Starting phenix.real_space_refine on Sun Oct 25 09:09:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vpc_21308/10_2026/6vpc_21308.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vpc_21308/10_2026/6vpc_21308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vpc_21308/10_2026/6vpc_21308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vpc_21308/10_2026/6vpc_21308.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vpc_21308/10_2026/6vpc_21308.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vpc_21308/10_2026/6vpc_21308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vpc_21308/10_2026/6vpc_21308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vpc_21308/10_2026/6vpc_21308.map" } resolution = 3.2 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= 0.004 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 2 6.06 5 P 154 5.49 5 Mg 3 5.21 5 S 44 5.16 5 C 9806 2.51 5 N 2880 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 16309 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1724 Classifications: {'RNAv2': 81} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 40, 'rna3p_pyr': 33} Link IDs: {'rna2p': 7, 'rna3p': 73} Chain: "B" Number of atoms: 10766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1332, 10766 Classifications: {'peptide': 1332} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 35, 'TRANS': 1296} Chain breaks: 3 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 8, 'ASP:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 83 Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 824 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "D" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 659 Classifications: {'DNA': 32, 'RNA': 1} Modifications used: {'rna2p': 1} Link IDs: {'rna2p': 1, 'rna3p': 31} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1131 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 4, 'TRANS': 140} Chain: "F" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1200 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" 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 14640 SG CYS E 87 61.313 28.543 137.297 1.00181.35 S ATOM 14661 SG CYS E 90 64.230 28.752 136.279 1.00186.75 S ATOM 15771 SG CYS F 87 60.016 41.060 133.993 1.00183.68 S ATOM 15792 SG CYS F 90 60.736 41.779 137.525 1.00184.30 S Time building chain proxies: 3.19, per 1000 atoms: 0.20 Number of scatterers: 16309 At special positions: 0 Unit cell: (94.94, 124.08, 168.26, 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 2 29.99 S 44 16.00 P 154 15.00 Mg 3 11.99 O 3420 8.00 N 2880 7.00 C 9806 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: 1.52 Conformation dependent library (CDL) restraints added in 572.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 90 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 57 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 87 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 57 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 87 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 90 " 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3090 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 12 sheets defined 53.9% alpha, 8.5% beta 55 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'B' and resid 256 through 291 removed outlier: 5.045A pdb=" N ASN B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 289 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 318 through 329 Processing helix chain 'B' and resid 331 through 342 removed outlier: 3.743A pdb=" N LEU B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 361 removed outlier: 3.602A pdb=" N PHE B 361 " --> pdb=" O HIS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 393 Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 414 through 425 Processing helix chain 'B' and resid 433 through 443 Processing helix chain 'B' and resid 467 through 480 Processing helix chain 'B' and resid 483 through 499 removed outlier: 4.469A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 removed outlier: 3.760A pdb=" N ARG B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 540 Processing helix chain 'B' and resid 543 through 549 Processing helix chain 'B' and resid 555 through 561 Processing helix chain 'B' and resid 565 through 580 Proline residue: B 575 - end of helix Processing helix chain 'B' and resid 583 through 592 removed outlier: 3.822A pdb=" N VAL B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 607 removed outlier: 3.926A pdb=" N SER B 606 " --> pdb=" O ASP B 603 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 607 " --> pdb=" O ASN B 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 603 through 607' Processing helix chain 'B' and resid 608 through 624 removed outlier: 4.162A pdb=" N HIS B 612 " --> pdb=" O PRO B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 removed outlier: 3.591A pdb=" N LYS B 631 " --> pdb=" O TYR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 643 Processing helix chain 'B' and resid 674 through 679 Processing helix chain 'B' and resid 680 through 691 Processing helix chain 'B' and resid 709 through 722 Processing helix chain 'B' and resid 738 through 749 Processing helix chain 'B' and resid 757 through 765 Processing helix chain 'B' and resid 765 through 771 Processing helix chain 'B' and resid 788 through 799 Processing helix chain 'B' and resid 800 through 806 Processing helix chain 'B' and resid 809 through 823 Processing helix chain 'B' and resid 825 through 834 Processing helix chain 'B' and resid 835 through 839 removed outlier: 4.336A pdb=" N HIS B 838 " --> pdb=" O THR B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 851 removed outlier: 3.538A pdb=" N MET B 845 " --> pdb=" O ASP B 841 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG B 850 " --> pdb=" O LYS B 846 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 851 " --> pdb=" O GLN B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 866 Processing helix chain 'B' and resid 875 through 882 Processing helix chain 'B' and resid 889 through 896 Processing helix chain 'B' and resid 900 through 906 Processing helix chain 'B' and resid 917 through 923 Processing helix chain 'B' and resid 927 through 948 Processing helix chain 'B' and resid 974 through 989 Processing helix chain 'B' and resid 991 through 996 Processing helix chain 'B' and resid 999 through 1003 Processing helix chain 'B' and resid 1005 through 1014 Processing helix chain 'B' and resid 1029 through 1033 Processing helix chain 'B' and resid 1048 through 1050 No H-bonds generated for 'chain 'B' and resid 1048 through 1050' Processing helix chain 'B' and resid 1057 through 1062 Processing helix chain 'B' and resid 1069 through 1086 removed outlier: 5.449A pdb=" N ASN B1078 " --> pdb=" O LYS B1074 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N TYR B1079 " --> pdb=" O LYS B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1102 Processing helix chain 'B' and resid 1122 through 1137 Processing helix chain 'B' and resid 1156 through 1168 removed outlier: 4.392A pdb=" N VAL B1160 " --> pdb=" O LYS B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1198 removed outlier: 4.270A pdb=" N ALA B1181 " --> pdb=" O ASN B1177 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B1184 " --> pdb=" O HIS B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1201 through 1206 Processing helix chain 'B' and resid 1216 through 1220 removed outlier: 3.562A pdb=" N ALA B1220 " --> pdb=" O LYS B1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1227 through 1240 removed outlier: 3.702A pdb=" N MET B1240 " --> pdb=" O TYR B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1241 through 1244 Processing helix chain 'B' and resid 1275 through 1285 Processing helix chain 'B' and resid 1324 through 1329 Processing helix chain 'B' and resid 1367 through 1374 Processing helix chain 'B' and resid 1374 through 1383 Processing helix chain 'B' and resid 1388 through 1392 Processing helix chain 'B' and resid 1404 through 1406 No H-bonds generated for 'chain 'B' and resid 1404 through 1406' Processing helix chain 'B' and resid 1426 through 1438 Processing helix chain 'B' and resid 1445 through 1459 removed outlier: 3.859A pdb=" N ASN B1449 " --> pdb=" O SER B1445 " (cutoff:3.500A) Processing helix chain 'B' and resid 1460 through 1477 removed outlier: 4.369A pdb=" N ASP B1464 " --> pdb=" O LYS B1460 " (cutoff:3.500A) Processing helix chain 'B' and resid 1480 through 1494 Processing helix chain 'B' and resid 1498 through 1509 Processing helix chain 'B' and resid 1510 through 1513 Processing helix chain 'B' and resid 1537 through 1541 Processing helix chain 'E' and resid 7 through 25 Processing helix chain 'E' and resid 47 through 52 Processing helix chain 'E' and resid 57 through 71 Processing helix chain 'E' and resid 87 through 98 Processing helix chain 'E' and resid 137 through 149 removed outlier: 3.565A pdb=" N CYS E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 25 Processing helix chain 'F' and resid 47 through 52 Processing helix chain 'F' and resid 57 through 71 Processing helix chain 'F' and resid 87 through 98 Processing helix chain 'F' and resid 137 through 150 Processing helix chain 'F' and resid 153 through 160 Processing sheet with id=AA1, first strand: chain 'B' and resid 1151 through 1155 removed outlier: 4.333A pdb=" N MET B 960 " --> pdb=" O LEU B1155 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN B 955 " --> pdb=" O TYR B 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 226 through 230 Processing sheet with id=AA3, first strand: chain 'B' and resid 232 through 233 removed outlier: 4.523A pdb=" N LEU B1400 " --> pdb=" O ILE B1545 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 725 through 726 Processing sheet with id=AA5, first strand: chain 'B' and resid 1034 through 1037 Processing sheet with id=AA6, first strand: chain 'B' and resid 1246 through 1248 Processing sheet with id=AA7, first strand: chain 'B' and resid 1260 through 1262 removed outlier: 6.674A pdb=" N GLU B1261 " --> pdb=" O VAL B1270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1317 through 1318 Processing sheet with id=AA9, first strand: chain 'B' and resid 1353 through 1364 removed outlier: 3.524A pdb=" N LYS B1355 " --> pdb=" O VAL B1346 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B1346 " --> pdb=" O LYS B1355 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B1338 " --> pdb=" O ILE B1363 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B1393 " --> pdb=" O LEU B1341 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1521 through 1523 Processing sheet with id=AB2, first strand: chain 'E' and resid 39 through 45 removed outlier: 6.594A pdb=" N LEU E 34 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU E 43 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA E 32 " --> pdb=" O GLU E 43 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU E 80 " --> pdb=" O VAL E 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 39 through 45 removed outlier: 5.206A pdb=" N VAL F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU F 36 " --> pdb=" O VAL F 40 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1830 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 137 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 1.99 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: 4484 1.34 - 1.46: 3647 1.46 - 1.58: 8413 1.58 - 1.70: 304 1.70 - 1.82: 78 Bond restraints: 16926 Sorted by residual: bond pdb=" C2 8AZ D 26 " pdb=" N3 8AZ D 26 " ideal model delta sigma weight residual 1.297 1.466 -0.169 2.00e-02 2.50e+03 7.16e+01 bond pdb=" N3 8AZ D 26 " pdb=" C4 8AZ D 26 " ideal model delta sigma weight residual 1.360 1.489 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" N1 8AZ D 26 " pdb=" C2 8AZ D 26 " ideal model delta sigma weight residual 1.341 1.449 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" N7 8AZ D 26 " pdb=" N8 8AZ D 26 " ideal model delta sigma weight residual 1.285 1.370 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5 8AZ D 26 " pdb=" C6 8AZ D 26 " ideal model delta sigma weight residual 1.480 1.551 -0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 16921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 23375 2.88 - 5.76: 137 5.76 - 8.64: 7 8.64 - 11.52: 3 11.52 - 14.40: 1 Bond angle restraints: 23523 Sorted by residual: angle pdb=" C5 8AZ D 26 " pdb=" C6 8AZ D 26 " pdb=" N1 8AZ D 26 " ideal model delta sigma weight residual 104.59 118.99 -14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" C LEU B 839 " pdb=" N PHE B 840 " pdb=" CA PHE B 840 " ideal model delta sigma weight residual 122.46 114.02 8.44 1.80e+00 3.09e-01 2.20e+01 angle pdb=" O4' DA C 13 " pdb=" C4' DA C 13 " pdb=" C3' DA C 13 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" N3 DT D 20 " pdb=" C4 DT D 20 " pdb=" O4 DT D 20 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT C 5 " pdb=" C4 DT C 5 " pdb=" O4 DT C 5 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 23518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 9319 34.88 - 69.76: 547 69.76 - 104.65: 33 104.65 - 139.53: 1 139.53 - 174.41: 3 Dihedral angle restraints: 9903 sinusoidal: 5121 harmonic: 4782 Sorted by residual: dihedral pdb=" C4' A A 29 " pdb=" C3' A A 29 " pdb=" C2' A A 29 " pdb=" C1' A A 29 " ideal model delta sinusoidal sigma weight residual 36.34 -36.42 72.77 1 3.10e+00 1.04e-01 7.03e+02 dihedral pdb=" C4' C A 56 " pdb=" C3' C A 56 " pdb=" C2' C A 56 " pdb=" C1' C A 56 " ideal model delta sinusoidal sigma weight residual 36.34 -35.70 72.04 1 3.10e+00 1.04e-01 6.91e+02 dihedral pdb=" C4' A A 58 " pdb=" C3' A A 58 " pdb=" C2' A A 58 " pdb=" C1' A A 58 " ideal model delta sinusoidal sigma weight residual 36.35 -35.24 71.59 1 3.10e+00 1.04e-01 6.83e+02 ... (remaining 9900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2270 0.060 - 0.119: 294 0.119 - 0.179: 24 0.179 - 0.239: 67 0.239 - 0.298: 31 Chirality restraints: 2686 Sorted by residual: chirality pdb=" P A A 29 " pdb=" OP1 A A 29 " pdb=" OP2 A A 29 " pdb=" O5' A A 29 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" P A A 70 " pdb=" OP1 A A 70 " pdb=" OP2 A A 70 " pdb=" O5' A A 70 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C2' C A 56 " pdb=" C3' C A 56 " pdb=" O2' C A 56 " pdb=" C1' C A 56 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 2683 not shown) Planarity restraints: 2463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 495 " 0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C ASP B 495 " -0.077 2.00e-02 2.50e+03 pdb=" O ASP B 495 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA B 496 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1202 " 0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C GLU B1202 " -0.060 2.00e-02 2.50e+03 pdb=" O GLU B1202 " 0.023 2.00e-02 2.50e+03 pdb=" N SER B1203 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 814 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C GLU B 814 " -0.059 2.00e-02 2.50e+03 pdb=" O GLU B 814 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP B 815 " 0.020 2.00e-02 2.50e+03 ... (remaining 2460 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 380 2.68 - 3.23: 14825 3.23 - 3.79: 25517 3.79 - 4.34: 34785 4.34 - 4.90: 53766 Nonbonded interactions: 129273 Sorted by model distance: nonbonded pdb=" O6 8AZ D 26 " pdb="ZN ZN F 201 " model vdw 2.121 2.230 nonbonded pdb=" OP1 C A 6 " pdb=" OH TYR B 712 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR B1439 " pdb=" OE1 GLN B1453 " model vdw 2.254 3.040 nonbonded pdb=" O2' U A 9 " pdb=" OP1 U A 10 " model vdw 2.256 3.040 nonbonded pdb=" OD1 ASP B1464 " pdb=" OH TYR B1491 " model vdw 2.263 3.040 ... (remaining 129268 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 Found NCS groups: ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 5 through 149 or resid 201)) } 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.100 Find NCS groups from input model: 0.070 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.004 0.169 16932 Z= 0.261 Angle : 0.684 14.400 23523 Z= 0.448 Chirality : 0.060 0.298 2686 Planarity : 0.004 0.045 2463 Dihedral : 18.173 174.412 6813 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.58 % Allowed : 8.75 % Favored : 89.68 % 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: -1.99 (0.18), residues: 1621 helix: -1.20 (0.15), residues: 796 sheet: -1.09 (0.41), residues: 145 loop : -1.33 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 101 TYR 0.014 0.001 TYR F 10 PHE 0.017 0.001 PHE B1234 TRP 0.009 0.001 TRP B1323 HIS 0.003 0.001 HIS B 895 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.25 (16926) covalent geometry : angle 0.68369 / 0.45 (23523) hydrogen bonds : bond 0.12108 / 6.27 ( 774) hydrogen bonds : angle 6.17504 / 2.53 ( 2096) metal coordination : bond 0.09673 / 4.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 303 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 379 ASP cc_start: 0.6544 (m-30) cc_final: 0.6255 (p0) REVERT: B 766 PHE cc_start: 0.8509 (m-80) cc_final: 0.7946 (m-80) REVERT: B 846 LYS cc_start: 0.8413 (tttp) cc_final: 0.8186 (mtpp) REVERT: B 890 PHE cc_start: 0.7343 (t80) cc_final: 0.7106 (t80) REVERT: B 900 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7434 (t) REVERT: E 96 HIS cc_start: 0.6189 (m-70) cc_final: 0.5637 (m-70) REVERT: F 10 TYR cc_start: 0.9221 (t80) cc_final: 0.8925 (t80) outliers start: 22 outliers final: 4 residues processed: 321 average time/residue: 0.1603 time to fit residues: 71.3745 Evaluate side-chains 158 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 153 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 819 THR Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 904 ASP Chi-restraints excluded: chain B residue 1539 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 30.0000 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 243 ASN B 462 GLN B 599 GLN B 760 GLN B1005 ASN ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1177 ASN B1180 HIS E 119 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS F 14 HIS F 46 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.163357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.111160 restraints weight = 32582.057| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.55 r_work: 0.3320 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16932 Z= 0.162 Angle : 0.808 15.987 23523 Z= 0.378 Chirality : 0.068 1.144 2686 Planarity : 0.004 0.063 2463 Dihedral : 17.954 172.839 3565 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.58 % Allowed : 14.41 % Favored : 83.01 % 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: 0.03 (0.20), residues: 1621 helix: 0.82 (0.18), residues: 778 sheet: -0.15 (0.41), residues: 153 loop : -0.80 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 13 TYR 0.030 0.002 TYR B1009 PHE 0.014 0.001 PHE B 766 TRP 0.010 0.001 TRP F 11 HIS 0.006 0.001 HIS B1461 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (16926) covalent geometry : angle 0.80762 / 0.38 (23523) hydrogen bonds : bond 0.04394 / 2.29 ( 774) hydrogen bonds : angle 4.95132 / 2.03 ( 2096) metal coordination : bond 0.00612 / 0.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 379 ASP cc_start: 0.7033 (m-30) cc_final: 0.6308 (p0) REVERT: B 437 ASN cc_start: 0.7141 (m-40) cc_final: 0.6480 (m-40) REVERT: B 528 ASP cc_start: 0.8561 (t70) cc_final: 0.8166 (t0) REVERT: B 567 GLU cc_start: 0.8070 (tp30) cc_final: 0.7778 (tm-30) REVERT: B 731 MET cc_start: 0.4910 (ptt) cc_final: 0.3621 (pmm) REVERT: B 1261 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: F 10 TYR cc_start: 0.9448 (t80) cc_final: 0.9225 (t80) REVERT: F 84 PHE cc_start: 0.6173 (t80) cc_final: 0.5770 (t80) REVERT: F 89 MET cc_start: 0.8514 (ttp) cc_final: 0.7676 (ptm) REVERT: F 116 SER cc_start: 0.8003 (OUTLIER) cc_final: 0.7720 (p) REVERT: F 126 MET cc_start: 0.8988 (mmm) cc_final: 0.8778 (mmm) outliers start: 36 outliers final: 13 residues processed: 186 average time/residue: 0.1269 time to fit residues: 35.2658 Evaluate side-chains 142 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1259 LEU Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1477 VAL Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 116 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [128, 34, 73, 172, 30, 105, 26, 131, 23, 147, 44] chunk 128 optimal weight: 2.9990 chunk 34 optimal weight: 0.0000 chunk 73 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 GLN B1238 ASN E 127 ASN ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.158635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.103766 restraints weight = 32964.135| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.13 r_work: 0.3155 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16932 Z= 0.218 Angle : 0.753 14.425 23523 Z= 0.368 Chirality : 0.059 0.902 2686 Planarity : 0.004 0.045 2463 Dihedral : 18.014 170.834 3561 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.51 % Allowed : 13.69 % Favored : 83.80 % 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: 0.33 (0.20), residues: 1621 helix: 1.04 (0.18), residues: 779 sheet: 0.25 (0.42), residues: 155 loop : -0.68 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 418 TYR 0.026 0.002 TYR B1009 PHE 0.026 0.002 PHE B 766 TRP 0.015 0.002 TRP F 45 HIS 0.009 0.001 HIS B 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (16926) covalent geometry : angle 0.75348 / 0.37 (23523) hydrogen bonds : bond 0.05126 / 2.66 ( 774) hydrogen bonds : angle 4.85961 / 1.98 ( 2096) metal coordination : bond 0.01482 / 0.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 379 ASP cc_start: 0.7008 (m-30) cc_final: 0.6206 (p0) REVERT: B 437 ASN cc_start: 0.7180 (m-40) cc_final: 0.6921 (t0) REVERT: B 528 ASP cc_start: 0.8664 (t70) cc_final: 0.8306 (t0) REVERT: B 567 GLU cc_start: 0.8243 (tp30) cc_final: 0.7989 (tm-30) REVERT: B 692 MET cc_start: 0.8552 (mtt) cc_final: 0.8240 (mtt) REVERT: B 731 MET cc_start: 0.5055 (ptt) cc_final: 0.3793 (pmm) REVERT: B 1240 MET cc_start: 0.9257 (tpp) cc_final: 0.9009 (tpp) REVERT: E 12 MET cc_start: 0.1304 (OUTLIER) cc_final: 0.0615 (tpp) REVERT: E 61 MET cc_start: 0.9321 (mmm) cc_final: 0.9011 (mmm) REVERT: E 70 MET cc_start: 0.8584 (ptp) cc_final: 0.8044 (ptp) REVERT: F 70 MET cc_start: 0.8440 (ptm) cc_final: 0.7777 (ppp) REVERT: F 96 HIS cc_start: 0.5837 (m90) cc_final: 0.5271 (m170) outliers start: 35 outliers final: 21 residues processed: 159 average time/residue: 0.1249 time to fit residues: 29.4727 Evaluate side-chains 144 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 819 THR Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1387 VAL Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 12 MET Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [143, 148, 61, 141, 50, 132, 162, 156, 168, 15, 60] chunk 143 optimal weight: 20.0000 chunk 148 optimal weight: 50.0000 chunk 61 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 156 optimal weight: 30.0000 chunk 168 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 GLN B1060 ASN B1418 GLN F 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.154165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.098364 restraints weight = 32712.610| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.13 r_work: 0.3059 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 16932 Z= 0.314 Angle : 0.860 16.860 23523 Z= 0.414 Chirality : 0.061 0.722 2686 Planarity : 0.005 0.044 2463 Dihedral : 18.121 169.574 3561 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.30 % Allowed : 13.48 % Favored : 83.23 % 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: 0.21 (0.21), residues: 1621 helix: 0.98 (0.18), residues: 781 sheet: 0.40 (0.40), residues: 166 loop : -0.87 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1368 TYR 0.028 0.002 TYR B1533 PHE 0.027 0.002 PHE B 766 TRP 0.009 0.002 TRP B1271 HIS 0.014 0.002 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.31 (16926) covalent geometry : angle 0.86003 / 0.41 (23523) hydrogen bonds : bond 0.06342 / 3.27 ( 774) hydrogen bonds : angle 5.00179 / 2.04 ( 2096) metal coordination : bond 0.00935 / 0.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 437 ASN cc_start: 0.7258 (m-40) cc_final: 0.6694 (m-40) REVERT: B 692 MET cc_start: 0.8647 (mtt) cc_final: 0.8391 (mtt) REVERT: B 731 MET cc_start: 0.5213 (OUTLIER) cc_final: 0.3928 (pmm) REVERT: B 765 TYR cc_start: 0.8587 (t80) cc_final: 0.8026 (t80) REVERT: B 1261 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: E 70 MET cc_start: 0.8622 (ptp) cc_final: 0.8279 (ptp) REVERT: F 61 MET cc_start: 0.8406 (mmm) cc_final: 0.8186 (mmm) REVERT: F 89 MET cc_start: 0.8779 (ttp) cc_final: 0.8526 (ptm) outliers start: 46 outliers final: 29 residues processed: 163 average time/residue: 0.1230 time to fit residues: 30.6846 Evaluate side-chains 152 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 819 THR Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 843 LYS Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1387 VAL Chi-restraints excluded: chain B residue 1391 LEU Chi-restraints excluded: chain B residue 1511 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [119, 156, 167, 43, 109, 14, 25, 5, 140, 125, 73] chunk 119 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 525 HIS B1418 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.157749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.102360 restraints weight = 32646.092| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.21 r_work: 0.3146 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16932 Z= 0.135 Angle : 0.679 11.313 23523 Z= 0.332 Chirality : 0.053 0.543 2686 Planarity : 0.003 0.042 2463 Dihedral : 18.024 170.591 3561 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.22 % Allowed : 14.34 % Favored : 83.44 % 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: 0.68 (0.21), residues: 1621 helix: 1.38 (0.18), residues: 781 sheet: 0.72 (0.40), residues: 176 loop : -0.72 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 418 TYR 0.008 0.001 TYR B1009 PHE 0.014 0.001 PHE B 772 TRP 0.006 0.001 TRP B 215 HIS 0.006 0.001 HIS B 525 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (16926) covalent geometry : angle 0.67943 / 0.33 (23523) hydrogen bonds : bond 0.04559 / 2.38 ( 774) hydrogen bonds : angle 4.68679 / 1.91 ( 2096) metal coordination : bond 0.00316 / 0.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 437 ASN cc_start: 0.7220 (m-40) cc_final: 0.6642 (m-40) REVERT: B 567 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7904 (tp30) REVERT: B 692 MET cc_start: 0.8614 (mtt) cc_final: 0.8333 (mtt) REVERT: B 731 MET cc_start: 0.5088 (ptt) cc_final: 0.3970 (pmm) REVERT: B 804 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7733 (mp) REVERT: B 824 GLU cc_start: 0.7696 (pp20) cc_final: 0.7011 (mm-30) REVERT: B 852 ARG cc_start: 0.7767 (ttm110) cc_final: 0.6938 (mmt-90) REVERT: B 978 MET cc_start: 0.5971 (mmm) cc_final: 0.5682 (mmm) REVERT: B 1240 MET cc_start: 0.9280 (tpp) cc_final: 0.8997 (tpp) REVERT: B 1261 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: E 61 MET cc_start: 0.9061 (mmp) cc_final: 0.8831 (mmm) REVERT: E 70 MET cc_start: 0.8605 (ptp) cc_final: 0.8302 (ptp) REVERT: F 61 MET cc_start: 0.8370 (mmm) cc_final: 0.8137 (mmm) REVERT: F 96 HIS cc_start: 0.6954 (m90) cc_final: 0.6681 (m90) REVERT: F 118 MET cc_start: 0.8871 (ptp) cc_final: 0.8513 (pmm) outliers start: 31 outliers final: 20 residues processed: 149 average time/residue: 0.1198 time to fit residues: 27.5389 Evaluate side-chains 144 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1439 TYR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [80, 25, 111, 16, 127, 121, 50, 161, 135, 149, 68] chunk 80 optimal weight: 7.9990 chunk 25 optimal weight: 0.0070 chunk 111 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 135 optimal weight: 0.8980 chunk 149 optimal weight: 30.0000 chunk 68 optimal weight: 7.9990 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 52 HIS E 96 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.156844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.101921 restraints weight = 32421.866| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.15 r_work: 0.3123 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16932 Z= 0.162 Angle : 0.678 11.600 23523 Z= 0.331 Chirality : 0.053 0.477 2686 Planarity : 0.003 0.042 2463 Dihedral : 17.954 170.026 3561 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.44 % Allowed : 14.84 % Favored : 82.72 % 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: 0.72 (0.21), residues: 1621 helix: 1.40 (0.18), residues: 788 sheet: 0.82 (0.39), residues: 184 loop : -0.75 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 977 TYR 0.011 0.001 TYR B1533 PHE 0.018 0.001 PHE B 766 TRP 0.006 0.001 TRP B 215 HIS 0.006 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (16926) covalent geometry : angle 0.67831 / 0.33 (23523) hydrogen bonds : bond 0.04662 / 2.41 ( 774) hydrogen bonds : angle 4.64264 / 1.89 ( 2096) metal coordination : bond 0.00575 / 0.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 437 ASN cc_start: 0.7262 (m-40) cc_final: 0.6713 (m-40) REVERT: B 567 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7926 (tp30) REVERT: B 692 MET cc_start: 0.8601 (mtt) cc_final: 0.8329 (mtt) REVERT: B 731 MET cc_start: 0.5103 (OUTLIER) cc_final: 0.3942 (pmm) REVERT: B 804 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7771 (mp) REVERT: B 824 GLU cc_start: 0.7718 (pp20) cc_final: 0.6807 (mm-30) REVERT: B 834 LYS cc_start: 0.8478 (ptmt) cc_final: 0.8229 (ptpt) REVERT: B 852 ARG cc_start: 0.7798 (ttm110) cc_final: 0.6896 (mmt-90) REVERT: B 1240 MET cc_start: 0.9277 (tpp) cc_final: 0.8975 (tpp) REVERT: B 1245 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8280 (m) REVERT: B 1261 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: B 1459 HIS cc_start: 0.8946 (m90) cc_final: 0.8446 (m90) REVERT: E 61 MET cc_start: 0.9071 (mmp) cc_final: 0.8847 (mmm) REVERT: E 70 MET cc_start: 0.8626 (ptp) cc_final: 0.8324 (ptp) REVERT: F 61 MET cc_start: 0.8551 (mmm) cc_final: 0.8270 (mmm) REVERT: F 70 MET cc_start: 0.8009 (ptm) cc_final: 0.7805 (ppp) REVERT: F 118 MET cc_start: 0.8849 (ptp) cc_final: 0.8502 (pmm) outliers start: 34 outliers final: 24 residues processed: 147 average time/residue: 0.1193 time to fit residues: 27.0469 Evaluate side-chains 153 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1245 THR Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1439 TYR Chi-restraints excluded: chain B residue 1511 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 73 TYR Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [14, 146, 7, 0, 140, 49, 108, 60, 107, 20, 66] chunk 14 optimal weight: 0.8980 chunk 146 optimal weight: 40.0000 chunk 7 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 617 HIS B1418 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.155422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.100358 restraints weight = 32569.873| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.05 r_work: 0.3087 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16932 Z= 0.217 Angle : 0.724 12.945 23523 Z= 0.351 Chirality : 0.054 0.462 2686 Planarity : 0.004 0.043 2463 Dihedral : 17.959 169.780 3559 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.37 % Allowed : 15.48 % Favored : 82.15 % 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: 0.61 (0.21), residues: 1621 helix: 1.34 (0.18), residues: 789 sheet: 0.59 (0.40), residues: 180 loop : -0.79 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 13 TYR 0.015 0.001 TYR B 352 PHE 0.020 0.002 PHE B 766 TRP 0.006 0.001 TRP B 215 HIS 0.008 0.001 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 (16926) covalent geometry : angle 0.72372 / 0.35 (23523) hydrogen bonds : bond 0.05129 / 2.65 ( 774) hydrogen bonds : angle 4.69245 / 1.91 ( 2096) metal coordination : bond 0.00667 / 0.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 437 ASN cc_start: 0.7302 (m-40) cc_final: 0.6779 (m-40) REVERT: B 567 GLU cc_start: 0.8232 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 692 MET cc_start: 0.8646 (mtt) cc_final: 0.8369 (mtt) REVERT: B 731 MET cc_start: 0.5343 (OUTLIER) cc_final: 0.4155 (pmm) REVERT: B 804 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7805 (mp) REVERT: B 824 GLU cc_start: 0.7806 (pp20) cc_final: 0.7200 (mm-30) REVERT: B 834 LYS cc_start: 0.8564 (ptmt) cc_final: 0.8324 (ptpt) REVERT: B 1240 MET cc_start: 0.9275 (tpp) cc_final: 0.8975 (tpp) REVERT: B 1245 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8329 (m) REVERT: B 1261 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: E 61 MET cc_start: 0.9039 (mmp) cc_final: 0.8826 (mmm) REVERT: F 61 MET cc_start: 0.8588 (mmm) cc_final: 0.8228 (mmm) REVERT: F 89 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8247 (ptt) REVERT: F 118 MET cc_start: 0.8820 (ptp) cc_final: 0.8523 (pmm) outliers start: 33 outliers final: 22 residues processed: 152 average time/residue: 0.1159 time to fit residues: 27.5538 Evaluate side-chains 149 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 669 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1245 THR Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1439 TYR Chi-restraints excluded: chain B residue 1511 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 73 TYR Chi-restraints excluded: chain F residue 89 MET Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [46, 106, 19, 93, 66, 92, 173, 163, 81, 142, 79] chunk 46 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 19 optimal weight: 0.2980 chunk 93 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 HIS E 96 HIS ** F 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.156559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.102974 restraints weight = 32434.298| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.87 r_work: 0.3127 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16932 Z= 0.156 Angle : 0.689 14.158 23523 Z= 0.335 Chirality : 0.052 0.444 2686 Planarity : 0.004 0.066 2463 Dihedral : 17.919 170.310 3559 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.44 % Allowed : 15.84 % Favored : 81.72 % 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: 0.74 (0.21), residues: 1621 helix: 1.45 (0.19), residues: 783 sheet: 0.79 (0.40), residues: 186 loop : -0.77 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 47 TYR 0.010 0.001 TYR B1533 PHE 0.020 0.001 PHE B 766 TRP 0.032 0.002 TRP F 45 HIS 0.009 0.001 HIS F 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (16926) covalent geometry : angle 0.68923 / 0.33 (23523) hydrogen bonds : bond 0.04556 / 2.37 ( 774) hydrogen bonds : angle 4.63025 / 1.89 ( 2096) metal coordination : bond 0.00300 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 437 ASN cc_start: 0.7330 (m-40) cc_final: 0.6814 (m-40) REVERT: B 567 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 692 MET cc_start: 0.8611 (mtt) cc_final: 0.8343 (mtt) REVERT: B 731 MET cc_start: 0.5445 (OUTLIER) cc_final: 0.4200 (pmm) REVERT: B 804 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7752 (mp) REVERT: B 824 GLU cc_start: 0.7732 (pp20) cc_final: 0.7174 (mm-30) REVERT: B 1240 MET cc_start: 0.9257 (tpp) cc_final: 0.8967 (tpp) REVERT: B 1261 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: B 1402 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: E 61 MET cc_start: 0.9002 (mmp) cc_final: 0.8787 (mmm) REVERT: F 61 MET cc_start: 0.8483 (mmm) cc_final: 0.8175 (mmm) REVERT: F 70 MET cc_start: 0.8301 (ppp) cc_final: 0.8070 (ppp) REVERT: F 118 MET cc_start: 0.8779 (ptp) cc_final: 0.8469 (pmm) outliers start: 34 outliers final: 23 residues processed: 151 average time/residue: 0.1123 time to fit residues: 26.5370 Evaluate side-chains 148 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1154 THR Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1316 LEU Chi-restraints excluded: chain B residue 1402 GLU Chi-restraints excluded: chain B residue 1511 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 73 TYR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 144 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [48, 28, 83, 116, 162, 153, 57, 82, 113, 154, 87] chunk 48 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 162 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 57 optimal weight: 0.0050 chunk 82 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1418 GLN ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.158051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.103050 restraints weight = 32684.619| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.07 r_work: 0.3176 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16932 Z= 0.122 Angle : 0.684 18.125 23523 Z= 0.328 Chirality : 0.050 0.412 2686 Planarity : 0.004 0.070 2463 Dihedral : 17.857 170.765 3559 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.86 % Allowed : 16.34 % Favored : 81.79 % 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: 0.92 (0.21), residues: 1621 helix: 1.60 (0.19), residues: 788 sheet: 0.88 (0.40), residues: 186 loop : -0.71 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 47 TYR 0.009 0.001 TYR F 73 PHE 0.018 0.001 PHE B 766 TRP 0.016 0.001 TRP F 45 HIS 0.003 0.001 HIS B 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (16926) covalent geometry : angle 0.68369 / 0.33 (23523) hydrogen bonds : bond 0.03998 / 2.09 ( 774) hydrogen bonds : angle 4.53560 / 1.85 ( 2096) metal coordination : bond 0.00126 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 437 ASN cc_start: 0.7283 (m-40) cc_final: 0.6740 (m-40) REVERT: B 692 MET cc_start: 0.8525 (mtt) cc_final: 0.8277 (mtt) REVERT: B 731 MET cc_start: 0.5455 (ptt) cc_final: 0.4263 (pmm) REVERT: B 804 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7765 (mp) REVERT: B 824 GLU cc_start: 0.7695 (pp20) cc_final: 0.7115 (mm-30) REVERT: B 1196 LYS cc_start: 0.8628 (ttpp) cc_final: 0.8063 (ttpp) REVERT: B 1240 MET cc_start: 0.9245 (tpp) cc_final: 0.8986 (tpp) REVERT: B 1261 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: E 12 MET cc_start: 0.0024 (tpt) cc_final: -0.0180 (tpt) REVERT: E 61 MET cc_start: 0.9091 (mmp) cc_final: 0.8871 (mmm) REVERT: E 70 MET cc_start: 0.8246 (ptt) cc_final: 0.7773 (ppp) REVERT: F 12 MET cc_start: 0.7706 (ptm) cc_final: 0.7421 (ppp) REVERT: F 61 MET cc_start: 0.8571 (mmm) cc_final: 0.8214 (mmm) REVERT: F 70 MET cc_start: 0.8146 (ppp) cc_final: 0.7892 (ppp) outliers start: 26 outliers final: 21 residues processed: 149 average time/residue: 0.1190 time to fit residues: 27.2934 Evaluate side-chains 148 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1439 TYR Chi-restraints excluded: chain B residue 1511 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 39 ARG Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 73 TYR Chi-restraints excluded: chain F residue 116 SER Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [68, 118, 84, 107, 52, 8, 104, 57, 117, 20, 163] chunk 68 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 107 optimal weight: 30.0000 chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 0.0570 chunk 20 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 96 HIS ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.158487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.104773 restraints weight = 32460.879| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.94 r_work: 0.3183 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16932 Z= 0.124 Angle : 0.697 19.383 23523 Z= 0.335 Chirality : 0.049 0.372 2686 Planarity : 0.003 0.050 2463 Dihedral : 17.820 170.837 3559 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.65 % Allowed : 16.92 % Favored : 81.43 % 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: 0.91 (0.21), residues: 1621 helix: 1.55 (0.19), residues: 793 sheet: 0.97 (0.39), residues: 185 loop : -0.68 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 111 TYR 0.008 0.001 TYR F 73 PHE 0.022 0.001 PHE B 766 TRP 0.012 0.001 TRP F 45 HIS 0.007 0.001 HIS F 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (16926) covalent geometry : angle 0.69747 / 0.33 (23523) hydrogen bonds : bond 0.03966 / 2.07 ( 774) hydrogen bonds : angle 4.52459 / 1.84 ( 2096) metal coordination : bond 0.00349 / 0.17 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3242 Ramachandran restraints generated. 1621 Oldfield, 0 Emsley, 1621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 437 ASN cc_start: 0.7297 (m-40) cc_final: 0.6778 (m-40) REVERT: B 692 MET cc_start: 0.8578 (mtt) cc_final: 0.8324 (mtt) REVERT: B 731 MET cc_start: 0.5712 (ptt) cc_final: 0.4435 (pmm) REVERT: B 804 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7750 (mp) REVERT: B 824 GLU cc_start: 0.7670 (pp20) cc_final: 0.7090 (mm-30) REVERT: B 1240 MET cc_start: 0.9277 (tpp) cc_final: 0.9013 (tpp) REVERT: B 1261 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: E 61 MET cc_start: 0.9016 (mmp) cc_final: 0.8656 (mmm) REVERT: E 70 MET cc_start: 0.8302 (ptt) cc_final: 0.7884 (ppp) REVERT: F 12 MET cc_start: 0.7584 (ptm) cc_final: 0.6695 (ppp) REVERT: F 70 MET cc_start: 0.8252 (ppp) cc_final: 0.8007 (ppp) outliers start: 23 outliers final: 19 residues processed: 148 average time/residue: 0.1212 time to fit residues: 28.0093 Evaluate side-chains 149 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 947 VAL Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1261 GLU Chi-restraints excluded: chain B residue 1511 THR Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 73 TYR Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: [115, 52, 24, 62, 47, 45, 81, 46, 44, 48, 153] chunk 115 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 153 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1459 HIS ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 HIS ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.158886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.105135 restraints weight = 32655.953| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.98 r_work: 0.3192 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16932 Z= 0.120 Angle : 0.685 16.362 23523 Z= 0.331 Chirality : 0.048 0.355 2686 Planarity : 0.003 0.068 2463 Dihedral : 17.785 171.038 3559 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.58 % Allowed : 17.56 % Favored : 80.86 % 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: 0.96 (0.21), residues: 1621 helix: 1.58 (0.19), residues: 794 sheet: 1.03 (0.40), residues: 185 loop : -0.65 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 39 TYR 0.008 0.001 TYR F 73 PHE 0.019 0.001 PHE B 766 TRP 0.013 0.001 TRP F 45 HIS 0.013 0.001 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (16926) covalent geometry : angle 0.68494 / 0.33 (23523) hydrogen bonds : bond 0.03865 / 2.01 ( 774) hydrogen bonds : angle 4.48591 / 1.82 ( 2096) metal coordination : bond 0.00330 / 0.17 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4937.43 seconds wall clock time: 84 minutes 48.22 seconds (5088.22 seconds total)