Starting phenix.real_space_refine on Thu Jul 2 20:52:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hdq_52072/07_2026/9hdq_52072.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hdq_52072/07_2026/9hdq_52072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hdq_52072/07_2026/9hdq_52072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hdq_52072/07_2026/9hdq_52072.map" model { file = "/net/cci-nas-00/data/ceres_data/9hdq_52072/07_2026/9hdq_52072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hdq_52072/07_2026/9hdq_52072.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 85 5.49 5 S 39 5.16 5 C 6349 2.51 5 N 1770 2.21 5 O 2017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10261 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8505 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 43, 'TRANS': 981} Chain: "B" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 198 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 7} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "E" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 524 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "F" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7304 SG CYS A1130 39.917 77.107 104.187 1.00 67.00 S ATOM 7339 SG CYS A1134 41.652 76.706 107.716 1.00 67.85 S ATOM 7445 SG CYS A1147 42.901 74.525 104.815 1.00 57.58 S Time building chain proxies: 1.67, per 1000 atoms: 0.16 Number of scatterers: 10261 At special positions: 0 Unit cell: (92.635, 146.115, 119.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 39 16.00 P 85 15.00 O 2017 8.00 N 1770 7.00 C 6349 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 331.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" NE2 HIS A1142 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1130 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1147 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1134 " Number of angles added : 3 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 67.4% alpha, 6.9% beta 36 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.856A pdb=" N ASN A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 259' Processing helix chain 'A' and resid 259 through 278 Processing helix chain 'A' and resid 283 through 311 removed outlier: 3.566A pdb=" N ASP A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 331 removed outlier: 3.693A pdb=" N SER A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 370 removed outlier: 3.734A pdb=" N ARG A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 369 " --> pdb=" O TRP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 removed outlier: 3.599A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.514A pdb=" N TYR A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 4.099A pdb=" N TYR A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 454 through 464 removed outlier: 3.614A pdb=" N SER A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 484 removed outlier: 3.652A pdb=" N TYR A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 503 Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 537 through 559 removed outlier: 3.517A pdb=" N GLN A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LYS A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 558 " --> pdb=" O HIS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 589 removed outlier: 3.585A pdb=" N ILE A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 609 through 621 Processing helix chain 'A' and resid 624 through 634 Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.727A pdb=" N VAL A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 4.128A pdb=" N GLN A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL A 728 " --> pdb=" O ASN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 779 through 800 removed outlier: 4.383A pdb=" N LYS A 786 " --> pdb=" O LYS A 782 " (cutoff:3.500A) Proline residue: A 787 - end of helix Processing helix chain 'A' and resid 805 through 828 removed outlier: 4.033A pdb=" N LEU A 818 " --> pdb=" O LYS A 814 " (cutoff:3.500A) Proline residue: A 819 - end of helix Processing helix chain 'A' and resid 833 through 849 removed outlier: 4.096A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 862 Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 885 through 893 removed outlier: 4.240A pdb=" N TYR A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.867A pdb=" N TYR A 914 " --> pdb=" O HIS A 910 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 947 Processing helix chain 'A' and resid 961 through 967 removed outlier: 3.911A pdb=" N LEU A 967 " --> pdb=" O TRP A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 982 Processing helix chain 'A' and resid 984 through 989 Processing helix chain 'A' and resid 990 through 994 removed outlier: 3.658A pdb=" N ASP A 993 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1006 removed outlier: 3.766A pdb=" N ASP A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 3.930A pdb=" N ILE A1014 " --> pdb=" O LYS A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1031 removed outlier: 3.899A pdb=" N ARG A1031 " --> pdb=" O ILE A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1043 removed outlier: 3.850A pdb=" N PHE A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR A1043 " --> pdb=" O ILE A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.641A pdb=" N GLN A1059 " --> pdb=" O ASN A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1076 Processing helix chain 'A' and resid 1081 through 1095 Processing helix chain 'A' and resid 1098 through 1110 removed outlier: 3.598A pdb=" N MET A1104 " --> pdb=" O ALA A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1123 Processing helix chain 'A' and resid 1139 through 1145 Processing helix chain 'A' and resid 1150 through 1164 removed outlier: 3.504A pdb=" N TRP A1154 " --> pdb=" O VAL A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1178 Processing helix chain 'A' and resid 1181 through 1185 removed outlier: 3.561A pdb=" N LYS A1185 " --> pdb=" O ASN A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1206 removed outlier: 3.575A pdb=" N ARG A1195 " --> pdb=" O ASP A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1237 removed outlier: 3.568A pdb=" N TYR A1232 " --> pdb=" O THR A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1258 removed outlier: 4.740A pdb=" N LYS A1249 " --> pdb=" O GLY A1245 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU A1250 " --> pdb=" O THR A1246 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A1258 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1267 Processing sheet with id=AA1, first strand: chain 'A' and resid 393 through 395 Processing sheet with id=AA2, first strand: chain 'A' and resid 530 through 536 removed outlier: 4.834A pdb=" N LEU A 516 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 530 through 536 removed outlier: 4.834A pdb=" N LEU A 516 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 697 through 700 removed outlier: 4.190A pdb=" N MET A 704 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 690 Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 768 485 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2211 1.33 - 1.45: 2711 1.45 - 1.58: 5514 1.58 - 1.70: 164 1.70 - 1.82: 63 Bond restraints: 10663 Sorted by residual: bond pdb=" P DA F 1 " pdb=" OP1 DA F 1 " ideal model delta sigma weight residual 1.480 1.546 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C1' DT E 41 " pdb=" N1 DT E 41 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.55e+00 bond pdb=" C3' DT E 42 " pdb=" O3' DT E 42 " ideal model delta sigma weight residual 1.435 1.398 0.037 1.30e-02 5.92e+03 8.09e+00 bond pdb=" C1' DT B 13 " pdb=" N1 DT B 13 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.59e+00 bond pdb=" C3' DA C 12 " pdb=" C2' DA C 12 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.24e+00 ... (remaining 10658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 12721 1.57 - 3.13: 1706 3.13 - 4.70: 277 4.70 - 6.27: 30 6.27 - 7.83: 12 Bond angle restraints: 14746 Sorted by residual: angle pdb=" O4' DT B 20 " pdb=" C4' DT B 20 " pdb=" C3' DT B 20 " ideal model delta sigma weight residual 106.00 103.05 2.95 6.00e-01 2.78e+00 2.42e+01 angle pdb=" O4' DT B 22 " pdb=" C4' DT B 22 " pdb=" C3' DT B 22 " ideal model delta sigma weight residual 106.00 103.18 2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" O4' DA F 1 " pdb=" C1' DA F 1 " pdb=" N9 DA F 1 " ideal model delta sigma weight residual 108.00 104.90 3.10 7.00e-01 2.04e+00 1.96e+01 angle pdb=" CA TYR A 914 " pdb=" CB TYR A 914 " pdb=" CG TYR A 914 " ideal model delta sigma weight residual 113.90 106.07 7.83 1.80e+00 3.09e-01 1.89e+01 angle pdb=" O4' DT B 19 " pdb=" C1' DT B 19 " pdb=" N1 DT B 19 " ideal model delta sigma weight residual 108.00 111.02 -3.02 7.00e-01 2.04e+00 1.87e+01 ... (remaining 14741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.08: 5866 33.08 - 66.15: 445 66.15 - 99.23: 18 99.23 - 132.30: 0 132.30 - 165.37: 1 Dihedral angle restraints: 6330 sinusoidal: 3290 harmonic: 3040 Sorted by residual: dihedral pdb=" CA ASP A 993 " pdb=" C ASP A 993 " pdb=" N PHE A 994 " pdb=" CA PHE A 994 " ideal model delta harmonic sigma weight residual -180.00 -151.24 -28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA LEU A 953 " pdb=" C LEU A 953 " pdb=" N THR A 954 " pdb=" CA THR A 954 " ideal model delta harmonic sigma weight residual -180.00 -151.29 -28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA LEU A 697 " pdb=" C LEU A 697 " pdb=" N SER A 698 " pdb=" CA SER A 698 " ideal model delta harmonic sigma weight residual 180.00 151.55 28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 6327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 1543 0.156 - 0.312: 85 0.312 - 0.468: 3 0.468 - 0.623: 3 0.623 - 0.779: 2 Chirality restraints: 1636 Sorted by residual: chirality pdb=" P DA F 1 " pdb=" OP1 DA F 1 " pdb=" OP2 DA F 1 " pdb=" O5' DA F 1 " both_signs ideal model delta sigma weight residual True 2.34 3.11 -0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" P DT E 25 " pdb=" OP1 DT E 25 " pdb=" OP2 DT E 25 " pdb=" O5' DT E 25 " both_signs ideal model delta sigma weight residual True 2.34 -3.01 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" P DA B 6 " pdb=" OP1 DA B 6 " pdb=" OP2 DA B 6 " pdb=" O5' DA B 6 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.65e+00 ... (remaining 1633 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT E 27 " -0.036 2.00e-02 2.50e+03 1.95e-02 9.50e+00 pdb=" N1 DT E 27 " 0.045 2.00e-02 2.50e+03 pdb=" C2 DT E 27 " -0.011 2.00e-02 2.50e+03 pdb=" O2 DT E 27 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DT E 27 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT E 27 " -0.005 2.00e-02 2.50e+03 pdb=" O4 DT E 27 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DT E 27 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT E 27 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DT E 27 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA F 1 " 0.034 2.00e-02 2.50e+03 1.85e-02 9.39e+00 pdb=" N9 DA F 1 " -0.048 2.00e-02 2.50e+03 pdb=" C8 DA F 1 " 0.010 2.00e-02 2.50e+03 pdb=" N7 DA F 1 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA F 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA F 1 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA F 1 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DA F 1 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA F 1 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA F 1 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DA F 1 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT B 10 " 0.033 2.00e-02 2.50e+03 1.88e-02 8.86e+00 pdb=" N1 DT B 10 " -0.046 2.00e-02 2.50e+03 pdb=" C2 DT B 10 " 0.013 2.00e-02 2.50e+03 pdb=" O2 DT B 10 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT B 10 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT B 10 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT B 10 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT B 10 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT B 10 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT B 10 " -0.004 2.00e-02 2.50e+03 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 2908 2.86 - 3.37: 9282 3.37 - 3.88: 17119 3.88 - 4.39: 20186 4.39 - 4.90: 31188 Nonbonded interactions: 80683 Sorted by model distance: nonbonded pdb=" O PHE A 273 " pdb=" ND2 ASN A 277 " model vdw 2.353 3.120 nonbonded pdb=" O ASP A 523 " pdb=" ND2 ASN A 529 " model vdw 2.359 3.120 nonbonded pdb=" O ALA A1073 " pdb=" O MET A1076 " model vdw 2.456 3.040 nonbonded pdb=" OG1 THR A 774 " pdb=" O ASP A 776 " model vdw 2.501 3.040 nonbonded pdb=" NH1 ARG A 311 " pdb=" OD1 ASP A 315 " model vdw 2.519 3.120 ... (remaining 80678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 13.600 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 : 0.008 0.066 10667 Z= 0.504 Angle : 1.135 7.832 14749 Z= 0.765 Chirality : 0.090 0.779 1636 Planarity : 0.010 0.096 1539 Dihedral : 19.146 165.375 4350 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.22), residues: 1023 helix: -0.81 (0.17), residues: 593 sheet: 0.14 (0.71), residues: 46 loop : -0.56 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.003 ARG A1052 TYR 0.039 0.006 TYR A 914 PHE 0.020 0.003 PHE A 367 TRP 0.032 0.004 TRP A1011 HIS 0.014 0.003 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00791 / 0.50 (10663) covalent geometry : angle 1.13324 / 0.76 (14746) hydrogen bonds : bond 0.24024 / 15.44 ( 549) hydrogen bonds : angle 6.82036 / 5.00 ( 1552) metal coordination : bond 0.01626 / 0.78 ( 4) metal coordination : angle 4.37063 / 2.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.430 Fit side-chains REVERT: A 271 LYS cc_start: 0.8494 (mttt) cc_final: 0.8238 (mtmm) REVERT: A 272 MET cc_start: 0.7557 (tpp) cc_final: 0.7306 (tpp) REVERT: A 358 LYS cc_start: 0.7812 (mttt) cc_final: 0.7314 (ttmt) REVERT: A 379 ARG cc_start: 0.7777 (mmm-85) cc_final: 0.7562 (mmm-85) REVERT: A 393 ILE cc_start: 0.7546 (pt) cc_final: 0.7306 (pp) REVERT: A 406 GLU cc_start: 0.7261 (tt0) cc_final: 0.6707 (tp30) REVERT: A 531 ARG cc_start: 0.8303 (ptt90) cc_final: 0.7767 (ppp80) REVERT: A 747 ARG cc_start: 0.6689 (mtt180) cc_final: 0.6297 (mpp-170) REVERT: A 765 ARG cc_start: 0.9030 (ptt90) cc_final: 0.8523 (ptp90) REVERT: A 776 ASP cc_start: 0.7970 (m-30) cc_final: 0.7740 (t70) REVERT: A 863 GLN cc_start: 0.8012 (tt0) cc_final: 0.7469 (tp40) REVERT: A 910 HIS cc_start: 0.7484 (m-70) cc_final: 0.6500 (p90) REVERT: A 929 ASP cc_start: 0.8160 (m-30) cc_final: 0.7871 (m-30) REVERT: A 1011 TRP cc_start: 0.6378 (m100) cc_final: 0.6103 (m-10) REVERT: A 1047 LYS cc_start: 0.7868 (mttt) cc_final: 0.7537 (mttm) REVERT: A 1063 LYS cc_start: 0.7656 (ptmt) cc_final: 0.7038 (tptp) REVERT: A 1064 LYS cc_start: 0.7377 (ttpt) cc_final: 0.6902 (mtmt) REVERT: A 1066 ASN cc_start: 0.7678 (m-40) cc_final: 0.7440 (m110) REVERT: A 1082 LYS cc_start: 0.8160 (mttt) cc_final: 0.7724 (tttm) REVERT: A 1104 MET cc_start: 0.8366 (tpt) cc_final: 0.8119 (tpp) REVERT: A 1182 ASN cc_start: 0.7554 (m-40) cc_final: 0.7253 (p0) REVERT: A 1191 ASP cc_start: 0.7980 (m-30) cc_final: 0.7435 (p0) REVERT: A 1240 PHE cc_start: 0.7922 (t80) cc_final: 0.7523 (t80) REVERT: A 1267 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7266 (mmm-85) REVERT: A 1269 PHE cc_start: 0.7482 (p90) cc_final: 0.7124 (p90) outliers start: 0 outliers final: 1 residues processed: 125 average time/residue: 0.7523 time to fit residues: 99.6093 Evaluate side-chains 95 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 ASN A 309 GLN A 618 ASN A 710 ASN A 851 GLN A 865 ASN A 910 HIS A1055 ASN A1077 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.172595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.123089 restraints weight = 11852.108| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.73 r_work: 0.3394 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10667 Z= 0.176 Angle : 0.705 6.903 14749 Z= 0.410 Chirality : 0.048 0.342 1636 Planarity : 0.005 0.040 1539 Dihedral : 22.095 179.905 2100 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.17 % Allowed : 4.78 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.25), residues: 1023 helix: 1.29 (0.20), residues: 610 sheet: 0.30 (0.69), residues: 46 loop : -0.08 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1052 TYR 0.013 0.002 TYR A 260 PHE 0.014 0.002 PHE A 741 TRP 0.014 0.002 TRP A1158 HIS 0.007 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.18 (10663) covalent geometry : angle 0.70424 / 0.41 (14746) hydrogen bonds : bond 0.07790 / 4.94 ( 549) hydrogen bonds : angle 4.46334 / 3.33 ( 1552) metal coordination : bond 0.00598 / 0.27 ( 4) metal coordination : angle 1.75290 / 0.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.301 Fit side-chains REVERT: A 272 MET cc_start: 0.7451 (tpp) cc_final: 0.7052 (tpt) REVERT: A 358 LYS cc_start: 0.7500 (mttt) cc_final: 0.7203 (ttpt) REVERT: A 379 ARG cc_start: 0.7413 (mmm-85) cc_final: 0.7092 (mmm-85) REVERT: A 406 GLU cc_start: 0.7002 (tt0) cc_final: 0.6676 (tp30) REVERT: A 444 GLU cc_start: 0.7486 (tt0) cc_final: 0.7045 (tm-30) REVERT: A 531 ARG cc_start: 0.8010 (ptt90) cc_final: 0.7493 (ppp80) REVERT: A 556 LYS cc_start: 0.8143 (mttt) cc_final: 0.7924 (mmpt) REVERT: A 765 ARG cc_start: 0.8990 (ptt90) cc_final: 0.8689 (ptp90) REVERT: A 863 GLN cc_start: 0.8012 (tt0) cc_final: 0.7676 (tp40) REVERT: A 910 HIS cc_start: 0.7098 (m90) cc_final: 0.6529 (p90) REVERT: A 1082 LYS cc_start: 0.7714 (mttt) cc_final: 0.7387 (tttm) REVERT: A 1104 MET cc_start: 0.8525 (tpt) cc_final: 0.8244 (tpp) REVERT: A 1162 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7189 (mtp180) REVERT: A 1191 ASP cc_start: 0.7852 (m-30) cc_final: 0.7515 (p0) REVERT: A 1240 PHE cc_start: 0.7559 (t80) cc_final: 0.7199 (t80) REVERT: A 1267 ARG cc_start: 0.8038 (mtt90) cc_final: 0.7695 (mmm-85) outliers start: 11 outliers final: 1 residues processed: 104 average time/residue: 0.6503 time to fit residues: 71.8037 Evaluate side-chains 93 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1162 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 865 ASN A1113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.171754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.122726 restraints weight = 11900.843| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.76 r_work: 0.3393 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10667 Z= 0.162 Angle : 0.625 6.672 14749 Z= 0.364 Chirality : 0.044 0.289 1636 Planarity : 0.005 0.052 1539 Dihedral : 22.055 162.707 2098 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.17 % Allowed : 7.44 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.26), residues: 1023 helix: 1.68 (0.20), residues: 609 sheet: 0.36 (0.66), residues: 46 loop : -0.12 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 363 TYR 0.014 0.002 TYR A 634 PHE 0.016 0.002 PHE A 367 TRP 0.013 0.002 TRP A 849 HIS 0.006 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (10663) covalent geometry : angle 0.62441 / 0.36 (14746) hydrogen bonds : bond 0.06819 / 4.32 ( 549) hydrogen bonds : angle 4.15322 / 3.11 ( 1552) metal coordination : bond 0.00476 / 0.20 ( 4) metal coordination : angle 2.08937 / 1.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.498 Fit side-chains REVERT: A 272 MET cc_start: 0.7516 (tpp) cc_final: 0.7206 (tpt) REVERT: A 320 GLN cc_start: 0.5669 (tt0) cc_final: 0.5310 (mt0) REVERT: A 358 LYS cc_start: 0.7539 (mttt) cc_final: 0.7167 (ttpt) REVERT: A 379 ARG cc_start: 0.7333 (mmm-85) cc_final: 0.7083 (mmm-85) REVERT: A 406 GLU cc_start: 0.6891 (tt0) cc_final: 0.6597 (tp30) REVERT: A 444 GLU cc_start: 0.7485 (tt0) cc_final: 0.7055 (tm-30) REVERT: A 531 ARG cc_start: 0.8071 (ptt90) cc_final: 0.7537 (ppp80) REVERT: A 603 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7460 (mmtm) REVERT: A 765 ARG cc_start: 0.9008 (ptt90) cc_final: 0.8773 (ptp90) REVERT: A 863 GLN cc_start: 0.7975 (tt0) cc_final: 0.7695 (mm110) REVERT: A 910 HIS cc_start: 0.7077 (m90) cc_final: 0.6438 (p90) REVERT: A 1013 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6171 (mm) REVERT: A 1064 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7572 (pmmt) REVERT: A 1104 MET cc_start: 0.8488 (tpt) cc_final: 0.8237 (tpp) REVERT: A 1162 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7019 (mtp180) REVERT: A 1191 ASP cc_start: 0.7838 (m-30) cc_final: 0.7468 (p0) REVERT: A 1267 ARG cc_start: 0.7992 (mtt90) cc_final: 0.7724 (mmm-85) outliers start: 11 outliers final: 3 residues processed: 102 average time/residue: 0.7156 time to fit residues: 77.5832 Evaluate side-chains 94 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 89 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 865 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.173575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.122998 restraints weight = 11872.062| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.74 r_work: 0.3407 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10667 Z= 0.143 Angle : 0.570 6.099 14749 Z= 0.332 Chirality : 0.041 0.142 1636 Planarity : 0.004 0.043 1539 Dihedral : 21.906 144.450 2098 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.70 % Allowed : 8.82 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.26), residues: 1023 helix: 1.85 (0.20), residues: 609 sheet: 0.38 (0.64), residues: 46 loop : -0.13 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1078 TYR 0.016 0.002 TYR A 284 PHE 0.015 0.002 PHE A1269 TRP 0.010 0.001 TRP A 573 HIS 0.006 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (10663) covalent geometry : angle 0.56940 / 0.33 (14746) hydrogen bonds : bond 0.05948 / 3.77 ( 549) hydrogen bonds : angle 4.02270 / 3.02 ( 1552) metal coordination : bond 0.00415 / 0.19 ( 4) metal coordination : angle 1.78877 / 0.84 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.398 Fit side-chains REVERT: A 253 ASN cc_start: 0.6896 (t0) cc_final: 0.6610 (t0) REVERT: A 358 LYS cc_start: 0.7503 (mttt) cc_final: 0.7084 (ttpt) REVERT: A 379 ARG cc_start: 0.7310 (mmm-85) cc_final: 0.7054 (mmm-85) REVERT: A 382 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.5794 (mppt) REVERT: A 444 GLU cc_start: 0.7422 (tt0) cc_final: 0.6961 (tm-30) REVERT: A 531 ARG cc_start: 0.7993 (ptt90) cc_final: 0.7449 (ppp80) REVERT: A 603 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7397 (mmmm) REVERT: A 765 ARG cc_start: 0.9000 (ptt90) cc_final: 0.8756 (ptp90) REVERT: A 863 GLN cc_start: 0.7976 (tt0) cc_final: 0.7652 (mm110) REVERT: A 910 HIS cc_start: 0.7135 (m90) cc_final: 0.6458 (p90) REVERT: A 1013 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6295 (mm) REVERT: A 1064 LYS cc_start: 0.7724 (mtmt) cc_final: 0.7289 (mmtm) REVERT: A 1104 MET cc_start: 0.8423 (tpt) cc_final: 0.8151 (tpp) REVERT: A 1119 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7835 (mmm) REVERT: A 1162 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6993 (mtp180) REVERT: A 1191 ASP cc_start: 0.7725 (m-30) cc_final: 0.7274 (p0) REVERT: A 1267 ARG cc_start: 0.8065 (mtt90) cc_final: 0.7705 (mmm-85) outliers start: 16 outliers final: 9 residues processed: 108 average time/residue: 0.7904 time to fit residues: 90.4087 Evaluate side-chains 97 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 35 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 76 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1077 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.173828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122503 restraints weight = 11718.853| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.71 r_work: 0.3412 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10667 Z= 0.137 Angle : 0.551 7.380 14749 Z= 0.320 Chirality : 0.039 0.139 1636 Planarity : 0.004 0.045 1539 Dihedral : 21.793 135.431 2098 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.59 % Allowed : 9.56 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.26), residues: 1023 helix: 2.00 (0.20), residues: 609 sheet: 0.31 (0.64), residues: 46 loop : -0.16 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 363 TYR 0.012 0.001 TYR A 284 PHE 0.016 0.002 PHE A1269 TRP 0.011 0.001 TRP A 849 HIS 0.006 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (10663) covalent geometry : angle 0.55069 / 0.32 (14746) hydrogen bonds : bond 0.05706 / 3.62 ( 549) hydrogen bonds : angle 3.95330 / 2.97 ( 1552) metal coordination : bond 0.00316 / 0.14 ( 4) metal coordination : angle 1.54581 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.431 Fit side-chains REVERT: A 272 MET cc_start: 0.7273 (tpp) cc_final: 0.6982 (tpt) REVERT: A 358 LYS cc_start: 0.7468 (mttt) cc_final: 0.7094 (ttpt) REVERT: A 379 ARG cc_start: 0.7308 (mmm-85) cc_final: 0.7056 (mmm-85) REVERT: A 444 GLU cc_start: 0.7290 (tt0) cc_final: 0.6943 (tm-30) REVERT: A 531 ARG cc_start: 0.7980 (ptt90) cc_final: 0.7443 (ppp80) REVERT: A 603 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7362 (mmmm) REVERT: A 765 ARG cc_start: 0.9025 (ptt90) cc_final: 0.8767 (ptp90) REVERT: A 863 GLN cc_start: 0.7950 (tt0) cc_final: 0.7634 (mm110) REVERT: A 910 HIS cc_start: 0.7161 (m90) cc_final: 0.6458 (p90) REVERT: A 1013 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6281 (mm) REVERT: A 1064 LYS cc_start: 0.7742 (mtmt) cc_final: 0.7474 (pmmt) REVERT: A 1090 LYS cc_start: 0.8362 (tmmt) cc_final: 0.8151 (ttmm) REVERT: A 1104 MET cc_start: 0.8400 (tpt) cc_final: 0.8177 (tpp) REVERT: A 1119 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7718 (mmm) REVERT: A 1162 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7021 (mtp180) REVERT: A 1191 ASP cc_start: 0.7709 (m-30) cc_final: 0.7217 (p0) REVERT: A 1267 ARG cc_start: 0.8085 (mtt90) cc_final: 0.7703 (mmm-85) outliers start: 15 outliers final: 9 residues processed: 100 average time/residue: 0.7369 time to fit residues: 78.2812 Evaluate side-chains 98 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 92 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 102 optimal weight: 40.0000 chunk 55 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 581 ASN A 851 GLN A1077 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.174006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123451 restraints weight = 11902.205| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.73 r_work: 0.3409 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10667 Z= 0.138 Angle : 0.548 6.133 14749 Z= 0.318 Chirality : 0.039 0.133 1636 Planarity : 0.004 0.042 1539 Dihedral : 21.720 133.923 2098 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.44 % Allowed : 9.88 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.26), residues: 1023 helix: 2.04 (0.21), residues: 609 sheet: 0.32 (0.64), residues: 46 loop : -0.21 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 363 TYR 0.015 0.002 TYR A 284 PHE 0.016 0.002 PHE A1269 TRP 0.011 0.001 TRP A 799 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (10663) covalent geometry : angle 0.54757 / 0.32 (14746) hydrogen bonds : bond 0.05679 / 3.60 ( 549) hydrogen bonds : angle 3.92571 / 2.95 ( 1552) metal coordination : bond 0.00343 / 0.15 ( 4) metal coordination : angle 1.38963 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.400 Fit side-chains REVERT: A 272 MET cc_start: 0.7270 (tpp) cc_final: 0.6965 (tpt) REVERT: A 358 LYS cc_start: 0.7504 (mttt) cc_final: 0.7115 (ttpt) REVERT: A 379 ARG cc_start: 0.7296 (mmm-85) cc_final: 0.7063 (mmm-85) REVERT: A 444 GLU cc_start: 0.7306 (tt0) cc_final: 0.6938 (tm-30) REVERT: A 531 ARG cc_start: 0.7956 (ptt90) cc_final: 0.7435 (ppp80) REVERT: A 603 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7401 (mmmm) REVERT: A 765 ARG cc_start: 0.9026 (ptt90) cc_final: 0.8771 (ptp90) REVERT: A 863 GLN cc_start: 0.7942 (tt0) cc_final: 0.7624 (mm110) REVERT: A 1064 LYS cc_start: 0.7753 (mtmt) cc_final: 0.7467 (pmmt) REVERT: A 1090 LYS cc_start: 0.8384 (tmmt) cc_final: 0.8151 (tppt) REVERT: A 1104 MET cc_start: 0.8391 (tpt) cc_final: 0.8134 (tpp) REVERT: A 1119 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7860 (mmm) REVERT: A 1162 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7019 (mtp180) REVERT: A 1191 ASP cc_start: 0.7715 (m-30) cc_final: 0.7220 (p0) REVERT: A 1267 ARG cc_start: 0.8086 (mtt90) cc_final: 0.7715 (mmm-85) outliers start: 23 outliers final: 9 residues processed: 104 average time/residue: 0.7503 time to fit residues: 82.9801 Evaluate side-chains 96 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1162 ARG Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 851 GLN A1077 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.174883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.126690 restraints weight = 11826.298| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.51 r_work: 0.3416 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10667 Z= 0.124 Angle : 0.516 6.146 14749 Z= 0.302 Chirality : 0.038 0.133 1636 Planarity : 0.004 0.042 1539 Dihedral : 21.608 131.894 2098 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.49 % Allowed : 11.58 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.26), residues: 1023 helix: 2.15 (0.21), residues: 609 sheet: 0.32 (0.64), residues: 46 loop : -0.16 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 363 TYR 0.011 0.001 TYR A1227 PHE 0.018 0.001 PHE A1269 TRP 0.016 0.001 TRP A 799 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.12 (10663) covalent geometry : angle 0.51578 / 0.30 (14746) hydrogen bonds : bond 0.05123 / 3.24 ( 549) hydrogen bonds : angle 3.82572 / 2.88 ( 1552) metal coordination : bond 0.00371 / 0.16 ( 4) metal coordination : angle 1.22468 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.397 Fit side-chains REVERT: A 272 MET cc_start: 0.7293 (tpp) cc_final: 0.7083 (tpp) REVERT: A 358 LYS cc_start: 0.7526 (mttt) cc_final: 0.7183 (ttpt) REVERT: A 379 ARG cc_start: 0.7399 (mmm-85) cc_final: 0.7160 (mmm-85) REVERT: A 382 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.5775 (mppt) REVERT: A 444 GLU cc_start: 0.7284 (tt0) cc_final: 0.6997 (tm-30) REVERT: A 531 ARG cc_start: 0.7932 (ptt90) cc_final: 0.7468 (ppp80) REVERT: A 603 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7311 (mmmm) REVERT: A 765 ARG cc_start: 0.9024 (ptt90) cc_final: 0.8806 (ptp90) REVERT: A 863 GLN cc_start: 0.7957 (tt0) cc_final: 0.7664 (mm110) REVERT: A 1064 LYS cc_start: 0.7704 (mtmt) cc_final: 0.7463 (pmmt) REVERT: A 1090 LYS cc_start: 0.8406 (tmmt) cc_final: 0.8198 (ttmm) REVERT: A 1104 MET cc_start: 0.8427 (tpt) cc_final: 0.8179 (tpp) REVERT: A 1119 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7942 (mmm) REVERT: A 1191 ASP cc_start: 0.7720 (m-30) cc_final: 0.7243 (m-30) REVERT: A 1267 ARG cc_start: 0.7997 (mtt90) cc_final: 0.7693 (mmm-85) outliers start: 14 outliers final: 5 residues processed: 96 average time/residue: 0.7201 time to fit residues: 73.8630 Evaluate side-chains 91 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1119 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 36 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 581 ASN A 851 GLN A1077 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.174092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.125655 restraints weight = 11858.877| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.53 r_work: 0.3400 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10667 Z= 0.133 Angle : 0.536 7.310 14749 Z= 0.310 Chirality : 0.039 0.135 1636 Planarity : 0.004 0.041 1539 Dihedral : 21.571 130.250 2098 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.91 % Allowed : 11.05 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.26), residues: 1023 helix: 2.12 (0.21), residues: 609 sheet: 0.39 (0.65), residues: 46 loop : -0.19 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 363 TYR 0.015 0.001 TYR A 284 PHE 0.020 0.001 PHE A1269 TRP 0.015 0.001 TRP A 799 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 (10663) covalent geometry : angle 0.53581 / 0.31 (14746) hydrogen bonds : bond 0.05455 / 3.46 ( 549) hydrogen bonds : angle 3.85290 / 2.89 ( 1552) metal coordination : bond 0.00246 / 0.11 ( 4) metal coordination : angle 1.23593 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.393 Fit side-chains REVERT: A 272 MET cc_start: 0.7279 (tpp) cc_final: 0.6953 (tpt) REVERT: A 358 LYS cc_start: 0.7533 (mttt) cc_final: 0.7175 (ttpt) REVERT: A 379 ARG cc_start: 0.7396 (mmm-85) cc_final: 0.7159 (mmm-85) REVERT: A 382 LYS cc_start: 0.6633 (OUTLIER) cc_final: 0.5779 (mppt) REVERT: A 444 GLU cc_start: 0.7373 (tt0) cc_final: 0.6990 (tm-30) REVERT: A 531 ARG cc_start: 0.7936 (ptt90) cc_final: 0.7468 (ppp80) REVERT: A 603 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7370 (mmmm) REVERT: A 765 ARG cc_start: 0.9047 (ptt90) cc_final: 0.8810 (ptp90) REVERT: A 863 GLN cc_start: 0.7939 (tt0) cc_final: 0.7661 (mm110) REVERT: A 1064 LYS cc_start: 0.7660 (mtmt) cc_final: 0.7437 (pmmt) REVERT: A 1090 LYS cc_start: 0.8410 (tmmt) cc_final: 0.8205 (ttmm) REVERT: A 1104 MET cc_start: 0.8430 (tpt) cc_final: 0.8166 (tpp) REVERT: A 1119 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7932 (mmm) REVERT: A 1162 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6991 (mtp180) REVERT: A 1191 ASP cc_start: 0.7704 (m-30) cc_final: 0.7225 (p0) REVERT: A 1267 ARG cc_start: 0.8001 (mtt90) cc_final: 0.7684 (mmm-85) outliers start: 18 outliers final: 9 residues processed: 99 average time/residue: 0.6851 time to fit residues: 72.4568 Evaluate side-chains 96 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1162 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 581 ASN A 851 GLN A1077 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.174048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.123017 restraints weight = 11831.635| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.83 r_work: 0.3407 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10667 Z= 0.134 Angle : 0.535 6.417 14749 Z= 0.310 Chirality : 0.039 0.136 1636 Planarity : 0.004 0.041 1539 Dihedral : 21.498 128.506 2098 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.70 % Allowed : 11.58 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.26), residues: 1023 helix: 2.12 (0.21), residues: 609 sheet: 0.42 (0.66), residues: 46 loop : -0.17 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 363 TYR 0.014 0.001 TYR A 284 PHE 0.021 0.001 PHE A1269 TRP 0.013 0.001 TRP A 799 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (10663) covalent geometry : angle 0.53487 / 0.31 (14746) hydrogen bonds : bond 0.05471 / 3.47 ( 549) hydrogen bonds : angle 3.85382 / 2.89 ( 1552) metal coordination : bond 0.00250 / 0.11 ( 4) metal coordination : angle 1.18322 / 0.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.394 Fit side-chains REVERT: A 272 MET cc_start: 0.7289 (tpp) cc_final: 0.6963 (tpt) REVERT: A 358 LYS cc_start: 0.7507 (mttt) cc_final: 0.7112 (ttpt) REVERT: A 379 ARG cc_start: 0.7296 (mmm-85) cc_final: 0.7069 (mmm160) REVERT: A 382 LYS cc_start: 0.6526 (OUTLIER) cc_final: 0.5739 (mppt) REVERT: A 444 GLU cc_start: 0.7365 (tt0) cc_final: 0.6896 (tm-30) REVERT: A 531 ARG cc_start: 0.7912 (ptt90) cc_final: 0.7413 (ppp80) REVERT: A 603 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7328 (mmmm) REVERT: A 765 ARG cc_start: 0.9053 (ptt90) cc_final: 0.8766 (ptp90) REVERT: A 863 GLN cc_start: 0.7923 (tt0) cc_final: 0.7592 (mm110) REVERT: A 1064 LYS cc_start: 0.7666 (mtmt) cc_final: 0.7339 (pmmt) REVERT: A 1090 LYS cc_start: 0.8365 (tmmt) cc_final: 0.8130 (ttmm) REVERT: A 1104 MET cc_start: 0.8402 (tpt) cc_final: 0.8142 (tpp) REVERT: A 1119 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7864 (mmm) REVERT: A 1162 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6934 (mtp180) REVERT: A 1191 ASP cc_start: 0.7700 (m-30) cc_final: 0.7109 (p0) REVERT: A 1267 ARG cc_start: 0.8041 (mtt90) cc_final: 0.7623 (mmm-85) outliers start: 16 outliers final: 10 residues processed: 96 average time/residue: 0.7600 time to fit residues: 77.7828 Evaluate side-chains 97 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1162 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.9990 chunk 58 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 851 GLN A1077 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.174923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.123955 restraints weight = 11676.282| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.70 r_work: 0.3433 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.002 0.034 10667 Z= 0.123 Angle : 0.522 8.137 14749 Z= 0.303 Chirality : 0.038 0.135 1636 Planarity : 0.004 0.040 1539 Dihedral : 21.390 127.401 2098 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.49 % Allowed : 11.90 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.26), residues: 1023 helix: 2.22 (0.21), residues: 610 sheet: 0.36 (0.65), residues: 46 loop : -0.13 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 363 TYR 0.011 0.001 TYR A1227 PHE 0.021 0.001 PHE A1269 TRP 0.021 0.001 TRP A 799 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.12 (10663) covalent geometry : angle 0.52146 / 0.30 (14746) hydrogen bonds : bond 0.05010 / 3.17 ( 549) hydrogen bonds : angle 3.77581 / 2.84 ( 1552) metal coordination : bond 0.00349 / 0.15 ( 4) metal coordination : angle 1.16824 / 0.55 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.390 Fit side-chains REVERT: A 272 MET cc_start: 0.7283 (tpp) cc_final: 0.6958 (tpt) REVERT: A 358 LYS cc_start: 0.7484 (mttt) cc_final: 0.7119 (ttpt) REVERT: A 379 ARG cc_start: 0.7277 (mmm-85) cc_final: 0.7018 (mmm-85) REVERT: A 382 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.5670 (mppt) REVERT: A 444 GLU cc_start: 0.7291 (tt0) cc_final: 0.6931 (tm-30) REVERT: A 531 ARG cc_start: 0.7898 (ptt90) cc_final: 0.7423 (ppp80) REVERT: A 603 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7416 (mttp) REVERT: A 765 ARG cc_start: 0.9046 (ptt90) cc_final: 0.8782 (ptp90) REVERT: A 853 ARG cc_start: 0.8627 (ttm-80) cc_final: 0.8289 (mmm160) REVERT: A 863 GLN cc_start: 0.7897 (tt0) cc_final: 0.7667 (mm110) REVERT: A 910 HIS cc_start: 0.7080 (m90) cc_final: 0.6655 (p-80) REVERT: A 1064 LYS cc_start: 0.7636 (mtmt) cc_final: 0.7385 (pmmt) REVERT: A 1090 LYS cc_start: 0.8363 (tmmt) cc_final: 0.8148 (ttmm) REVERT: A 1104 MET cc_start: 0.8348 (tpt) cc_final: 0.8091 (tpp) REVERT: A 1119 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7872 (mmm) REVERT: A 1162 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7009 (mtp180) REVERT: A 1191 ASP cc_start: 0.7603 (m-30) cc_final: 0.7110 (m-30) REVERT: A 1267 ARG cc_start: 0.8016 (mtt90) cc_final: 0.7654 (mmm-85) outliers start: 14 outliers final: 8 residues processed: 96 average time/residue: 0.7896 time to fit residues: 80.6745 Evaluate side-chains 96 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1119 MET Chi-restraints excluded: chain A residue 1162 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 102 optimal weight: 40.0000 chunk 23 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 581 ASN A 851 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.172036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.123153 restraints weight = 11852.253| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.56 r_work: 0.3360 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10667 Z= 0.188 Angle : 0.616 6.459 14749 Z= 0.350 Chirality : 0.042 0.150 1636 Planarity : 0.005 0.044 1539 Dihedral : 21.505 124.274 2098 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.70 % Allowed : 12.11 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.26), residues: 1023 helix: 1.87 (0.20), residues: 611 sheet: 0.36 (0.65), residues: 46 loop : -0.23 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 363 TYR 0.022 0.002 TYR A 284 PHE 0.021 0.002 PHE A1269 TRP 0.016 0.002 TRP A 849 HIS 0.007 0.002 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (10663) covalent geometry : angle 0.61546 / 0.35 (14746) hydrogen bonds : bond 0.06781 / 4.30 ( 549) hydrogen bonds : angle 4.06450 / 3.04 ( 1552) metal coordination : bond 0.00160 / 0.07 ( 4) metal coordination : angle 1.02996 / 0.48 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5343.61 seconds wall clock time: 91 minutes 38.81 seconds (5498.81 seconds total)