Starting phenix.real_space_refine on Fri Oct 23 14:15:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hdp_52071/10_2026/9hdp_52071.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hdp_52071/10_2026/9hdp_52071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hdp_52071/10_2026/9hdp_52071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hdp_52071/10_2026/9hdp_52071.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hdp_52071/10_2026/9hdp_52071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hdp_52071/10_2026/9hdp_52071.map" } resolution = 2.5 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 88 5.49 5 Mg 1 5.21 5 S 39 5.16 5 C 6359 2.51 5 N 1772 2.21 5 O 2030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10290 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' MG': 1, ' ZN': 1, 'D3T': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7304 SG CYS A1130 41.134 74.334 103.581 1.00 62.25 S ATOM 7339 SG CYS A1134 43.194 74.227 106.843 1.00 78.94 S ATOM 7445 SG CYS A1147 44.272 71.919 104.061 1.00 62.85 S Time building chain proxies: 2.43, per 1000 atoms: 0.24 Number of scatterers: 10290 At special positions: 0 Unit cell: (91.68, 142.295, 118.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 39 16.00 P 88 15.00 Mg 1 11.99 O 2030 8.00 N 1772 7.00 C 6359 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: 0.95 Conformation dependent library (CDL) restraints added in 316.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A1142 " pdb="ZN ZN A1302 " - pdb=" SG CYS A1147 " pdb="ZN ZN A1302 " - pdb=" SG CYS A1130 " pdb="ZN ZN A1302 " - 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: 52 helices and 6 sheets defined 66.0% alpha, 6.6% beta 36 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 259 through 278 removed outlier: 3.543A pdb=" N LYS A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 310 removed outlier: 3.778A pdb=" N ASP A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 333 through 370 removed outlier: 3.638A pdb=" N ARG A 369 " --> pdb=" O TRP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.634A pdb=" N TYR A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.503A pdb=" N MET A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.880A 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: 3.593A pdb=" N SER A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 484 removed outlier: 3.751A 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 507 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: 3.611A pdb=" N GLN A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N HIS A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LYS A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 558 " --> pdb=" O HIS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 589 removed outlier: 3.584A pdb=" N ILE A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 624 through 634 Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.737A pdb=" N VAL A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 3.889A pdb=" N GLN A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.561A 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 799 removed outlier: 4.026A 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: 3.702A 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: 4.044A 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 removed outlier: 3.936A pdb=" N GLY A 869 " --> pdb=" O LYS A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 886 through 893 Processing helix chain 'A' and resid 897 through 902 removed outlier: 3.885A pdb=" N ARG A 901 " --> pdb=" O ASP A 897 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 902 " --> pdb=" O GLN A 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 897 through 902' Processing helix chain 'A' and resid 910 through 916 removed outlier: 4.082A pdb=" N TYR A 914 " --> pdb=" O HIS A 910 " (cutoff:3.500A) removed outlier: 4.875A 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: 3.596A pdb=" N LEU A 967 " --> pdb=" O TRP A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 984 through 989 removed outlier: 3.513A pdb=" N ILE A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 994 Processing helix chain 'A' and resid 998 through 1006 removed outlier: 4.095A pdb=" N ASP A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 4.133A pdb=" N ILE A1014 " --> pdb=" O LYS A1010 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A1015 " --> pdb=" O TRP A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1031 removed outlier: 3.631A pdb=" N ARG A1031 " --> pdb=" O ILE A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1043 removed outlier: 3.763A pdb=" N PHE A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR A1043 " --> pdb=" O ILE A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 removed outlier: 3.616A pdb=" N GLN A1059 " --> pdb=" O ASN A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1076 removed outlier: 3.589A pdb=" N LYS A1071 " --> pdb=" O ASN A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1095 Processing helix chain 'A' and resid 1098 through 1110 removed outlier: 3.542A 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: 3.533A pdb=" N TRP A1154 " --> pdb=" O VAL A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1185 Processing helix chain 'A' and resid 1189 through 1206 removed outlier: 3.537A pdb=" N ARG A1195 " --> pdb=" O ASP A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1238 Processing helix chain 'A' and resid 1239 through 1258 removed outlier: 3.568A pdb=" N GLY A1245 " --> pdb=" O ILE A1241 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS A1249 " --> pdb=" O GLY A1245 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A1250 " --> pdb=" O THR A1246 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A1252 " --> pdb=" O MET A1248 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A1253 " --> pdb=" O LYS A1249 " (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 394 Processing sheet with id=AA2, first strand: chain 'A' and resid 530 through 536 removed outlier: 3.564A pdb=" N ALA A 512 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 5.281A 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: 3.564A pdb=" N ALA A 512 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 5.281A 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 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 768 471 hydrogen bonds defined for protein. 1359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2498 1.34 - 1.46: 2790 1.46 - 1.58: 5172 1.58 - 1.70: 169 1.70 - 1.82: 63 Bond restraints: 10692 Sorted by residual: bond pdb=" O3B D3T A1303 " pdb=" PG D3T A1303 " ideal model delta sigma weight residual 1.743 1.614 0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" C1' D3T A1303 " pdb=" N1 D3T A1303 " ideal model delta sigma weight residual 1.485 1.555 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" P DT E 25 " pdb=" O5' DT E 25 " ideal model delta sigma weight residual 1.593 1.627 -0.034 1.00e-02 1.00e+04 1.15e+01 bond pdb=" P DA F 1 " pdb=" OP1 DA F 1 " ideal model delta sigma weight residual 1.480 1.544 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C1' DT E 43 " pdb=" N1 DT E 43 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.63e+00 ... (remaining 10687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 13329 1.86 - 3.73: 1288 3.73 - 5.59: 141 5.59 - 7.46: 28 7.46 - 9.32: 5 Bond angle restraints: 14791 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 106.00 102.97 3.03 6.00e-01 2.78e+00 2.55e+01 angle pdb=" CA TYR A 914 " pdb=" CB TYR A 914 " pdb=" CG TYR A 914 " ideal model delta sigma weight residual 113.90 105.75 8.15 1.80e+00 3.09e-01 2.05e+01 angle pdb=" C4' DT B 16 " pdb=" O4' DT B 16 " pdb=" C1' DT B 16 " ideal model delta sigma weight residual 110.10 105.64 4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" O4' DT B 19 " pdb=" C1' DT B 19 " pdb=" N1 DT B 19 " ideal model delta sigma weight residual 108.00 111.12 -3.12 7.00e-01 2.04e+00 1.98e+01 angle pdb=" O4' DA F 1 " pdb=" C1' DA F 1 " pdb=" N9 DA F 1 " ideal model delta sigma weight residual 108.00 104.94 3.06 7.00e-01 2.04e+00 1.92e+01 ... (remaining 14786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5365 17.67 - 35.34: 581 35.34 - 53.00: 327 53.00 - 70.67: 80 70.67 - 88.34: 11 Dihedral angle restraints: 6364 sinusoidal: 3324 harmonic: 3040 Sorted by residual: dihedral pdb=" CA ASP A 918 " pdb=" C ASP A 918 " pdb=" N LYS A 919 " pdb=" CA LYS A 919 " ideal model delta harmonic sigma weight residual -180.00 -150.54 -29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA TRP A1145 " pdb=" C TRP A1145 " pdb=" N ASP A1146 " pdb=" CA ASP A1146 " ideal model delta harmonic sigma weight residual -180.00 -151.17 -28.83 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ASN A 277 " pdb=" C ASN A 277 " pdb=" N GLU A 278 " pdb=" CA GLU A 278 " ideal model delta harmonic sigma weight residual -180.00 -151.73 -28.27 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 6361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 1540 0.157 - 0.313: 92 0.313 - 0.469: 0 0.469 - 0.626: 3 0.626 - 0.782: 3 Chirality restraints: 1638 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 3.12 -0.78 2.00e-01 2.50e+01 1.53e+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 -3.05 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" P DA G 1 " pdb=" OP1 DA G 1 " pdb=" OP2 DA G 1 " pdb=" O5' DA G 1 " both_signs ideal model delta sigma weight residual True 2.34 2.97 -0.63 2.00e-01 2.50e+01 9.95e+00 ... (remaining 1635 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT B 18 " -0.034 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" N1 DT B 18 " 0.051 2.00e-02 2.50e+03 pdb=" C2 DT B 18 " -0.009 2.00e-02 2.50e+03 pdb=" O2 DT B 18 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DT B 18 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT B 18 " -0.010 2.00e-02 2.50e+03 pdb=" O4 DT B 18 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DT B 18 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT B 18 " -0.014 2.00e-02 2.50e+03 pdb=" C6 DT B 18 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1227 " 0.016 2.00e-02 2.50e+03 2.15e-02 9.28e+00 pdb=" CG TYR A1227 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A1227 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A1227 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A1227 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR A1227 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1227 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR A1227 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA F 1 " 0.029 2.00e-02 2.50e+03 1.84e-02 9.27e+00 pdb=" N9 DA F 1 " -0.051 2.00e-02 2.50e+03 pdb=" C8 DA F 1 " 0.015 2.00e-02 2.50e+03 pdb=" N7 DA F 1 " -0.001 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 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA F 1 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA F 1 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA F 1 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DA F 1 " -0.000 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 36 2.62 - 3.19: 8416 3.19 - 3.76: 15307 3.76 - 4.33: 22649 4.33 - 4.90: 34649 Nonbonded interactions: 81057 Sorted by model distance: nonbonded pdb=" OD2 ASP A 600 " pdb="MG MG A1301 " model vdw 2.053 2.170 nonbonded pdb="MG MG A1301 " pdb=" O2B D3T A1303 " model vdw 2.072 2.170 nonbonded pdb="MG MG A1301 " pdb=" O1G D3T A1303 " model vdw 2.176 2.170 nonbonded pdb=" O ALA A 601 " pdb="MG MG A1301 " model vdw 2.180 2.170 nonbonded pdb="MG MG A1301 " pdb=" O2A D3T A1303 " model vdw 2.216 2.170 ... (remaining 81052 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: 5.390 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.870 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 0.129 10696 Z= 0.514 Angle : 1.158 9.323 14794 Z= 0.777 Chirality : 0.090 0.782 1638 Planarity : 0.010 0.103 1540 Dihedral : 18.883 88.340 4384 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: -1.14 (0.22), residues: 1023 helix: -0.92 (0.17), residues: 592 sheet: 0.37 (0.68), residues: 46 loop : -0.32 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.003 ARG A 577 TYR 0.039 0.006 TYR A 284 PHE 0.026 0.004 PHE A 367 TRP 0.026 0.004 TRP A1158 HIS 0.013 0.002 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00820 / 0.51 (10692) covalent geometry : angle 1.15630 / 0.78 (14791) hydrogen bonds : bond 0.23130 / 14.80 ( 536) hydrogen bonds : angle 6.57222 / 4.71 ( 1507) metal coordination : bond 0.01890 / 0.88 ( 4) metal coordination : angle 4.88935 / 2.37 ( 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 147 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.352 Fit side-chains REVERT: A 266 MET cc_start: 0.7377 (tpt) cc_final: 0.7072 (tpt) REVERT: A 305 TYR cc_start: 0.6520 (t80) cc_final: 0.5920 (t80) REVERT: A 310 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7121 (pp20) REVERT: A 361 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7536 (mm-30) REVERT: A 379 ARG cc_start: 0.7741 (ttt-90) cc_final: 0.7473 (mmm160) REVERT: A 427 GLU cc_start: 0.7162 (tt0) cc_final: 0.6542 (mp0) REVERT: A 444 GLU cc_start: 0.6973 (tt0) cc_final: 0.6460 (mp0) REVERT: A 553 GLN cc_start: 0.7520 (mt0) cc_final: 0.7172 (mt0) REVERT: A 556 LYS cc_start: 0.7510 (mttt) cc_final: 0.6873 (mmpt) REVERT: A 682 GLU cc_start: 0.8099 (tt0) cc_final: 0.7715 (tp30) REVERT: A 703 ASP cc_start: 0.7599 (t0) cc_final: 0.7341 (t70) REVERT: A 748 GLN cc_start: 0.6178 (mt0) cc_final: 0.5893 (tm130) REVERT: A 798 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7744 (tttm) REVERT: A 815 MET cc_start: 0.8509 (ttp) cc_final: 0.8143 (ttm) REVERT: A 846 LYS cc_start: 0.8280 (tttp) cc_final: 0.7765 (ttpp) REVERT: A 851 GLN cc_start: 0.8534 (mt0) cc_final: 0.8203 (mp10) REVERT: A 853 ARG cc_start: 0.8444 (ptm160) cc_final: 0.7290 (ptt90) REVERT: A 863 GLN cc_start: 0.8026 (mt0) cc_final: 0.7186 (mm110) REVERT: A 864 LYS cc_start: 0.8190 (mttt) cc_final: 0.7976 (mttm) REVERT: A 908 MET cc_start: 0.6449 (mtt) cc_final: 0.5486 (tpt) REVERT: A 910 HIS cc_start: 0.7347 (m-70) cc_final: 0.6933 (m-70) REVERT: A 971 PRO cc_start: 0.7591 (Cg_exo) cc_final: 0.6345 (Cg_endo) REVERT: A 980 ASN cc_start: 0.6048 (m-40) cc_final: 0.5592 (m110) REVERT: A 1002 MET cc_start: 0.6192 (tpp) cc_final: 0.5653 (tpt) REVERT: A 1017 LYS cc_start: 0.6732 (ttpt) cc_final: 0.6461 (ttpp) REVERT: A 1064 LYS cc_start: 0.6026 (ttpt) cc_final: 0.5710 (mmtp) REVERT: A 1070 LYS cc_start: 0.7342 (mmtp) cc_final: 0.6990 (mmmm) REVERT: A 1077 ASN cc_start: 0.7676 (m-40) cc_final: 0.7466 (m110) REVERT: A 1122 ILE cc_start: 0.8304 (mt) cc_final: 0.8028 (mt) REVERT: A 1180 TYR cc_start: 0.8377 (m-80) cc_final: 0.8120 (m-80) REVERT: A 1191 ASP cc_start: 0.7415 (m-30) cc_final: 0.7146 (OUTLIER) REVERT: A 1249 LYS cc_start: 0.7690 (mttt) cc_final: 0.7153 (tptp) REVERT: A 1267 ARG cc_start: 0.8048 (mtt180) cc_final: 0.7593 (tpt-90) outliers start: 0 outliers final: 1 residues processed: 147 average time/residue: 0.7422 time to fit residues: 115.5855 Evaluate side-chains 102 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 106, 38] chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN A 443 GLN A 554 HIS A 587 ASN A 618 ASN A1055 ASN A1127 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.186317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.139869 restraints weight = 11352.722| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.66 r_work: 0.3523 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10696 Z= 0.179 Angle : 0.732 9.360 14794 Z= 0.408 Chirality : 0.047 0.177 1638 Planarity : 0.005 0.043 1540 Dihedral : 21.666 59.537 2132 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.17 % Allowed : 6.70 % Favored : 92.14 % 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: 1.11 (0.25), residues: 1023 helix: 1.39 (0.20), residues: 586 sheet: 0.15 (0.65), residues: 48 loop : -0.09 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 588 TYR 0.016 0.002 TYR A1184 PHE 0.016 0.002 PHE A 741 TRP 0.012 0.002 TRP A1224 HIS 0.004 0.001 HIS A1113 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (10692) covalent geometry : angle 0.73084 / 0.41 (14791) hydrogen bonds : bond 0.07196 / 4.71 ( 536) hydrogen bonds : angle 4.25136 / 3.06 ( 1507) metal coordination : bond 0.00355 / 0.17 ( 4) metal coordination : angle 2.59835 / 1.19 ( 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 127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.361 Fit side-chains REVERT: A 553 GLN cc_start: 0.7884 (mt0) cc_final: 0.7522 (mt0) REVERT: A 703 ASP cc_start: 0.7555 (t0) cc_final: 0.7353 (t70) REVERT: A 846 LYS cc_start: 0.8257 (tttp) cc_final: 0.7935 (ttpp) REVERT: A 863 GLN cc_start: 0.7870 (mt0) cc_final: 0.7219 (mm110) REVERT: A 908 MET cc_start: 0.5891 (mtt) cc_final: 0.5351 (tpt) REVERT: A 910 HIS cc_start: 0.7202 (m-70) cc_final: 0.6884 (m-70) REVERT: A 914 TYR cc_start: 0.6619 (m-80) cc_final: 0.6417 (m-10) REVERT: A 980 ASN cc_start: 0.5779 (m-40) cc_final: 0.5377 (m110) REVERT: A 1002 MET cc_start: 0.6436 (tpp) cc_final: 0.5902 (tpt) REVERT: A 1017 LYS cc_start: 0.6425 (ttpt) cc_final: 0.6153 (ttpp) REVERT: A 1118 ARG cc_start: 0.7833 (mmm-85) cc_final: 0.7594 (mmm-85) outliers start: 11 outliers final: 3 residues processed: 121 average time/residue: 0.7531 time to fit residues: 96.6247 Evaluate side-chains 96 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 1191 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [5, 49, 91, 73, 36, 31, 16, 71, 12, 44, 102] chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 102 optimal weight: 30.0000 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.187729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141894 restraints weight = 11214.786| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.72 r_work: 0.3499 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10696 Z= 0.150 Angle : 0.611 9.064 14794 Z= 0.350 Chirality : 0.042 0.166 1638 Planarity : 0.004 0.048 1540 Dihedral : 21.520 59.617 2132 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.13 % Allowed : 9.25 % Favored : 88.63 % 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: 1.56 (0.26), residues: 1023 helix: 1.82 (0.21), residues: 587 sheet: 0.52 (0.65), residues: 46 loop : -0.04 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 588 TYR 0.012 0.002 TYR A 284 PHE 0.017 0.002 PHE A 367 TRP 0.016 0.001 TRP A 799 HIS 0.004 0.001 HIS A1113 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (10692) covalent geometry : angle 0.60940 / 0.35 (14791) hydrogen bonds : bond 0.06243 / 4.08 ( 536) hydrogen bonds : angle 3.88503 / 2.81 ( 1507) metal coordination : bond 0.00501 / 0.21 ( 4) metal coordination : angle 2.84888 / 1.31 ( 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 126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.368 Fit side-chains REVERT: A 522 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6757 (mtt-85) REVERT: A 553 GLN cc_start: 0.8071 (mt0) cc_final: 0.7689 (mt0) REVERT: A 839 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7651 (mm-30) REVERT: A 846 LYS cc_start: 0.8260 (tttp) cc_final: 0.8013 (ttpp) REVERT: A 853 ARG cc_start: 0.8338 (ptp-170) cc_final: 0.7354 (ppt-90) REVERT: A 863 GLN cc_start: 0.7839 (mt0) cc_final: 0.7237 (mm110) REVERT: A 908 MET cc_start: 0.6089 (mtt) cc_final: 0.5448 (tpt) REVERT: A 910 HIS cc_start: 0.7077 (m-70) cc_final: 0.6728 (m-70) REVERT: A 980 ASN cc_start: 0.5755 (m-40) cc_final: 0.5225 (m-40) REVERT: A 1002 MET cc_start: 0.6410 (tpp) cc_final: 0.5938 (tpt) REVERT: A 1017 LYS cc_start: 0.6449 (ttpt) cc_final: 0.6127 (tmmt) outliers start: 20 outliers final: 4 residues processed: 116 average time/residue: 0.6634 time to fit residues: 81.9532 Evaluate side-chains 96 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 839 GLU Chi-restraints excluded: chain A residue 1269 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [47, 1, 92, 58, 70, 97, 33, 83, 9, 96, 36] chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN A 710 ASN A 772 GLN A 925 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.186216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.138867 restraints weight = 11124.652| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.73 r_work: 0.3507 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10696 Z= 0.148 Angle : 0.599 9.141 14794 Z= 0.336 Chirality : 0.040 0.168 1638 Planarity : 0.004 0.051 1540 Dihedral : 21.509 59.926 2132 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.23 % Allowed : 10.41 % Favored : 87.35 % 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: 1.62 (0.26), residues: 1023 helix: 1.94 (0.21), residues: 585 sheet: 0.21 (0.66), residues: 48 loop : -0.09 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1267 TYR 0.015 0.002 TYR A1189 PHE 0.017 0.002 PHE A 367 TRP 0.019 0.001 TRP A 799 HIS 0.004 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (10692) covalent geometry : angle 0.59760 / 0.34 (14791) hydrogen bonds : bond 0.05807 / 3.82 ( 536) hydrogen bonds : angle 3.76052 / 2.70 ( 1507) metal coordination : bond 0.00354 / 0.15 ( 4) metal coordination : angle 2.77406 / 1.26 ( 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 121 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.381 Fit side-chains REVERT: A 379 ARG cc_start: 0.7604 (mmm160) cc_final: 0.7177 (mmm160) REVERT: A 522 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6908 (mtt-85) REVERT: A 553 GLN cc_start: 0.8232 (mt0) cc_final: 0.7834 (mt0) REVERT: A 694 GLU cc_start: 0.7464 (tt0) cc_final: 0.7249 (tt0) REVERT: A 846 LYS cc_start: 0.8272 (tttp) cc_final: 0.8026 (ttpp) REVERT: A 863 GLN cc_start: 0.7813 (mt0) cc_final: 0.7217 (mm110) REVERT: A 870 ILE cc_start: 0.8204 (mt) cc_final: 0.7999 (mm) REVERT: A 910 HIS cc_start: 0.6944 (m-70) cc_final: 0.6594 (m-70) REVERT: A 914 TYR cc_start: 0.7216 (m-80) cc_final: 0.7012 (m-10) REVERT: A 919 LYS cc_start: 0.8392 (tttt) cc_final: 0.8076 (ttpp) REVERT: A 1002 MET cc_start: 0.6604 (tpp) cc_final: 0.6153 (tpt) REVERT: A 1076 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.5376 (mtt) outliers start: 21 outliers final: 6 residues processed: 108 average time/residue: 0.6216 time to fit residues: 71.7274 Evaluate side-chains 99 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 1076 MET 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: [100, 68, 74, 40, 13, 43, 36, 15, 24, 97, 55] chunk 100 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 13 optimal weight: 0.0370 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.186684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139833 restraints weight = 11101.601| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.87 r_work: 0.3501 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10696 Z= 0.131 Angle : 0.556 9.064 14794 Z= 0.315 Chirality : 0.039 0.158 1638 Planarity : 0.004 0.054 1540 Dihedral : 21.401 59.957 2132 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.49 % Allowed : 11.37 % Favored : 87.14 % 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: 1.71 (0.26), residues: 1023 helix: 2.05 (0.21), residues: 590 sheet: 0.19 (0.65), residues: 48 loop : -0.15 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.009 0.001 TYR A1112 PHE 0.015 0.001 PHE A 367 TRP 0.019 0.001 TRP A 799 HIS 0.003 0.001 HIS A1113 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (10692) covalent geometry : angle 0.55497 / 0.32 (14791) hydrogen bonds : bond 0.05356 / 3.53 ( 536) hydrogen bonds : angle 3.65017 / 2.63 ( 1507) metal coordination : bond 0.00530 / 0.21 ( 4) metal coordination : angle 2.53607 / 1.16 ( 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 114 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.282 Fit side-chains REVERT: A 271 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7927 (mttt) REVERT: A 379 ARG cc_start: 0.7474 (mmm160) cc_final: 0.6973 (mmm160) REVERT: A 381 ILE cc_start: 0.7445 (pt) cc_final: 0.7206 (pp) REVERT: A 522 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6787 (mtt-85) REVERT: A 553 GLN cc_start: 0.8224 (mt0) cc_final: 0.7823 (mt0) REVERT: A 846 LYS cc_start: 0.8282 (tttp) cc_final: 0.8031 (ttpp) REVERT: A 863 GLN cc_start: 0.7794 (mt0) cc_final: 0.7233 (mm110) REVERT: A 870 ILE cc_start: 0.8183 (mt) cc_final: 0.7969 (mm) REVERT: A 908 MET cc_start: 0.6262 (mtp) cc_final: 0.5388 (mmm) REVERT: A 910 HIS cc_start: 0.6813 (m-70) cc_final: 0.6479 (m-70) REVERT: A 928 LYS cc_start: 0.7561 (tttt) cc_final: 0.7286 (tttm) REVERT: A 1002 MET cc_start: 0.6737 (tpp) cc_final: 0.6313 (tpt) outliers start: 14 outliers final: 7 residues processed: 108 average time/residue: 0.6332 time to fit residues: 73.1813 Evaluate side-chains 95 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 1227 TYR 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: [58, 66, 104, 83, 20, 61, 96, 92, 97, 0, 35] chunk 58 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 30.0000 chunk 83 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.187178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.139349 restraints weight = 11350.422| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.88 r_work: 0.3507 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10696 Z= 0.128 Angle : 0.558 8.628 14794 Z= 0.314 Chirality : 0.038 0.153 1638 Planarity : 0.004 0.055 1540 Dihedral : 21.328 62.473 2132 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.91 % Allowed : 11.90 % 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: 1.78 (0.26), residues: 1023 helix: 2.11 (0.21), residues: 590 sheet: 0.14 (0.67), residues: 48 loop : -0.10 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 588 TYR 0.014 0.001 TYR A1232 PHE 0.015 0.001 PHE A 367 TRP 0.018 0.001 TRP A 799 HIS 0.003 0.001 HIS A1113 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 (10692) covalent geometry : angle 0.55703 / 0.31 (14791) hydrogen bonds : bond 0.05238 / 3.47 ( 536) hydrogen bonds : angle 3.60253 / 2.59 ( 1507) metal coordination : bond 0.00461 / 0.18 ( 4) metal coordination : angle 2.39347 / 1.09 ( 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 115 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.379 Fit side-chains REVERT: A 271 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7877 (mttt) REVERT: A 375 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7090 (tpp-160) REVERT: A 379 ARG cc_start: 0.7405 (mmm160) cc_final: 0.6882 (mmm160) REVERT: A 381 ILE cc_start: 0.7448 (pt) cc_final: 0.7199 (pp) REVERT: A 501 LYS cc_start: 0.7493 (tptp) cc_final: 0.7192 (tptp) REVERT: A 522 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6779 (mtt-85) REVERT: A 553 GLN cc_start: 0.8262 (mt0) cc_final: 0.8011 (mt0) REVERT: A 748 GLN cc_start: 0.6811 (mp10) cc_final: 0.6082 (tm130) REVERT: A 846 LYS cc_start: 0.8299 (tttp) cc_final: 0.8039 (ttpp) REVERT: A 863 GLN cc_start: 0.7810 (mt0) cc_final: 0.7228 (mm110) REVERT: A 870 ILE cc_start: 0.8179 (mt) cc_final: 0.7955 (mm) REVERT: A 908 MET cc_start: 0.6265 (mtp) cc_final: 0.5351 (mmm) REVERT: A 910 HIS cc_start: 0.6785 (m-70) cc_final: 0.6448 (m-70) REVERT: A 928 LYS cc_start: 0.7556 (tttt) cc_final: 0.7255 (tttm) REVERT: A 976 THR cc_start: 0.6097 (m) cc_final: 0.5604 (p) REVERT: A 1002 MET cc_start: 0.6740 (tpp) cc_final: 0.6304 (tpt) REVERT: A 1076 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.5519 (mtt) outliers start: 18 outliers final: 7 residues processed: 107 average time/residue: 0.6774 time to fit residues: 77.3595 Evaluate side-chains 100 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 1076 MET Chi-restraints excluded: chain A residue 1227 TYR 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: [88, 77, 89, 45, 78, 86, 81, 76, 97, 2, 102] chunk 88 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 86 optimal weight: 0.2980 chunk 81 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 102 optimal weight: 40.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.187946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140753 restraints weight = 11214.781| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.02 r_work: 0.3520 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10696 Z= 0.122 Angle : 0.542 9.211 14794 Z= 0.307 Chirality : 0.038 0.143 1638 Planarity : 0.004 0.055 1540 Dihedral : 21.236 63.675 2132 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.59 % Allowed : 12.75 % Favored : 85.65 % 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: 1.86 (0.26), residues: 1023 helix: 2.17 (0.21), residues: 590 sheet: 0.14 (0.67), residues: 48 loop : -0.05 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1118 TYR 0.010 0.001 TYR A1232 PHE 0.013 0.001 PHE A 367 TRP 0.033 0.001 TRP A 799 HIS 0.003 0.001 HIS A1113 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.12 (10692) covalent geometry : angle 0.54071 / 0.31 (14791) hydrogen bonds : bond 0.04948 / 3.29 ( 536) hydrogen bonds : angle 3.56759 / 2.57 ( 1507) metal coordination : bond 0.00501 / 0.20 ( 4) metal coordination : angle 2.31404 / 1.06 ( 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 111 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.364 Fit side-chains REVERT: A 264 ASN cc_start: 0.7244 (OUTLIER) cc_final: 0.6795 (m-40) REVERT: A 271 LYS cc_start: 0.8188 (mtpp) cc_final: 0.7929 (mttt) REVERT: A 368 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: A 375 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7060 (tpp-160) REVERT: A 379 ARG cc_start: 0.7353 (mmm160) cc_final: 0.6812 (mmm160) REVERT: A 381 ILE cc_start: 0.7297 (pt) cc_final: 0.7071 (pp) REVERT: A 501 LYS cc_start: 0.7514 (tptp) cc_final: 0.7223 (tptp) REVERT: A 522 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6794 (mtt-85) REVERT: A 553 GLN cc_start: 0.8252 (mt0) cc_final: 0.8003 (mt0) REVERT: A 748 GLN cc_start: 0.6872 (mp10) cc_final: 0.6121 (tm130) REVERT: A 846 LYS cc_start: 0.8282 (tttp) cc_final: 0.7977 (ttpp) REVERT: A 863 GLN cc_start: 0.7783 (mt0) cc_final: 0.7261 (mm110) REVERT: A 870 ILE cc_start: 0.8160 (mt) cc_final: 0.7931 (mm) REVERT: A 908 MET cc_start: 0.6135 (mtp) cc_final: 0.5270 (mmm) REVERT: A 910 HIS cc_start: 0.6738 (m-70) cc_final: 0.6393 (m-70) REVERT: A 928 LYS cc_start: 0.7539 (tttt) cc_final: 0.7231 (tttm) REVERT: A 1002 MET cc_start: 0.6829 (tpp) cc_final: 0.6418 (tpt) outliers start: 15 outliers final: 8 residues processed: 105 average time/residue: 0.6970 time to fit residues: 77.7426 Evaluate side-chains 103 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 1063 LYS Chi-restraints excluded: chain A residue 1227 TYR Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [15, 106, 54, 16, 91, 42, 0, 87, 45, 58, 12] chunk 15 optimal weight: 0.0870 chunk 106 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.188110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140428 restraints weight = 11219.464| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.99 r_work: 0.3516 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10696 Z= 0.121 Angle : 0.537 8.735 14794 Z= 0.302 Chirality : 0.038 0.141 1638 Planarity : 0.004 0.055 1540 Dihedral : 21.131 64.122 2132 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.02 % Allowed : 12.96 % Favored : 85.02 % 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: 1.90 (0.26), residues: 1023 helix: 2.19 (0.21), residues: 590 sheet: 0.14 (0.67), residues: 48 loop : -0.02 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1118 TYR 0.010 0.001 TYR A 731 PHE 0.014 0.001 PHE A 367 TRP 0.032 0.001 TRP A 799 HIS 0.002 0.001 HIS A1113 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.12 (10692) covalent geometry : angle 0.53628 / 0.30 (14791) hydrogen bonds : bond 0.04923 / 3.28 ( 536) hydrogen bonds : angle 3.54740 / 2.55 ( 1507) metal coordination : bond 0.00435 / 0.17 ( 4) metal coordination : angle 2.12987 / 0.97 ( 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 113 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.383 Fit side-chains REVERT: A 264 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.6795 (m-40) REVERT: A 271 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7936 (mttt) REVERT: A 368 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: A 375 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7108 (tpp-160) REVERT: A 379 ARG cc_start: 0.7433 (mmm160) cc_final: 0.6836 (mmm160) REVERT: A 501 LYS cc_start: 0.7584 (tptp) cc_final: 0.7374 (tptp) REVERT: A 522 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6761 (mtt-85) REVERT: A 553 GLN cc_start: 0.8293 (mt0) cc_final: 0.8005 (mt0) REVERT: A 683 LYS cc_start: 0.8029 (mttp) cc_final: 0.7807 (mttp) REVERT: A 846 LYS cc_start: 0.8288 (tttp) cc_final: 0.7987 (ttpp) REVERT: A 863 GLN cc_start: 0.7799 (mt0) cc_final: 0.7278 (mm110) REVERT: A 870 ILE cc_start: 0.8152 (mt) cc_final: 0.7901 (mm) REVERT: A 910 HIS cc_start: 0.6542 (m-70) cc_final: 0.6221 (m-70) REVERT: A 928 LYS cc_start: 0.7572 (tttt) cc_final: 0.7266 (tttm) REVERT: A 1002 MET cc_start: 0.6745 (tpp) cc_final: 0.6398 (tpt) REVERT: A 1076 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.5666 (mtt) REVERT: A 1129 ARG cc_start: 0.7645 (mtp85) cc_final: 0.7384 (mtt90) outliers start: 19 outliers final: 9 residues processed: 105 average time/residue: 0.7005 time to fit residues: 78.2470 Evaluate side-chains 103 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 1063 LYS Chi-restraints excluded: chain A residue 1076 MET Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1227 TYR Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [105, 57, 85, 25, 88, 41, 37, 77, 34, 81, 18] chunk 105 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 88 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 GLN A 443 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.187876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140752 restraints weight = 11239.826| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.05 r_work: 0.3521 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10696 Z= 0.123 Angle : 0.546 9.080 14794 Z= 0.306 Chirality : 0.038 0.142 1638 Planarity : 0.004 0.054 1540 Dihedral : 21.085 64.106 2132 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.70 % Allowed : 13.60 % Favored : 84.70 % 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: 1.91 (0.26), residues: 1023 helix: 2.19 (0.21), residues: 590 sheet: 0.20 (0.67), residues: 48 loop : -0.01 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1267 TYR 0.010 0.001 TYR A 731 PHE 0.015 0.001 PHE A 367 TRP 0.032 0.001 TRP A 799 HIS 0.003 0.001 HIS A1113 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (10692) covalent geometry : angle 0.54525 / 0.31 (14791) hydrogen bonds : bond 0.04989 / 3.32 ( 536) hydrogen bonds : angle 3.57301 / 2.57 ( 1507) metal coordination : bond 0.00408 / 0.16 ( 4) metal coordination : angle 2.11164 / 0.97 ( 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 112 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.348 Fit side-chains REVERT: A 264 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6792 (m-40) REVERT: A 271 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7943 (mttt) REVERT: A 368 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: A 375 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7087 (tpp-160) REVERT: A 379 ARG cc_start: 0.7430 (mmm160) cc_final: 0.6837 (mmm160) REVERT: A 522 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6752 (mtt-85) REVERT: A 553 GLN cc_start: 0.8283 (mt0) cc_final: 0.8001 (mt0) REVERT: A 846 LYS cc_start: 0.8288 (tttp) cc_final: 0.7982 (ttpp) REVERT: A 863 GLN cc_start: 0.7796 (mt0) cc_final: 0.7279 (mm110) REVERT: A 870 ILE cc_start: 0.8165 (mt) cc_final: 0.7920 (mm) REVERT: A 910 HIS cc_start: 0.6543 (m-70) cc_final: 0.6217 (m-70) REVERT: A 928 LYS cc_start: 0.7540 (tttt) cc_final: 0.7222 (tttm) REVERT: A 1076 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.5668 (mtt) REVERT: A 1129 ARG cc_start: 0.7683 (mtp85) cc_final: 0.7443 (mtt90) outliers start: 16 outliers final: 9 residues processed: 104 average time/residue: 0.7088 time to fit residues: 78.3213 Evaluate side-chains 105 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 1063 LYS Chi-restraints excluded: chain A residue 1076 MET Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1227 TYR Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [62, 11, 54, 64, 3, 36, 89, 42, 70, 104, 59] chunk 62 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 0.0170 chunk 104 optimal weight: 30.0000 chunk 59 optimal weight: 0.8980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 GLN A1066 ASN A1182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.188584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.139896 restraints weight = 11051.309| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.80 r_work: 0.3536 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10696 Z= 0.118 Angle : 0.538 9.376 14794 Z= 0.301 Chirality : 0.037 0.142 1638 Planarity : 0.004 0.055 1540 Dihedral : 21.013 63.380 2132 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.59 % Allowed : 14.03 % Favored : 84.38 % 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: 1.89 (0.26), residues: 1023 helix: 2.21 (0.21), residues: 593 sheet: 0.19 (0.67), residues: 48 loop : -0.09 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1267 TYR 0.009 0.001 TYR A 731 PHE 0.013 0.001 PHE A 367 TRP 0.038 0.001 TRP A 799 HIS 0.002 0.001 HIS A1113 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.12 (10692) covalent geometry : angle 0.53684 / 0.30 (14791) hydrogen bonds : bond 0.04703 / 3.13 ( 536) hydrogen bonds : angle 3.51373 / 2.53 ( 1507) metal coordination : bond 0.00397 / 0.16 ( 4) metal coordination : angle 1.98313 / 0.91 ( 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 111 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.366 Fit side-chains REVERT: A 260 TYR cc_start: 0.6072 (OUTLIER) cc_final: 0.5662 (t80) REVERT: A 264 ASN cc_start: 0.7228 (OUTLIER) cc_final: 0.6699 (m-40) REVERT: A 271 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7914 (mttt) REVERT: A 368 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: A 375 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7080 (tpp-160) REVERT: A 379 ARG cc_start: 0.7425 (mmm160) cc_final: 0.6813 (mmm160) REVERT: A 522 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6760 (mtt-85) REVERT: A 553 GLN cc_start: 0.8267 (mt0) cc_final: 0.7978 (mt0) REVERT: A 846 LYS cc_start: 0.8274 (tttp) cc_final: 0.7968 (ttpp) REVERT: A 863 GLN cc_start: 0.7780 (mt0) cc_final: 0.7266 (mm110) REVERT: A 870 ILE cc_start: 0.8141 (mt) cc_final: 0.7903 (mm) REVERT: A 910 HIS cc_start: 0.6551 (m-70) cc_final: 0.6234 (m-70) REVERT: A 928 LYS cc_start: 0.7540 (tttt) cc_final: 0.7224 (tttm) REVERT: A 1002 MET cc_start: 0.6655 (tpt) cc_final: 0.5896 (mmt) REVERT: A 1076 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.5657 (mtt) REVERT: A 1129 ARG cc_start: 0.7636 (mtp85) cc_final: 0.7415 (mtt90) outliers start: 15 outliers final: 8 residues processed: 104 average time/residue: 0.7012 time to fit residues: 77.6975 Evaluate side-chains 104 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 TYR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 1063 LYS Chi-restraints excluded: chain A residue 1076 MET Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1227 TYR Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: [31, 23, 105, 27, 88, 51, 94, 71, 13, 47, 4] chunk 31 optimal weight: 0.0270 chunk 23 optimal weight: 3.9990 chunk 105 optimal weight: 30.0000 chunk 27 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 51 optimal weight: 0.0770 chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 ASN A 443 GLN A 851 GLN A1066 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.188171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.139563 restraints weight = 11152.227| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.78 r_work: 0.3529 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10696 Z= 0.122 Angle : 0.542 9.415 14794 Z= 0.304 Chirality : 0.037 0.141 1638 Planarity : 0.004 0.055 1540 Dihedral : 20.968 63.413 2132 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.70 % Allowed : 13.82 % Favored : 84.48 % 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: 1.89 (0.26), residues: 1023 helix: 2.20 (0.21), residues: 593 sheet: 0.19 (0.67), residues: 48 loop : -0.08 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1118 TYR 0.010 0.001 TYR A 731 PHE 0.015 0.001 PHE A 367 TRP 0.039 0.002 TRP A 799 HIS 0.002 0.001 HIS A1113 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.12 (10692) covalent geometry : angle 0.54131 / 0.30 (14791) hydrogen bonds : bond 0.04836 / 3.22 ( 536) hydrogen bonds : angle 3.54497 / 2.55 ( 1507) metal coordination : bond 0.00394 / 0.16 ( 4) metal coordination : angle 1.99118 / 0.91 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4798.95 seconds wall clock time: 82 minutes 7.57 seconds (4927.57 seconds total)