Starting phenix.real_space_refine on Fri Oct 23 20:13:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/26kb_80708/10_2026/26kb_80708.cif Found real_map, /net/cci-nas-00/data/ceres_data/26kb_80708/10_2026/26kb_80708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/26kb_80708/10_2026/26kb_80708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/26kb_80708/10_2026/26kb_80708.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/26kb_80708/10_2026/26kb_80708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/26kb_80708/10_2026/26kb_80708.map" } resolution = 2.76 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= 0.014 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 Mn 1 7.51 5 Zn 2 6.06 5 Mg 1 5.21 5 S 78 5.16 5 C 6727 2.51 5 N 1832 2.21 5 O 1986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 10627 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1368, 10623 Classifications: {'peptide': 1368} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 38, 'TRANS': 1329} Chain breaks: 15 Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 17, 'ARG:plan': 11, 'ASN:plan1': 3, 'TYR:plan': 3, 'GLN:plan1': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 199 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' MN': 1, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 796 SG CYS A1028 44.287 17.097 90.882 1.00 92.05 S ATOM 815 SG CYS A1031 47.368 14.911 90.960 1.00 95.51 S ATOM 1058 SG CYS A1062 44.054 13.459 89.685 1.00 96.30 S ATOM 1078 SG CYS A1065 45.912 16.009 87.622 1.00 99.43 S ATOM 2238 SG CYS A1294 57.162 25.964 40.167 1.00 71.76 S Time building chain proxies: 2.32, per 1000 atoms: 0.22 Number of scatterers: 10627 At special positions: 0 Unit cell: (114.61, 88.33, 122.64, 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 Mn 1 24.99 S 78 16.00 Mg 1 11.99 O 1986 8.00 N 1832 7.00 C 6727 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 279.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4001 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1065 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1028 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1031 " pdb="ZN ZN A4001 " - pdb=" SG CYS A1062 " pdb=" ZN A4002 " pdb="ZN ZN A4002 " - pdb=" SG CYS A1294 " pdb="ZN ZN A4002 " - pdb=" NE2 HIS A1090 " Number of angles added : 6 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2620 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 10 sheets defined 64.0% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 930 through 947 removed outlier: 3.571A pdb=" N VAL A 934 " --> pdb=" O SER A 930 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N HIS A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 967 Processing helix chain 'A' and resid 973 through 987 Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1008 through 1025 removed outlier: 3.850A pdb=" N SER A1025 " --> pdb=" O GLU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1042 Processing helix chain 'A' and resid 1044 through 1056 Processing helix chain 'A' and resid 1057 through 1061 Processing helix chain 'A' and resid 1062 through 1066 removed outlier: 3.846A pdb=" N HIS A1066 " --> pdb=" O SER A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 3.510A pdb=" N VAL A1088 " --> pdb=" O ILE A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1111 removed outlier: 3.547A pdb=" N ARG A1111 " --> pdb=" O ASP A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1139 Processing helix chain 'A' and resid 1178 through 1192 Processing helix chain 'A' and resid 1196 through 1209 Processing helix chain 'A' and resid 1221 through 1232 Processing helix chain 'A' and resid 1266 through 1279 removed outlier: 4.300A pdb=" N PHE A1279 " --> pdb=" O ASP A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1282 No H-bonds generated for 'chain 'A' and resid 1280 through 1282' Processing helix chain 'A' and resid 1291 through 1296 removed outlier: 3.537A pdb=" N ILE A1295 " --> pdb=" O GLN A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1309 Processing helix chain 'A' and resid 1315 through 1329 Processing helix chain 'A' and resid 1330 through 1350 Processing helix chain 'A' and resid 1401 through 1426 removed outlier: 4.214A pdb=" N LEU A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR A1413 " --> pdb=" O SER A1409 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A1416 " --> pdb=" O LEU A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1435 removed outlier: 3.935A pdb=" N VAL A1435 " --> pdb=" O ILE A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1463 Processing helix chain 'A' and resid 1465 through 1481 removed outlier: 3.554A pdb=" N SER A1469 " --> pdb=" O ARG A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1505 Processing helix chain 'A' and resid 1507 through 1514 removed outlier: 3.724A pdb=" N ASN A1514 " --> pdb=" O ASN A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1531 removed outlier: 4.060A pdb=" N ARG A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A1527 " --> pdb=" O GLN A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1534 No H-bonds generated for 'chain 'A' and resid 1532 through 1534' Processing helix chain 'A' and resid 1538 through 1547 removed outlier: 3.791A pdb=" N SER A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1570 Processing helix chain 'A' and resid 1572 through 1581 removed outlier: 4.027A pdb=" N LYS A1581 " --> pdb=" O VAL A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1612 Processing helix chain 'A' and resid 1613 through 1616 Processing helix chain 'A' and resid 1631 through 1651 Processing helix chain 'A' and resid 1658 through 1666 Processing helix chain 'A' and resid 1758 through 1773 Processing helix chain 'A' and resid 1780 through 1792 Processing helix chain 'A' and resid 1793 through 1795 No H-bonds generated for 'chain 'A' and resid 1793 through 1795' Processing helix chain 'A' and resid 1796 through 1805 Processing helix chain 'A' and resid 1806 through 1810 removed outlier: 4.262A pdb=" N TRP A1810 " --> pdb=" O PRO A1807 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2306 removed outlier: 3.628A pdb=" N THR A2306 " --> pdb=" O ASN A2302 " (cutoff:3.500A) Processing helix chain 'A' and resid 2316 through 2336 Processing helix chain 'A' and resid 2367 through 2379 Processing helix chain 'A' and resid 2382 through 2397 Processing helix chain 'A' and resid 2404 through 2417 removed outlier: 3.711A pdb=" N ILE A2408 " --> pdb=" O PRO A2404 " (cutoff:3.500A) Processing helix chain 'A' and resid 2436 through 2441 Processing helix chain 'A' and resid 2442 through 2444 No H-bonds generated for 'chain 'A' and resid 2442 through 2444' Processing helix chain 'A' and resid 2447 through 2457 removed outlier: 3.848A pdb=" N LYS A2451 " --> pdb=" O ASN A2447 " (cutoff:3.500A) Processing helix chain 'A' and resid 2476 through 2503 removed outlier: 3.851A pdb=" N VAL A2489 " --> pdb=" O SER A2485 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A2490 " --> pdb=" O LEU A2486 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2559 removed outlier: 4.935A pdb=" N TRP A2542 " --> pdb=" O ASP A2538 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LYS A2543 " --> pdb=" O GLU A2539 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2594 removed outlier: 3.512A pdb=" N MET A2594 " --> pdb=" O ILE A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2595 through 2600 removed outlier: 3.692A pdb=" N ASN A2600 " --> pdb=" O THR A2596 " (cutoff:3.500A) Processing helix chain 'A' and resid 2605 through 2623 Processing helix chain 'A' and resid 2626 through 2645 removed outlier: 3.813A pdb=" N PHE A2641 " --> pdb=" O ARG A2637 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N HIS A2644 " --> pdb=" O ILE A2640 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A2645 " --> pdb=" O PHE A2641 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2657 removed outlier: 6.822A pdb=" N ILE A2654 " --> pdb=" O ARG A2650 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A2655 " --> pdb=" O ARG A2651 " (cutoff:3.500A) Processing helix chain 'A' and resid 2660 through 2664 removed outlier: 3.532A pdb=" N PHE A2663 " --> pdb=" O LEU A2660 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A2664 " --> pdb=" O SER A2661 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2660 through 2664' Processing helix chain 'A' and resid 2670 through 2675 removed outlier: 3.778A pdb=" N VAL A2675 " --> pdb=" O TYR A2671 " (cutoff:3.500A) Processing helix chain 'A' and resid 2678 through 2696 Processing helix chain 'A' and resid 2753 through 2764 Processing helix chain 'A' and resid 2770 through 2783 Processing helix chain 'A' and resid 2801 through 2805 Processing helix chain 'A' and resid 2806 through 2816 Processing helix chain 'A' and resid 2816 through 2836 Processing helix chain 'A' and resid 2993 through 3003 Processing helix chain 'A' and resid 3043 through 3060 Processing helix chain 'A' and resid 3062 through 3072 Processing helix chain 'A' and resid 3208 through 3217 removed outlier: 3.663A pdb=" N ILE A3217 " --> pdb=" O VAL A3213 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 971 through 972 removed outlier: 6.731A pdb=" N VAL A 971 " --> pdb=" O TYR A1755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1003 through 1004 Processing sheet with id=AA3, first strand: chain 'A' and resid 1151 through 1153 removed outlier: 4.772A pdb=" N CYS A1143 " --> pdb=" O VAL A1220 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A1220 " --> pdb=" O CYS A1143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1357 through 1362 removed outlier: 3.890A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU A1386 " --> pdb=" O GLY A1396 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY A1396 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2507 through 2514 Processing sheet with id=AA6, first strand: chain 'A' and resid 2399 through 2402 Processing sheet with id=AA7, first strand: chain 'A' and resid 2574 through 2576 removed outlier: 4.517A pdb=" N PHE A2580 " --> pdb=" O THR A2587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 3005 through 3009 Processing sheet with id=AA9, first strand: chain 'A' and resid 3078 through 3081 removed outlier: 3.772A pdb=" N SER A3078 " --> pdb=" O ARG A3224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 3086 through 3089 646 hydrogen bonds defined for protein. 1863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.24 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: 3469 1.34 - 1.46: 2023 1.46 - 1.58: 5200 1.58 - 1.69: 0 1.69 - 1.81: 109 Bond restraints: 10801 Sorted by residual: bond pdb=" CB PRO A2662 " pdb=" CG PRO A2662 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.16e+00 bond pdb=" C VAL A1288 " pdb=" N PRO A1289 " ideal model delta sigma weight residual 1.334 1.360 -0.027 2.34e-02 1.83e+03 1.29e+00 bond pdb=" CB GLU A2773 " pdb=" CG GLU A2773 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.24e+00 bond pdb=" CB PRO A2364 " pdb=" CG PRO A2364 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.33e-01 bond pdb=" CA GLN A3059 " pdb=" C GLN A3059 " ideal model delta sigma weight residual 1.522 1.533 -0.011 1.40e-02 5.10e+03 6.65e-01 ... (remaining 10796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 14381 1.43 - 2.87: 182 2.87 - 4.30: 31 4.30 - 5.73: 9 5.73 - 7.16: 5 Bond angle restraints: 14608 Sorted by residual: angle pdb=" CA PRO A2662 " pdb=" N PRO A2662 " pdb=" CD PRO A2662 " ideal model delta sigma weight residual 112.00 107.16 4.84 1.40e+00 5.10e-01 1.19e+01 angle pdb=" C ASP A1657 " pdb=" N THR A1658 " pdb=" CA THR A1658 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 1.00e+01 angle pdb=" CA GLU A2773 " pdb=" CB GLU A2773 " pdb=" CG GLU A2773 " ideal model delta sigma weight residual 114.10 119.98 -5.88 2.00e+00 2.50e-01 8.63e+00 angle pdb=" CA GLU A3038 " pdb=" CB GLU A3038 " pdb=" CG GLU A3038 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.46e+00 angle pdb=" CB MET A1448 " pdb=" CG MET A1448 " pdb=" SD MET A1448 " ideal model delta sigma weight residual 112.70 119.59 -6.89 3.00e+00 1.11e-01 5.27e+00 ... (remaining 14603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5628 17.98 - 35.95: 717 35.95 - 53.93: 167 53.93 - 71.91: 33 71.91 - 89.89: 5 Dihedral angle restraints: 6550 sinusoidal: 2538 harmonic: 4012 Sorted by residual: dihedral pdb=" CA ASP A 989 " pdb=" CB ASP A 989 " pdb=" CG ASP A 989 " pdb=" OD1 ASP A 989 " ideal model delta sinusoidal sigma weight residual -30.00 -84.81 54.81 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CG ARG A1027 " pdb=" CD ARG A1027 " pdb=" NE ARG A1027 " pdb=" CZ ARG A1027 " ideal model delta sinusoidal sigma weight residual 180.00 136.68 43.32 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CG ARG A1551 " pdb=" CD ARG A1551 " pdb=" NE ARG A1551 " pdb=" CZ ARG A1551 " ideal model delta sinusoidal sigma weight residual -90.00 -133.23 43.23 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 6547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1107 0.027 - 0.054: 377 0.054 - 0.081: 150 0.081 - 0.108: 57 0.108 - 0.135: 22 Chirality restraints: 1713 Sorted by residual: chirality pdb=" CA ILE A2353 " pdb=" N ILE A2353 " pdb=" C ILE A2353 " pdb=" CB ILE A2353 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE A1144 " pdb=" N ILE A1144 " pdb=" C ILE A1144 " pdb=" CB ILE A1144 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE A2403 " pdb=" N ILE A2403 " pdb=" C ILE A2403 " pdb=" CB ILE A2403 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1710 not shown) Planarity restraints: 1850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A2661 " -0.039 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO A2662 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A2662 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A2662 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A1286 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C GLN A1286 " -0.032 2.00e-02 2.50e+03 pdb=" O GLN A1286 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A1287 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A3062 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A3063 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A3063 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A3063 " -0.022 5.00e-02 4.00e+02 ... (remaining 1847 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 127 2.64 - 3.20: 9647 3.20 - 3.77: 17532 3.77 - 4.33: 23234 4.33 - 4.90: 39028 Nonbonded interactions: 89568 Sorted by model distance: nonbonded pdb=" OE2 GLU A2788 " pdb="ZN ZN A4002 " model vdw 2.074 2.230 nonbonded pdb=" OE2 GLU A3081 " pdb="MG MG A4004 " model vdw 2.106 2.170 nonbonded pdb=" OE2 GLU A2575 " pdb="MN MN A4003 " model vdw 2.129 2.320 nonbonded pdb=" OD2 ASP A2518 " pdb="MN MN A4003 " model vdw 2.161 2.320 nonbonded pdb=" OD1 ASP A2518 " pdb="MN MN A4003 " model vdw 2.169 2.320 ... (remaining 89563 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.420 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.100 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 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 : 0.002 0.074 10807 Z= 0.093 Angle : 0.444 7.164 14614 Z= 0.235 Chirality : 0.036 0.135 1713 Planarity : 0.003 0.057 1850 Dihedral : 16.688 89.885 3930 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.25 % Favored : 97.68 % Rotamer: Outliers : 0.34 % Allowed : 22.57 % Favored : 77.09 % 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: 2.06 (0.24), residues: 1336 helix: 2.62 (0.19), residues: 777 sheet: 1.82 (0.61), residues: 69 loop : -0.86 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1364 TYR 0.010 0.001 TYR A2457 PHE 0.014 0.001 PHE A2633 TRP 0.012 0.001 TRP A2542 HIS 0.002 0.000 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (10801) covalent geometry : angle 0.44314 / 0.24 (14608) hydrogen bonds : bond 0.10344 / 7.23 ( 646) hydrogen bonds : angle 4.30793 / 3.02 ( 1863) metal coordination : bond 0.00137 / 0.08 ( 6) metal coordination : angle 1.06691 / 0.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.361 Fit side-chains REVERT: A 1621 MET cc_start: 0.7766 (mtp) cc_final: 0.7266 (mpp) REVERT: A 2773 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7361 (tm-30) REVERT: A 2814 ARG cc_start: 0.8390 (tmm160) cc_final: 0.8177 (tmm160) REVERT: A 3062 ASP cc_start: 0.7282 (m-30) cc_final: 0.6991 (t0) outliers start: 4 outliers final: 2 residues processed: 135 average time/residue: 0.4091 time to fit residues: 61.0868 Evaluate side-chains 115 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1401 ASN Chi-restraints excluded: chain A residue 2820 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 944 HIS A1034 ASN A2376 GLN A2692 GLN ** A2825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3043 GLN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.088710 restraints weight = 16278.874| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.55 r_work: 0.2961 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10807 Z= 0.261 Angle : 0.566 7.629 14614 Z= 0.294 Chirality : 0.042 0.172 1713 Planarity : 0.004 0.056 1850 Dihedral : 3.820 25.840 1461 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.01 % Rotamer: Outliers : 2.47 % Allowed : 21.98 % Favored : 75.55 % 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: 1.65 (0.23), residues: 1336 helix: 2.22 (0.19), residues: 789 sheet: 1.24 (0.59), residues: 76 loop : -0.94 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1805 TYR 0.019 0.002 TYR A1503 PHE 0.021 0.002 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.005 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.26 (10801) covalent geometry : angle 0.56536 / 0.29 (14608) hydrogen bonds : bond 0.03979 / 2.72 ( 646) hydrogen bonds : angle 3.98155 / 2.79 ( 1863) metal coordination : bond 0.00706 / 0.42 ( 6) metal coordination : angle 1.55700 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.246 Fit side-chains REVERT: A 968 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8543 (mm-30) REVERT: A 1621 MET cc_start: 0.7946 (mtp) cc_final: 0.7414 (mpp) REVERT: A 2358 ASP cc_start: 0.8798 (t70) cc_final: 0.8596 (t0) REVERT: A 2543 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8215 (mtpt) REVERT: A 3091 LYS cc_start: 0.8954 (ptmt) cc_final: 0.8535 (pttp) REVERT: A 3203 MET cc_start: 0.7485 (mtp) cc_final: 0.6914 (mtm) outliers start: 29 outliers final: 15 residues processed: 142 average time/residue: 0.4385 time to fit residues: 68.3485 Evaluate side-chains 123 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2347 VAL Chi-restraints excluded: chain A residue 2458 ILE Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2654 ILE Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3090 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [96, 107, 112, 95, 109, 66, 71, 74, 86, 0, 93] chunk 96 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 944 HIS A2692 GLN ** A2825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3045 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 = 0.3665 r_free = 0.3665 target = 0.126793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.091142 restraints weight = 16274.364| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.58 r_work: 0.3058 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10807 Z= 0.125 Angle : 0.474 8.273 14614 Z= 0.246 Chirality : 0.038 0.145 1713 Planarity : 0.003 0.054 1850 Dihedral : 3.631 19.390 1457 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.40 % Favored : 97.53 % Rotamer: Outliers : 2.39 % Allowed : 22.57 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.24), residues: 1336 helix: 2.26 (0.19), residues: 791 sheet: 1.15 (0.58), residues: 76 loop : -0.99 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2801 TYR 0.010 0.001 TYR A2457 PHE 0.021 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.003 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10801) covalent geometry : angle 0.47409 / 0.25 (14608) hydrogen bonds : bond 0.03421 / 2.31 ( 646) hydrogen bonds : angle 3.81753 / 2.68 ( 1863) metal coordination : bond 0.00353 / 0.22 ( 6) metal coordination : angle 0.83310 / 0.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.408 Fit side-chains REVERT: A 968 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8498 (mm-30) REVERT: A 1373 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7394 (tttt) REVERT: A 1456 ARG cc_start: 0.7702 (mmm-85) cc_final: 0.7352 (mtm-85) REVERT: A 1621 MET cc_start: 0.7933 (mtp) cc_final: 0.7395 (mpp) REVERT: A 2358 ASP cc_start: 0.8837 (t70) cc_final: 0.8621 (t0) REVERT: A 2543 LYS cc_start: 0.8511 (ttpp) cc_final: 0.8173 (mtpt) REVERT: A 3091 LYS cc_start: 0.8962 (ptmt) cc_final: 0.8559 (pttp) REVERT: A 3203 MET cc_start: 0.7430 (mtp) cc_final: 0.6906 (mtm) outliers start: 28 outliers final: 9 residues processed: 136 average time/residue: 0.4539 time to fit residues: 67.8338 Evaluate side-chains 123 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1373 LYS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3071 VAL Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3090 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [15, 134, 90, 95, 11, 33, 129, 68, 2, 122, 82] chunk 15 optimal weight: 0.3980 chunk 134 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 0.0870 chunk 82 optimal weight: 2.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 944 HIS ** A1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2692 GLN ** A2825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3045 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 = 0.3662 r_free = 0.3662 target = 0.126668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.090884 restraints weight = 16227.271| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.59 r_work: 0.3044 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10807 Z= 0.131 Angle : 0.465 8.138 14614 Z= 0.241 Chirality : 0.038 0.143 1713 Planarity : 0.003 0.055 1850 Dihedral : 3.593 19.308 1457 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 3.07 % Allowed : 22.49 % Favored : 74.45 % 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: 1.65 (0.23), residues: 1336 helix: 2.25 (0.19), residues: 792 sheet: 1.09 (0.57), residues: 76 loop : -0.99 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1348 TYR 0.010 0.001 TYR A1503 PHE 0.024 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.004 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (10801) covalent geometry : angle 0.46362 / 0.24 (14608) hydrogen bonds : bond 0.03335 / 2.25 ( 646) hydrogen bonds : angle 3.75729 / 2.64 ( 1863) metal coordination : bond 0.00365 / 0.23 ( 6) metal coordination : angle 2.06182 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 968 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8375 (mm-30) REVERT: A 1141 ILE cc_start: 0.8381 (mt) cc_final: 0.8050 (pp) REVERT: A 1373 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7348 (tttt) REVERT: A 1456 ARG cc_start: 0.7626 (mmm-85) cc_final: 0.7277 (mtm-85) REVERT: A 1621 MET cc_start: 0.7900 (mtp) cc_final: 0.7377 (mpp) REVERT: A 2358 ASP cc_start: 0.8703 (t70) cc_final: 0.8489 (t0) REVERT: A 3091 LYS cc_start: 0.8932 (ptmt) cc_final: 0.8559 (pttp) outliers start: 36 outliers final: 16 residues processed: 142 average time/residue: 0.4215 time to fit residues: 66.2217 Evaluate side-chains 129 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1373 LYS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 2347 VAL Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3071 VAL Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3090 THR Chi-restraints excluded: chain A residue 3198 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [84, 93, 30, 132, 89, 54, 134, 73, 37, 101, 48] chunk 84 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 134 optimal weight: 0.0570 chunk 73 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 944 HIS ** A1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2692 GLN ** A3045 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 = 0.3672 r_free = 0.3672 target = 0.127324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.091513 restraints weight = 16035.639| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.59 r_work: 0.3050 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10807 Z= 0.117 Angle : 0.470 7.948 14614 Z= 0.243 Chirality : 0.038 0.143 1713 Planarity : 0.003 0.054 1850 Dihedral : 3.557 19.137 1457 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 2.81 % Allowed : 22.83 % Favored : 74.36 % 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: 1.68 (0.23), residues: 1336 helix: 2.26 (0.19), residues: 795 sheet: 1.10 (0.58), residues: 76 loop : -0.99 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1478 TYR 0.009 0.001 TYR A1503 PHE 0.023 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.002 0.001 HIS A1066 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10801) covalent geometry : angle 0.46945 / 0.24 (14608) hydrogen bonds : bond 0.03230 / 2.17 ( 646) hydrogen bonds : angle 3.75879 / 2.63 ( 1863) metal coordination : bond 0.00334 / 0.21 ( 6) metal coordination : angle 1.54991 / 0.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 968 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8350 (mm-30) REVERT: A 1141 ILE cc_start: 0.8424 (mt) cc_final: 0.8086 (pp) REVERT: A 1373 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7393 (tttm) REVERT: A 1621 MET cc_start: 0.7868 (mtp) cc_final: 0.7350 (mpp) REVERT: A 2358 ASP cc_start: 0.8706 (t70) cc_final: 0.8491 (t0) REVERT: A 3091 LYS cc_start: 0.8929 (ptmt) cc_final: 0.8566 (pttp) outliers start: 33 outliers final: 16 residues processed: 141 average time/residue: 0.4140 time to fit residues: 64.3903 Evaluate side-chains 127 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1373 LYS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1647 MET Chi-restraints excluded: chain A residue 2347 VAL Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3071 VAL Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3090 THR Chi-restraints excluded: chain A residue 3198 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [27, 6, 128, 108, 119, 9, 69, 72, 117, 51, 132] chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 128 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 51 optimal weight: 0.2980 chunk 132 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 944 HIS ** A1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2692 GLN ** A3045 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 = 0.3676 r_free = 0.3676 target = 0.127556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.091766 restraints weight = 16287.539| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.61 r_work: 0.3046 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10807 Z= 0.113 Angle : 0.464 7.293 14614 Z= 0.243 Chirality : 0.038 0.143 1713 Planarity : 0.003 0.054 1850 Dihedral : 3.541 18.776 1457 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.98 % Allowed : 22.66 % Favored : 74.36 % 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: 1.73 (0.23), residues: 1336 helix: 2.32 (0.19), residues: 792 sheet: 1.18 (0.58), residues: 76 loop : -0.99 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2814 TYR 0.014 0.001 TYR A1413 PHE 0.023 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.002 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (10801) covalent geometry : angle 0.46352 / 0.24 (14608) hydrogen bonds : bond 0.03161 / 2.13 ( 646) hydrogen bonds : angle 3.73858 / 2.62 ( 1863) metal coordination : bond 0.00313 / 0.19 ( 6) metal coordination : angle 1.42233 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 968 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8343 (mm-30) REVERT: A 1141 ILE cc_start: 0.8423 (mt) cc_final: 0.8085 (pp) REVERT: A 1373 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7324 (tttt) REVERT: A 1456 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.7231 (mtm-85) REVERT: A 1621 MET cc_start: 0.7901 (mtp) cc_final: 0.7378 (mpp) REVERT: A 2358 ASP cc_start: 0.8695 (t70) cc_final: 0.8474 (t0) REVERT: A 3091 LYS cc_start: 0.8936 (ptmt) cc_final: 0.8570 (pttp) outliers start: 35 outliers final: 17 residues processed: 141 average time/residue: 0.4208 time to fit residues: 65.7069 Evaluate side-chains 129 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1373 LYS Chi-restraints excluded: chain A residue 1392 GLU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 2347 VAL Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3071 VAL Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3090 THR Chi-restraints excluded: chain A residue 3198 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [54, 105, 129, 116, 130, 126, 7, 66, 63, 38, 26] chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 129 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 944 HIS ** A1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2692 GLN ** A2825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3045 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 = 0.3662 r_free = 0.3662 target = 0.126520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.090549 restraints weight = 16181.490| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.59 r_work: 0.3036 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10807 Z= 0.146 Angle : 0.500 10.245 14614 Z= 0.256 Chirality : 0.039 0.144 1713 Planarity : 0.003 0.054 1850 Dihedral : 3.586 19.201 1457 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.98 % Allowed : 23.08 % Favored : 73.94 % 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: 1.66 (0.23), residues: 1336 helix: 2.27 (0.19), residues: 792 sheet: 1.15 (0.58), residues: 76 loop : -1.02 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1478 TYR 0.011 0.001 TYR A1413 PHE 0.023 0.001 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.002 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (10801) covalent geometry : angle 0.49922 / 0.26 (14608) hydrogen bonds : bond 0.03336 / 2.25 ( 646) hydrogen bonds : angle 3.81033 / 2.66 ( 1863) metal coordination : bond 0.00409 / 0.25 ( 6) metal coordination : angle 1.19546 / 0.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 968 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8406 (mm-30) REVERT: A 1062 CYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8104 (p) REVERT: A 1373 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7462 (tttt) REVERT: A 1456 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.7244 (mtm-85) REVERT: A 1621 MET cc_start: 0.7866 (mtp) cc_final: 0.7355 (mpp) REVERT: A 2358 ASP cc_start: 0.8717 (t70) cc_final: 0.8461 (t0) REVERT: A 3091 LYS cc_start: 0.8946 (ptmt) cc_final: 0.8577 (pttp) outliers start: 35 outliers final: 21 residues processed: 141 average time/residue: 0.4133 time to fit residues: 64.4979 Evaluate side-chains 138 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1062 CYS Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1373 LYS Chi-restraints excluded: chain A residue 1392 GLU Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2347 VAL Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2458 ILE Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2654 ILE Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2796 VAL Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3071 VAL Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3090 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [13, 10, 92, 14, 23, 4, 82, 125, 72, 84, 86] chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 944 HIS A1034 ASN A2692 GLN ** A2825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.127624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.092000 restraints weight = 16156.256| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.55 r_work: 0.3024 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10807 Z= 0.112 Angle : 0.478 7.594 14614 Z= 0.247 Chirality : 0.038 0.142 1713 Planarity : 0.003 0.054 1850 Dihedral : 3.546 18.907 1457 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.56 % Allowed : 23.59 % Favored : 73.85 % 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: 1.70 (0.23), residues: 1336 helix: 2.32 (0.19), residues: 792 sheet: 1.17 (0.58), residues: 76 loop : -1.04 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1478 TYR 0.011 0.001 TYR A1413 PHE 0.022 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.002 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (10801) covalent geometry : angle 0.47750 / 0.25 (14608) hydrogen bonds : bond 0.03186 / 2.14 ( 646) hydrogen bonds : angle 3.76650 / 2.63 ( 1863) metal coordination : bond 0.00321 / 0.20 ( 6) metal coordination : angle 1.49067 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 941 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8105 (mtt) REVERT: A 968 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8410 (mm-30) REVERT: A 1373 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7306 (tttt) REVERT: A 1456 ARG cc_start: 0.7635 (mmm-85) cc_final: 0.7247 (mtm-85) REVERT: A 1621 MET cc_start: 0.7877 (mtp) cc_final: 0.7370 (mpp) REVERT: A 2358 ASP cc_start: 0.8694 (t70) cc_final: 0.8445 (t0) outliers start: 30 outliers final: 18 residues processed: 140 average time/residue: 0.4127 time to fit residues: 63.9641 Evaluate side-chains 132 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1373 LYS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2347 VAL Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2654 ILE Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3071 VAL Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3090 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [88, 53, 77, 102, 81, 133, 83, 48, 92, 29, 114] chunk 88 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 102 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 92 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 114 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 944 HIS A2692 GLN ** A2825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3045 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 = 0.3685 r_free = 0.3685 target = 0.128299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.092670 restraints weight = 16144.399| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.56 r_work: 0.3030 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10807 Z= 0.106 Angle : 0.484 11.758 14614 Z= 0.247 Chirality : 0.038 0.142 1713 Planarity : 0.003 0.054 1850 Dihedral : 3.515 18.468 1457 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.56 % Allowed : 23.68 % Favored : 73.76 % 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: 1.70 (0.23), residues: 1336 helix: 2.33 (0.19), residues: 792 sheet: 1.14 (0.58), residues: 76 loop : -1.06 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2815 TYR 0.010 0.001 TYR A1413 PHE 0.021 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.002 0.000 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (10801) covalent geometry : angle 0.48297 / 0.25 (14608) hydrogen bonds : bond 0.03124 / 2.10 ( 646) hydrogen bonds : angle 3.75285 / 2.63 ( 1863) metal coordination : bond 0.00296 / 0.18 ( 6) metal coordination : angle 1.49177 / 0.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 941 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8092 (mtt) REVERT: A 968 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8424 (mm-30) REVERT: A 1373 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7266 (tttt) REVERT: A 1456 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.7171 (mtm-85) REVERT: A 1578 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8473 (tttm) REVERT: A 1621 MET cc_start: 0.7851 (mtp) cc_final: 0.7345 (mpp) REVERT: A 2358 ASP cc_start: 0.8690 (t70) cc_final: 0.8447 (t0) outliers start: 30 outliers final: 17 residues processed: 142 average time/residue: 0.4211 time to fit residues: 66.1464 Evaluate side-chains 133 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1373 LYS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2347 VAL Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2458 ILE Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2654 ILE Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3071 VAL Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3090 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [69, 97, 50, 109, 133, 72, 66, 96, 100, 47, 86] chunk 69 optimal weight: 0.0170 chunk 97 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 944 HIS A1034 ASN ** A1421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2692 GLN ** A3045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.128038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092294 restraints weight = 16012.886| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.60 r_work: 0.3067 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10807 Z= 0.113 Angle : 0.494 12.005 14614 Z= 0.252 Chirality : 0.038 0.140 1713 Planarity : 0.003 0.054 1850 Dihedral : 3.503 18.219 1457 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.96 % Allowed : 24.11 % Favored : 73.94 % 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: 1.70 (0.23), residues: 1336 helix: 2.33 (0.19), residues: 792 sheet: 1.17 (0.58), residues: 76 loop : -1.08 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2815 TYR 0.009 0.001 TYR A1413 PHE 0.021 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.002 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (10801) covalent geometry : angle 0.49329 / 0.25 (14608) hydrogen bonds : bond 0.03163 / 2.13 ( 646) hydrogen bonds : angle 3.74658 / 2.62 ( 1863) metal coordination : bond 0.00336 / 0.20 ( 6) metal coordination : angle 1.38519 / 0.80 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 941 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8140 (mtt) REVERT: A 968 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8421 (mm-30) REVERT: A 1456 ARG cc_start: 0.7545 (mmm-85) cc_final: 0.7171 (mtm-85) REVERT: A 1529 MET cc_start: 0.8799 (ttm) cc_final: 0.8584 (mtt) REVERT: A 1621 MET cc_start: 0.7831 (mtp) cc_final: 0.7324 (mpp) REVERT: A 2358 ASP cc_start: 0.8678 (t70) cc_final: 0.8467 (t0) outliers start: 23 outliers final: 19 residues processed: 134 average time/residue: 0.4222 time to fit residues: 62.5811 Evaluate side-chains 134 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 941 MET Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1349 CYS Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1573 VAL Chi-restraints excluded: chain A residue 1647 MET Chi-restraints excluded: chain A residue 2295 THR Chi-restraints excluded: chain A residue 2347 VAL Chi-restraints excluded: chain A residue 2352 VAL Chi-restraints excluded: chain A residue 2356 SER Chi-restraints excluded: chain A residue 2458 ILE Chi-restraints excluded: chain A residue 2467 SER Chi-restraints excluded: chain A residue 2654 ILE Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 3006 VAL Chi-restraints excluded: chain A residue 3029 LEU Chi-restraints excluded: chain A residue 3049 PHE Chi-restraints excluded: chain A residue 3071 VAL Chi-restraints excluded: chain A residue 3081 GLU Chi-restraints excluded: chain A residue 3090 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: [108, 9, 77, 23, 28, 34, 48, 8, 68, 55, 71] chunk 108 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 23 optimal weight: 30.0000 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 944 HIS A2692 GLN ** A3045 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 = 0.3681 r_free = 0.3681 target = 0.127821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.092138 restraints weight = 16144.584| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.61 r_work: 0.3060 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10807 Z= 0.120 Angle : 0.497 11.675 14614 Z= 0.254 Chirality : 0.038 0.142 1713 Planarity : 0.003 0.054 1850 Dihedral : 3.520 18.201 1457 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.04 % Allowed : 24.19 % Favored : 73.76 % 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: 1.68 (0.23), residues: 1336 helix: 2.31 (0.19), residues: 791 sheet: 1.18 (0.58), residues: 76 loop : -1.08 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1478 TYR 0.010 0.001 TYR A1413 PHE 0.021 0.001 PHE A2633 TRP 0.014 0.001 TRP A2542 HIS 0.002 0.001 HIS A1491 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (10801) covalent geometry : angle 0.49605 / 0.25 (14608) hydrogen bonds : bond 0.03201 / 2.15 ( 646) hydrogen bonds : angle 3.75834 / 2.63 ( 1863) metal coordination : bond 0.00348 / 0.21 ( 6) metal coordination : angle 1.29620 / 0.74 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3315.68 seconds wall clock time: 57 minutes 40.94 seconds (3460.94 seconds total)