Starting phenix.real_space_refine on Fri Feb 14 23:07:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rpk_24617/02_2025/7rpk_24617.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rpk_24617/02_2025/7rpk_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_24617/02_2025/7rpk_24617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rpk_24617/02_2025/7rpk_24617.map" model { file = "/net/cci-nas-00/data/ceres_data/7rpk_24617/02_2025/7rpk_24617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rpk_24617/02_2025/7rpk_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 9.17, per 1000 atoms: 0.92 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: 2.41 Conformation dependent library (CDL) restraints added in 2.0 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: 1.05 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: 2.82 Time building geometry restraints manager: 2.82 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 30.070 Find NCS groups from input model: 0.100 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:10.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.670 ------------------------------------------------------------------------------- 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 : 1.004 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: 1.3462 time to fit residues: 229.2661 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 : 1.095 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.163690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111658 restraints weight = 28696.171| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.95 r_work: 0.3097 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 : 1.082 Fit side-chains REVERT: A 436 MET cc_start: 0.6479 (mmt) cc_final: 0.6124 (mpt) REVERT: A 449 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7744 (tptm) REVERT: A 531 MET cc_start: 0.8990 (tpt) cc_final: 0.8761 (tpp) REVERT: A 690 ARG cc_start: 0.6256 (mtt180) cc_final: 0.5955 (ptp-170) REVERT: A 698 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7131 (mm-30) REVERT: A 701 ARG cc_start: 0.8294 (tmm160) cc_final: 0.7651 (tpm170) REVERT: A 940 GLN cc_start: 0.8456 (tt0) cc_final: 0.8067 (tm-30) REVERT: A 986 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8568 (ttt) REVERT: A 997 MET cc_start: 0.8334 (tpp) cc_final: 0.8031 (tpt) REVERT: A 1140 GLN cc_start: 0.7915 (tt0) cc_final: 0.7480 (mt0) REVERT: H 55 LYS cc_start: 0.8291 (ptmt) cc_final: 0.7694 (mmtm) REVERT: H 76 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7600 (tt0) REVERT: H 112 ILE cc_start: 0.7893 (mt) cc_final: 0.7621 (mp) REVERT: H 115 MET cc_start: 0.7395 (mtp) cc_final: 0.7038 (mtt) REVERT: H 122 LYS cc_start: 0.7275 (mttt) cc_final: 0.6843 (mptm) REVERT: H 165 LEU cc_start: 0.8279 (mt) cc_final: 0.8061 (mt) outliers start: 15 outliers final: 2 residues processed: 135 average time/residue: 1.1745 time to fit residues: 171.6521 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 : 1.072 ------------------------------------------------------------------------------- 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 2 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.162610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111945 restraints weight = 15595.702| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.33 r_work: 0.3161 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2484 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= 0.177 Angle : 0.595 8.211 14107 Z= 0.288 Chirality : 0.044 0.625 1647 Planarity : 0.004 0.041 1607 Dihedral : 11.044 178.779 3421 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.27 % Allowed : 9.30 % Favored : 88.43 % 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: 2.30 (0.21), residues: 594 sheet: 0.11 (0.74), residues: 49 loop : 0.80 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 313 HIS 0.009 0.001 HIS A 874 PHE 0.015 0.001 PHE A 608 TYR 0.015 0.002 TYR A 619 ARG 0.002 0.000 ARG A 372 *********************** 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 131 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.024 Fit side-chains REVERT: A 223 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: A 449 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7657 (tptm) REVERT: A 698 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7193 (mm-30) REVERT: A 701 ARG cc_start: 0.8249 (tmm160) cc_final: 0.7665 (mmp-170) REVERT: A 940 GLN cc_start: 0.8282 (tt0) cc_final: 0.7876 (tm-30) REVERT: A 997 MET cc_start: 0.8085 (tpp) cc_final: 0.7847 (tpt) REVERT: A 1140 GLN cc_start: 0.7876 (tt0) cc_final: 0.7454 (mt0) REVERT: H 55 LYS cc_start: 0.8199 (ptmt) cc_final: 0.7661 (mmtm) REVERT: H 76 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7637 (mt-10) REVERT: H 112 ILE cc_start: 0.7868 (mt) cc_final: 0.7611 (mp) REVERT: H 165 LEU cc_start: 0.8179 (mt) cc_final: 0.7937 (mt) outliers start: 21 outliers final: 7 residues processed: 121 average time/residue: 1.2361 time to fit residues: 161.3335 Evaluate side-chains 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 A residue 947 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 14 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.162957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113122 restraints weight = 16305.812| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.30 r_work: 0.3175 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 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 = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10284 Z= 0.163 Angle : 0.545 5.950 14107 Z= 0.266 Chirality : 0.041 0.475 1647 Planarity : 0.004 0.040 1607 Dihedral : 10.579 178.760 3421 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.96 % Allowed : 10.74 % Favored : 87.29 % 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: 2.46 (0.21), residues: 593 sheet: 0.13 (0.74), residues: 49 loop : 0.79 (0.31), residues: 457 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 0.012 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: 18 poor density : 100 time to evaluate : 1.046 Fit side-chains REVERT: A 223 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: A 387 HIS cc_start: 0.7377 (m-70) cc_final: 0.7168 (m-70) REVERT: A 449 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7525 (tptm) REVERT: A 690 ARG cc_start: 0.7574 (ttp-170) cc_final: 0.7087 (tpp-160) REVERT: A 698 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7143 (mm-30) REVERT: A 701 ARG cc_start: 0.8259 (tmm160) cc_final: 0.7709 (mmp-170) REVERT: A 940 GLN cc_start: 0.8176 (tt0) cc_final: 0.7789 (tm-30) REVERT: A 997 MET cc_start: 0.8033 (tpp) cc_final: 0.7697 (tpt) REVERT: A 1140 GLN cc_start: 0.7856 (tt0) cc_final: 0.7416 (mt0) REVERT: H 55 LYS cc_start: 0.8090 (ptmt) cc_final: 0.7556 (mptt) REVERT: H 76 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7483 (mt-10) REVERT: H 112 ILE cc_start: 0.7810 (mt) cc_final: 0.7553 (mp) REVERT: H 165 LEU cc_start: 0.8171 (mt) cc_final: 0.7896 (mt) outliers start: 18 outliers final: 4 residues processed: 112 average time/residue: 1.1212 time to fit residues: 136.4194 Evaluate side-chains 100 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 57 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.161090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.108785 restraints weight = 25462.378| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.85 r_work: 0.3057 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10284 Z= 0.202 Angle : 0.575 6.010 14107 Z= 0.280 Chirality : 0.042 0.439 1647 Planarity : 0.004 0.039 1607 Dihedral : 10.691 177.363 3421 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.38 % Allowed : 10.95 % 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 (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: 2.33 (0.26), residues: 1099 helix: 2.44 (0.21), residues: 595 sheet: 0.19 (0.75), residues: 49 loop : 0.60 (0.31), residues: 455 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 0.016 0.001 PHE A 608 TYR 0.016 0.002 TYR A 644 ARG 0.003 0.000 ARG H 145 *********************** 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 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 1.021 Fit side-chains REVERT: A 223 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: A 449 LYS cc_start: 0.8139 (ttmt) cc_final: 0.7762 (tptm) REVERT: A 647 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8611 (mmp) REVERT: A 698 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7376 (mm-30) REVERT: A 701 ARG cc_start: 0.8399 (tmm160) cc_final: 0.7880 (mmp-170) REVERT: A 940 GLN cc_start: 0.8397 (tt0) cc_final: 0.8026 (tm-30) REVERT: A 997 MET cc_start: 0.8191 (tpp) cc_final: 0.7969 (tpt) REVERT: A 1140 GLN cc_start: 0.7963 (tt0) cc_final: 0.7563 (mt0) REVERT: H 55 LYS cc_start: 0.8154 (ptmt) cc_final: 0.7669 (mptt) REVERT: H 76 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7664 (mt-10) REVERT: H 165 LEU cc_start: 0.8401 (mt) cc_final: 0.8122 (mt) outliers start: 22 outliers final: 10 residues processed: 110 average time/residue: 1.2454 time to fit residues: 147.8082 Evaluate side-chains 103 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 647 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 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 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 = 0.162168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110800 restraints weight = 22182.027| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.84 r_work: 0.3094 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10284 Z= 0.174 Angle : 0.545 5.966 14107 Z= 0.266 Chirality : 0.041 0.428 1647 Planarity : 0.004 0.040 1607 Dihedral : 10.535 178.626 3421 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.07 % Allowed : 11.88 % 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: 2.38 (0.26), residues: 1099 helix: 2.51 (0.21), residues: 596 sheet: 0.26 (0.76), residues: 49 loop : 0.55 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 313 HIS 0.008 0.001 HIS A 777 PHE 0.012 0.001 PHE A 608 TYR 0.013 0.001 TYR A 644 ARG 0.002 0.000 ARG A 774 *********************** 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 115 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.053 Fit side-chains REVERT: A 223 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: A 449 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7666 (tptt) REVERT: A 698 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 701 ARG cc_start: 0.8337 (tmm160) cc_final: 0.7704 (mmm160) REVERT: A 940 GLN cc_start: 0.8330 (tt0) cc_final: 0.7935 (tm-30) REVERT: A 997 MET cc_start: 0.8125 (tpp) cc_final: 0.7898 (tpt) REVERT: A 1008 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8013 (mm) REVERT: A 1140 GLN cc_start: 0.7924 (tt0) cc_final: 0.7496 (mt0) REVERT: H 55 LYS cc_start: 0.8091 (ptmt) cc_final: 0.7560 (mptt) REVERT: H 76 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7573 (mt-10) REVERT: H 165 LEU cc_start: 0.8334 (mt) cc_final: 0.8034 (mt) outliers start: 19 outliers final: 12 residues processed: 108 average time/residue: 1.1140 time to fit residues: 131.3948 Evaluate side-chains 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 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 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 72 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.161753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110077 restraints weight = 20381.470| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.76 r_work: 0.3095 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10284 Z= 0.189 Angle : 0.554 5.996 14107 Z= 0.270 Chirality : 0.041 0.431 1647 Planarity : 0.004 0.039 1607 Dihedral : 10.526 178.121 3421 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.48 % Allowed : 11.16 % 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 (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: 2.45 (0.21), residues: 597 sheet: 0.24 (0.76), residues: 49 loop : 0.52 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 313 HIS 0.008 0.001 HIS A 777 PHE 0.014 0.001 PHE A 608 TYR 0.015 0.001 TYR A 644 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 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: A 449 LYS cc_start: 0.8044 (ttmt) cc_final: 0.7589 (tptt) REVERT: A 587 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7044 (mtpt) REVERT: A 698 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7231 (mm-30) REVERT: A 701 ARG cc_start: 0.8281 (tmm160) cc_final: 0.7703 (mmp-170) REVERT: A 940 GLN cc_start: 0.8304 (tt0) cc_final: 0.7859 (tm-30) REVERT: A 997 MET cc_start: 0.8110 (tpp) cc_final: 0.7885 (tpt) REVERT: A 1008 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.7927 (mm) REVERT: A 1140 GLN cc_start: 0.7896 (tt0) cc_final: 0.7441 (mt0) REVERT: H 55 LYS cc_start: 0.8058 (ptmt) cc_final: 0.7563 (mptt) REVERT: H 76 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7464 (mt-10) REVERT: H 165 LEU cc_start: 0.8300 (mt) cc_final: 0.8017 (mt) outliers start: 23 outliers final: 11 residues processed: 113 average time/residue: 1.0778 time to fit residues: 132.9300 Evaluate side-chains 108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 587 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN A 874 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.162716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111195 restraints weight = 19757.013| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.50 r_work: 0.3132 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10284 Z= 0.168 Angle : 0.535 6.794 14107 Z= 0.262 Chirality : 0.040 0.423 1647 Planarity : 0.003 0.039 1607 Dihedral : 10.375 178.232 3421 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.55 % Allowed : 12.19 % 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: 2.39 (0.26), residues: 1099 helix: 2.54 (0.21), residues: 596 sheet: 0.42 (0.77), residues: 46 loop : 0.50 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 313 HIS 0.009 0.001 HIS A 874 PHE 0.011 0.001 PHE A 608 TYR 0.013 0.001 TYR A 644 ARG 0.003 0.000 ARG A 372 *********************** 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 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: A 449 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7563 (tptt) REVERT: A 587 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6991 (mtpt) REVERT: A 698 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7219 (mm-30) REVERT: A 701 ARG cc_start: 0.8275 (tmm160) cc_final: 0.7620 (mmm160) REVERT: A 940 GLN cc_start: 0.8246 (tt0) cc_final: 0.7820 (tm-30) REVERT: A 1008 LEU cc_start: 0.8648 (tp) cc_final: 0.7868 (mm) REVERT: A 1140 GLN cc_start: 0.7880 (tt0) cc_final: 0.7433 (mt0) REVERT: H 55 LYS cc_start: 0.7979 (ptmt) cc_final: 0.7508 (mptt) REVERT: H 76 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7442 (mt-10) REVERT: H 165 LEU cc_start: 0.8325 (mt) cc_final: 0.8068 (mt) outliers start: 14 outliers final: 11 residues processed: 111 average time/residue: 1.1352 time to fit residues: 137.4707 Evaluate side-chains 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 587 LYS 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 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 12 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 874 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.162091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110706 restraints weight = 16669.766| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.53 r_work: 0.3140 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- 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 = 0.44 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 = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10284 Z= 0.191 Angle : 0.558 7.068 14107 Z= 0.275 Chirality : 0.041 0.437 1647 Planarity : 0.004 0.039 1607 Dihedral : 10.426 177.503 3421 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.96 % Allowed : 12.09 % Favored : 85.95 % 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: 2.34 (0.26), residues: 1099 helix: 2.49 (0.21), residues: 598 sheet: 0.50 (0.78), residues: 44 loop : 0.47 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 313 HIS 0.010 0.001 HIS A 874 PHE 0.014 0.001 PHE A 608 TYR 0.015 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 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: A 449 LYS cc_start: 0.8016 (ttmt) cc_final: 0.7642 (tptt) REVERT: A 587 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7075 (mtpt) REVERT: A 698 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7284 (mm-30) REVERT: A 701 ARG cc_start: 0.8295 (tmm160) cc_final: 0.7776 (mmp-170) REVERT: A 940 GLN cc_start: 0.8240 (tt0) cc_final: 0.7833 (tm-30) REVERT: A 1008 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.7986 (mm) REVERT: A 1140 GLN cc_start: 0.7862 (tt0) cc_final: 0.7424 (mt0) REVERT: H 55 LYS cc_start: 0.7964 (ptmt) cc_final: 0.7551 (mptt) REVERT: H 76 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7449 (mt-10) REVERT: H 165 LEU cc_start: 0.8356 (mt) cc_final: 0.8080 (mt) outliers start: 18 outliers final: 11 residues processed: 106 average time/residue: 1.1950 time to fit residues: 138.8041 Evaluate side-chains 107 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 587 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 874 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.162058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111231 restraints weight = 16430.407| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.57 r_work: 0.3146 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- 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 = 0.44 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 = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3241 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= 0.186 Angle : 0.553 7.286 14107 Z= 0.272 Chirality : 0.041 0.441 1647 Planarity : 0.003 0.039 1607 Dihedral : 10.449 177.298 3421 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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: 2.35 (0.26), residues: 1099 helix: 2.51 (0.21), residues: 597 sheet: 0.56 (0.82), residues: 41 loop : 0.44 (0.30), residues: 461 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 0.013 0.001 PHE A 608 TYR 0.015 0.001 TYR A 644 ARG 0.002 0.000 ARG A 774 ********************** 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 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: A 377 THR cc_start: 0.9091 (m) cc_final: 0.8849 (p) REVERT: A 449 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7634 (tptt) REVERT: A 587 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7041 (mtpt) REVERT: A 698 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7169 (pp20) REVERT: A 701 ARG cc_start: 0.8295 (tmm160) cc_final: 0.7732 (mmp-170) REVERT: A 940 GLN cc_start: 0.8252 (tt0) cc_final: 0.7832 (tm-30) REVERT: A 1008 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.7972 (mm) REVERT: A 1140 GLN cc_start: 0.7864 (tt0) cc_final: 0.7428 (mt0) REVERT: H 55 LYS cc_start: 0.7947 (ptmt) cc_final: 0.7537 (mptt) REVERT: H 76 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7453 (mt-10) REVERT: H 165 LEU cc_start: 0.8378 (mt) cc_final: 0.8146 (mt) outliers start: 15 outliers final: 10 residues processed: 102 average time/residue: 1.1378 time to fit residues: 126.2694 Evaluate side-chains 106 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 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 587 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 49 optimal weight: 0.0370 chunk 93 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN A 874 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.163422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111730 restraints weight = 22022.026| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.76 r_work: 0.3127 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 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 = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10284 Z= 0.155 Angle : 0.531 6.936 14107 Z= 0.261 Chirality : 0.040 0.441 1647 Planarity : 0.003 0.039 1607 Dihedral : 10.309 177.593 3421 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.45 % Allowed : 12.71 % 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: 2.41 (0.26), residues: 1099 helix: 2.58 (0.21), residues: 597 sheet: 0.36 (0.79), residues: 43 loop : 0.47 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 313 HIS 0.010 0.001 HIS A 874 PHE 0.009 0.001 PHE A 495 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: 7249.05 seconds wall clock time: 128 minutes 36.99 seconds (7716.99 seconds total)