A 940 GLN cc_start: 0.7571 (tt0) cc_final: 0.7092 (tm-30) REVERT: A 980 ASP cc_start: 0.7456 (m-30) cc_final: 0.7175 (m-30) REVERT: A 986 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7216 (ttt) REVERT: A 997 MET cc_start: 0.8062 (tpp) cc_final: 0.7736 (tpt) REVERT: A 1140 GLN cc_start: 0.7566 (tt0) cc_final: 0.7239 (mt0) REVERT: H 55 LYS cc_start: 0.7989 (ptmt) cc_final: 0.7408 (mmtm) REVERT: H 76 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6971 (tt0) REVERT: H 112 ILE cc_start: 0.7875 (mt) cc_final: 0.7613 (mp) REVERT: H 115 MET cc_start: 0.7322 (mtp) cc_final: 0.6968 (mtt) REVERT: H 122 LYS cc_start: 0.7307 (mttt) cc_final: 0.6936 (mptm) REVERT: H 165 LEU cc_start: 0.8189 (mt) cc_final: 0.7968 (mt) outliers start: 15 outliers final: 2 residues processed: 135 average time/residue: 1.2245 time to fit residues: 179.0443 Evaluate side-chains 99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 986 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 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 874 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10284 Z= 0.172 Angle : 0.589 8.224 14107 Z= 0.285 Chirality : 0.044 0.673 1647 Planarity : 0.004 0.046 1607 Dihedral : 11.014 178.255 3421 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.96 % Allowed : 9.71 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.26), residues: 1099 helix: 2.29 (0.21), residues: 594 sheet: 0.11 (0.74), residues: 49 loop : 0.82 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 313 HIS 0.009 0.001 HIS A 777 PHE 0.014 0.001 PHE A 608 TYR 0.014 0.001 TYR A 545 ARG 0.004 0.000 ARG A 690 *********************** 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 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.066 Fit side-chains REVERT: A 223 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: A 449 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7361 (tptm) REVERT: A 698 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6894 (mm-30) REVERT: A 701 ARG cc_start: 0.7944 (tmm160) cc_final: 0.7507 (mmp-170) REVERT: A 940 GLN cc_start: 0.7552 (tt0) cc_final: 0.7094 (tm-30) REVERT: A 980 ASP cc_start: 0.7462 (m-30) cc_final: 0.7105 (m-30) REVERT: A 997 MET cc_start: 0.7904 (tpp) cc_final: 0.7644 (tpt) REVERT: A 1140 GLN cc_start: 0.7593 (tt0) cc_final: 0.7280 (mt0) REVERT: H 55 LYS cc_start: 0.8023 (ptmt) cc_final: 0.7463 (mmtm) REVERT: H 76 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6967 (mt-10) REVERT: H 112 ILE cc_start: 0.7823 (mt) cc_final: 0.7575 (mp) REVERT: H 122 LYS cc_start: 0.7361 (mttt) cc_final: 0.7092 (mptm) REVERT: H 165 LEU cc_start: 0.8142 (mt) cc_final: 0.7886 (mt) outliers start: 18 outliers final: 6 residues processed: 118 average time/residue: 1.3004 time to fit residues: 165.1193 Evaluate side-chains 104 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 410 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 813 THR 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 98 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10284 Z= 0.146 Angle : 0.537 5.879 14107 Z= 0.261 Chirality : 0.041 0.474 1647 Planarity : 0.004 0.040 1607 Dihedral : 10.517 179.226 3421 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.86 % Allowed : 10.64 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.26), residues: 1099 helix: 2.45 (0.21), residues: 593 sheet: 0.65 (0.77), residues: 44 loop : 0.77 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 313 HIS 0.008 0.001 HIS A 777 PHE 0.010 0.001 PHE A 608 TYR 0.013 0.001 TYR A 545 ARG 0.003 0.000 ARG A 774 *********************** 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 118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.972 Fit side-chains REVERT: A 223 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: A 449 LYS cc_start: 0.7784 (ttmt) cc_final: 0.7317 (tptm) REVERT: A 690 ARG cc_start: 0.6848 (ptp-170) cc_final: 0.6552 (ptp-170) REVERT: A 698 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6927 (mm-30) REVERT: A 701 ARG cc_start: 0.8012 (tmm160) cc_final: 0.7565 (mmm160) REVERT: A 815 ASN cc_start: 0.8563 (t0) cc_final: 0.8174 (t0) REVERT: A 846 PHE cc_start: 0.8211 (m-80) cc_final: 0.7977 (m-10) REVERT: A 962 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7959 (mtm110) REVERT: A 980 ASP cc_start: 0.7475 (m-30) cc_final: 0.7105 (m-30) REVERT: A 997 MET cc_start: 0.7849 (tpp) cc_final: 0.7609 (tpt) REVERT: A 1140 GLN cc_start: 0.7584 (tt0) cc_final: 0.7289 (mt0) REVERT: H 55 LYS cc_start: 0.7898 (ptmt) cc_final: 0.7367 (mptt) REVERT: H 76 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6854 (mt-10) REVERT: H 112 ILE cc_start: 0.7839 (mt) cc_final: 0.7453 (mp) REVERT: H 165 LEU cc_start: 0.8134 (mt) cc_final: 0.7866 (mt) outliers start: 17 outliers final: 4 residues processed: 113 average time/residue: 1.1499 time to fit residues: 141.5387 Evaluate side-chains 99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 947 SER Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 996 VAL 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 88 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 90 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.0040 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN A 860 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10284 Z= 0.158 Angle : 0.535 5.988 14107 Z= 0.261 Chirality : 0.041 0.425 1647 Planarity : 0.003 0.040 1607 Dihedral : 10.320 178.581 3421 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.86 % Allowed : 11.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.26), residues: 1099 helix: 2.50 (0.21), residues: 596 sheet: 0.28 (0.75), residues: 49 loop : 0.68 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 650 HIS 0.008 0.001 HIS A 777 PHE 0.012 0.001 PHE A 608 TYR 0.014 0.001 TYR A 545 ARG 0.002 0.000 ARG A 774 *********************** 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 114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.108 Fit side-chains REVERT: A 223 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: A 449 LYS cc_start: 0.7763 (ttmt) cc_final: 0.7340 (tptt) REVERT: A 690 ARG cc_start: 0.6882 (ptp-170) cc_final: 0.6666 (ptp-170) REVERT: A 698 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6951 (mm-30) REVERT: A 701 ARG cc_start: 0.8006 (tmm160) cc_final: 0.7635 (mmp-170) REVERT: A 815 ASN cc_start: 0.8567 (t0) cc_final: 0.8306 (t0) REVERT: A 846 PHE cc_start: 0.8318 (m-80) cc_final: 0.8053 (m-10) REVERT: A 980 ASP cc_start: 0.7489 (m-30) cc_final: 0.7122 (m-30) REVERT: A 997 MET cc_start: 0.7815 (tpp) cc_final: 0.7604 (tpt) REVERT: A 1140 GLN cc_start: 0.7546 (tt0) cc_final: 0.7269 (mt0) REVERT: H 55 LYS cc_start: 0.7879 (ptmt) cc_final: 0.7360 (mptt) REVERT: H 76 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6823 (mt-10) REVERT: H 112 ILE cc_start: 0.7829 (mt) cc_final: 0.7420 (mp) REVERT: H 165 LEU cc_start: 0.8235 (mt) cc_final: 0.7935 (mt) outliers start: 17 outliers final: 8 residues processed: 109 average time/residue: 1.1852 time to fit residues: 140.0154 Evaluate side-chains 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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 35 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN A 643 ASN ** A 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10284 Z= 0.245 Angle : 0.596 7.541 14107 Z= 0.293 Chirality : 0.043 0.434 1647 Planarity : 0.004 0.040 1607 Dihedral : 10.636 177.462 3421 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.48 % Allowed : 11.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.26), residues: 1099 helix: 2.37 (0.21), residues: 597 sheet: 0.23 (0.75), residues: 49 loop : 0.56 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 313 HIS 0.008 0.001 HIS A 777 PHE 0.021 0.002 PHE A 608 TYR 0.017 0.002 TYR A 644 ARG 0.003 0.000 ARG H 145 *********************** 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 119 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: A 449 LYS cc_start: 0.7912 (ttmt) cc_final: 0.7426 (tptt) REVERT: A 690 ARG cc_start: 0.6880 (ptp-170) cc_final: 0.6627 (ptp-170) REVERT: A 698 GLU cc_start: 0.7224 (mm-30) cc_final: 0.7001 (mm-30) REVERT: A 701 ARG cc_start: 0.7958 (tmm160) cc_final: 0.7557 (mmp-170) REVERT: A 846 PHE cc_start: 0.8430 (m-80) cc_final: 0.8120 (m-10) REVERT: A 980 ASP cc_start: 0.7465 (m-30) cc_final: 0.7124 (m-30) REVERT: A 997 MET cc_start: 0.7999 (tpp) cc_final: 0.7765 (tpt) REVERT: A 1140 GLN cc_start: 0.7578 (tt0) cc_final: 0.7261 (mt0) REVERT: H 55 LYS cc_start: 0.7866 (ptmt) cc_final: 0.7374 (mptt) REVERT: H 76 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6788 (mt-10) REVERT: H 165 LEU cc_start: 0.8312 (mt) cc_final: 0.8022 (mt) outliers start: 23 outliers final: 12 residues processed: 111 average time/residue: 1.1081 time to fit residues: 134.1920 Evaluate side-chains 105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 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 996 VAL Chi-restraints excluded: chain A residue 1008 LEU Chi-restraints excluded: chain H residue 48 PHE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 89 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN A 874 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10284 Z= 0.156 Angle : 0.534 6.105 14107 Z= 0.261 Chirality : 0.040 0.423 1647 Planarity : 0.003 0.039 1607 Dihedral : 10.355 178.316 3421 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.65 % Allowed : 12.29 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.26), residues: 1099 helix: 2.55 (0.21), residues: 595 sheet: 0.29 (0.76), residues: 49 loop : 0.53 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 313 HIS 0.010 0.001 HIS A 874 PHE 0.010 0.001 PHE A 495 TYR 0.013 0.001 TYR A 545 ARG 0.002 0.000 ARG A 774 *********************** 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 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: A 449 LYS cc_start: 0.7846 (ttmt) cc_final: 0.7383 (tptt) REVERT: A 690 ARG cc_start: 0.6869 (ptp-170) cc_final: 0.6614 (ptp-170) REVERT: A 698 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6997 (mm-30) REVERT: A 701 ARG cc_start: 0.7994 (tmm160) cc_final: 0.7553 (mmm160) REVERT: A 846 PHE cc_start: 0.8425 (m-80) cc_final: 0.8115 (m-10) REVERT: A 980 ASP cc_start: 0.7461 (m-30) cc_final: 0.7111 (m-30) REVERT: A 997 MET cc_start: 0.7850 (tpp) cc_final: 0.7644 (tpt) REVERT: A 1008 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7573 (mm) REVERT: A 1140 GLN cc_start: 0.7570 (tt0) cc_final: 0.7277 (mt0) REVERT: H 55 LYS cc_start: 0.7845 (ptmt) cc_final: 0.7376 (mptt) REVERT: H 76 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6763 (mt-10) REVERT: H 165 LEU cc_start: 0.8305 (mt) cc_final: 0.8009 (mt) outliers start: 15 outliers final: 9 residues processed: 109 average time/residue: 1.1103 time to fit residues: 131.9333 Evaluate side-chains 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 996 VAL 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 63 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN A 874 HIS A 940 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10284 Z= 0.268 Angle : 0.601 6.627 14107 Z= 0.295 Chirality : 0.043 0.453 1647 Planarity : 0.004 0.039 1607 Dihedral : 10.716 176.436 3421 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.27 % Allowed : 11.67 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.26), residues: 1099 helix: 2.36 (0.21), residues: 597 sheet: 0.15 (0.75), residues: 49 loop : 0.48 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 313 HIS 0.010 0.001 HIS A 874 PHE 0.018 0.002 PHE A 608 TYR 0.017 0.002 TYR A 644 ARG 0.003 0.000 ARG H 145 *********************** 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 114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: A 449 LYS cc_start: 0.7946 (ttmt) cc_final: 0.7456 (tptt) REVERT: A 690 ARG cc_start: 0.6891 (ptp-170) cc_final: 0.6646 (ptp-170) REVERT: A 698 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7034 (mm-30) REVERT: A 701 ARG cc_start: 0.7952 (tmm160) cc_final: 0.7493 (mmm160) REVERT: A 846 PHE cc_start: 0.8517 (m-80) cc_final: 0.8195 (m-10) REVERT: A 980 ASP cc_start: 0.7484 (m-30) cc_final: 0.7262 (m-30) REVERT: A 997 MET cc_start: 0.8014 (tpp) cc_final: 0.7790 (tpt) REVERT: A 1140 GLN cc_start: 0.7575 (tt0) cc_final: 0.7230 (mt0) REVERT: H 55 LYS cc_start: 0.7851 (ptmt) cc_final: 0.7388 (mptt) REVERT: H 76 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6793 (mt-10) REVERT: H 165 LEU cc_start: 0.8347 (mt) cc_final: 0.8049 (mt) outliers start: 21 outliers final: 14 residues processed: 105 average time/residue: 1.1224 time to fit residues: 128.3634 Evaluate side-chains 105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 360 LEU Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 663 LEU 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 996 VAL 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 98 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN A 874 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10284 Z= 0.190 Angle : 0.554 6.924 14107 Z= 0.271 Chirality : 0.041 0.446 1647 Planarity : 0.004 0.039 1607 Dihedral : 10.531 177.068 3421 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.55 % Allowed : 12.81 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.26), residues: 1099 helix: 2.48 (0.21), residues: 597 sheet: 0.18 (0.76), residues: 49 loop : 0.48 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 313 HIS 0.010 0.001 HIS A 874 PHE 0.014 0.001 PHE A 608 TYR 0.014 0.001 TYR A 644 ARG 0.002 0.000 ARG A 774 *********************** 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 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.022 Fit side-chains REVERT: A 223 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: A 449 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7430 (tptt) REVERT: A 690 ARG cc_start: 0.6877 (ptp-170) cc_final: 0.6619 (ptp-170) REVERT: A 698 GLU cc_start: 0.7221 (mm-30) cc_final: 0.7015 (mm-30) REVERT: A 701 ARG cc_start: 0.7996 (tmm160) cc_final: 0.7625 (mmp-170) REVERT: A 846 PHE cc_start: 0.8505 (m-80) cc_final: 0.8183 (m-10) REVERT: A 980 ASP cc_start: 0.7486 (m-30) cc_final: 0.7149 (m-30) REVERT: A 997 MET cc_start: 0.7933 (tpp) cc_final: 0.7702 (tpt) REVERT: A 1008 LEU cc_start: 0.8478 (tp) cc_final: 0.7604 (mm) REVERT: A 1140 GLN cc_start: 0.7570 (tt0) cc_final: 0.7240 (mt0) REVERT: H 55 LYS cc_start: 0.7848 (ptmt) cc_final: 0.7395 (mptt) REVERT: H 76 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6766 (mt-10) REVERT: H 165 LEU cc_start: 0.8361 (mt) cc_final: 0.8043 (mt) outliers start: 14 outliers final: 9 residues processed: 105 average time/residue: 1.1258 time to fit residues: 128.9861 Evaluate side-chains 103 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 996 VAL 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 49 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN A 874 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10284 Z= 0.188 Angle : 0.551 7.886 14107 Z= 0.270 Chirality : 0.041 0.451 1647 Planarity : 0.004 0.039 1607 Dihedral : 10.504 176.946 3421 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.55 % Allowed : 12.60 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.26), residues: 1099 helix: 2.49 (0.21), residues: 597 sheet: 0.57 (0.80), residues: 44 loop : 0.41 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 313 HIS 0.010 0.001 HIS A 874 PHE 0.014 0.001 PHE A 608 TYR 0.014 0.001 TYR A 644 ARG 0.003 0.000 ARG A 372 ********************** 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 111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.077 Fit side-chains REVERT: A 223 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: A 449 LYS cc_start: 0.7881 (ttmt) cc_final: 0.7410 (tptt) REVERT: A 587 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6994 (mtpt) REVERT: A 690 ARG cc_start: 0.6873 (ptp-170) cc_final: 0.6612 (ptp-170) REVERT: A 698 GLU cc_start: 0.7223 (mm-30) cc_final: 0.7023 (mm-30) REVERT: A 701 ARG cc_start: 0.7992 (tmm160) cc_final: 0.7622 (mmp-170) REVERT: A 846 PHE cc_start: 0.8448 (m-80) cc_final: 0.8128 (m-10) REVERT: A 980 ASP cc_start: 0.7505 (m-30) cc_final: 0.7159 (m-30) REVERT: A 997 MET cc_start: 0.7913 (tpp) cc_final: 0.7688 (tpt) REVERT: A 1008 LEU cc_start: 0.8467 (tp) cc_final: 0.7592 (mm) REVERT: A 1140 GLN cc_start: 0.7572 (tt0) cc_final: 0.7246 (mt0) REVERT: H 55 LYS cc_start: 0.7804 (ptmt) cc_final: 0.7362 (mptt) REVERT: H 76 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6765 (mt-10) REVERT: H 165 LEU cc_start: 0.8357 (mt) cc_final: 0.8032 (mt) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 1.1027 time to fit residues: 129.1845 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 : 1.101 ------------------------------------------------------------------------------- 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 587 LYS Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 996 VAL 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 80 optimal weight: 0.9990 chunk 12 optimal weight: 0.0570 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN A 860 ASN A 874 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.163169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111287 restraints weight = 20602.895| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.66 r_work: 0.3138 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10284 Z= 0.146 Angle : 0.524 7.365 14107 Z= 0.255 Chirality : 0.040 0.443 1647 Planarity : 0.003 0.039 1607 Dihedral : 10.357 177.807 3421 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.45 % Allowed : 12.29 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.26), residues: 1099 helix: 2.60 (0.21), residues: 596 sheet: 0.65 (0.80), residues: 44 loop : 0.48 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 313 HIS 0.010 0.001 HIS A 874 PHE 0.010 0.001 PHE A 585 TYR 0.013 0.001 TYR A 545 ARG 0.002 0.000 ARG A 774 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3301.32 seconds wall clock time: 60 minutes 22.80 seconds (3622.80 seconds total)