Starting phenix.real_space_refine on Wed Jul 30 22:50:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eak_47834/07_2025/9eak_47834.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eak_47834/07_2025/9eak_47834.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9eak_47834/07_2025/9eak_47834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eak_47834/07_2025/9eak_47834.map" model { file = "/net/cci-nas-00/data/ceres_data/9eak_47834/07_2025/9eak_47834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eak_47834/07_2025/9eak_47834.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 149 5.49 5 Mg 1 5.21 5 S 18 5.16 5 C 7648 2.51 5 N 2308 2.21 5 O 2755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12879 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2038 Classifications: {'RNA': 95} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 83} Chain: "C" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 648 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 457 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 9735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1356, 9735 Classifications: {'peptide': 1356} Incomplete info: {'truncation_to_alanine': 358} Link IDs: {'PTRANS': 35, 'TRANS': 1320} Chain breaks: 2 Unresolved non-hydrogen bonds: 1377 Unresolved non-hydrogen angles: 1703 Unresolved non-hydrogen dihedrals: 1103 Unresolved non-hydrogen chiralities: 95 Planarities with less than four sites: {'GLN:plan1': 26, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 27, 'TRP:plan': 1, 'ASP:plan': 46, 'PHE:plan': 11, 'GLU:plan': 62, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 782 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.10, per 1000 atoms: 0.78 Number of scatterers: 12879 At special positions: 0 Unit cell: (96.6512, 135.812, 124.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 149 15.00 Mg 1 11.99 O 2755 8.00 N 2308 7.00 C 7648 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: 3.29 Conformation dependent library (CDL) restraints added in 1.5 seconds 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2578 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 10 sheets defined 52.7% alpha, 9.1% beta 50 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'A' and resid 60 through 91 removed outlier: 5.092A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.716A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 236 through 246 removed outlier: 3.844A pdb=" N ASN A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 269 through 283 removed outlier: 4.134A pdb=" N ASP A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 303 removed outlier: 3.587A pdb=" N ALA A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.566A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.154A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.755A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.716A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.091A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 561 through 571 Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.554A pdb=" N ASP A 596 " --> pdb=" O GLY A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.904A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 629 through 637 Processing helix chain 'A' and resid 638 through 643 removed outlier: 4.999A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 653 removed outlier: 3.942A pdb=" N ARG A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 702 through 716 removed outlier: 3.554A pdb=" N GLU A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 776 through 792 Processing helix chain 'A' and resid 794 through 799 Processing helix chain 'A' and resid 811 through 817 Processing helix chain 'A' and resid 832 through 836 Processing helix chain 'A' and resid 873 through 889 removed outlier: 3.777A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 902 Processing helix chain 'A' and resid 909 through 922 Processing helix chain 'A' and resid 925 through 940 removed outlier: 3.637A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.090A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.391A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.823A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1022 removed outlier: 3.712A pdb=" N MET A1021 " --> pdb=" O ASP A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.754A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 3.518A pdb=" N GLU A1268 " --> pdb=" O HIS A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1312 removed outlier: 3.580A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1316 Processing helix chain 'A' and resid 1341 through 1344 removed outlier: 3.640A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1341 through 1344' Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 7.008A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.614A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 251 Processing sheet with id=AA4, first strand: chain 'A' and resid 838 through 840 Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.673A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.516A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.516A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1324 through 1325 510 hydrogen bonds defined for protein. 1479 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 8.00 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2794 1.33 - 1.45: 3769 1.45 - 1.58: 6537 1.58 - 1.70: 296 1.70 - 1.82: 34 Bond restraints: 13430 Sorted by residual: bond pdb=" N TYR A 639 " pdb=" CA TYR A 639 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.22e-02 6.72e+03 9.11e+00 bond pdb=" N ASP A 384 " pdb=" CA ASP A 384 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.19e-02 7.06e+03 9.01e+00 bond pdb=" N VAL A 339 " pdb=" CA VAL A 339 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.18e-02 7.18e+03 8.30e+00 bond pdb=" N MET A 383 " pdb=" CA MET A 383 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.24e+00 bond pdb=" N LYS A 942 " pdb=" CA LYS A 942 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.40e+00 ... (remaining 13425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 18348 2.09 - 4.19: 480 4.19 - 6.28: 72 6.28 - 8.37: 17 8.37 - 10.47: 5 Bond angle restraints: 18922 Sorted by residual: angle pdb=" C ALA A 287 " pdb=" N ASP A 288 " pdb=" CA ASP A 288 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 angle pdb=" N VAL A 583 " pdb=" CA VAL A 583 " pdb=" C VAL A 583 " ideal model delta sigma weight residual 110.21 105.57 4.64 1.13e+00 7.83e-01 1.69e+01 angle pdb=" C ASP A 628 " pdb=" N ARG A 629 " pdb=" CA ARG A 629 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" CB GLU A1150 " pdb=" CG GLU A1150 " pdb=" CD GLU A1150 " ideal model delta sigma weight residual 112.60 119.08 -6.48 1.70e+00 3.46e-01 1.45e+01 angle pdb=" CA GLU A 345 " pdb=" CB GLU A 345 " pdb=" CG GLU A 345 " ideal model delta sigma weight residual 114.10 121.47 -7.37 2.00e+00 2.50e-01 1.36e+01 ... (remaining 18917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 7423 34.83 - 69.65: 505 69.65 - 104.48: 32 104.48 - 139.31: 1 139.31 - 174.13: 6 Dihedral angle restraints: 7967 sinusoidal: 3988 harmonic: 3979 Sorted by residual: dihedral pdb=" O4' C B 70 " pdb=" C1' C B 70 " pdb=" N1 C B 70 " pdb=" C2 C B 70 " ideal model delta sinusoidal sigma weight residual 200.00 32.88 167.12 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" O4' G B 5 " pdb=" C1' G B 5 " pdb=" N9 G B 5 " pdb=" C4 G B 5 " ideal model delta sinusoidal sigma weight residual 70.00 -5.54 75.54 1 2.00e+01 2.50e-03 1.80e+01 dihedral pdb=" C4' DC D 34 " pdb=" C3' DC D 34 " pdb=" O3' DC D 34 " pdb=" P DG D 35 " ideal model delta sinusoidal sigma weight residual -140.00 34.13 -174.13 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2139 0.103 - 0.206: 114 0.206 - 0.309: 4 0.309 - 0.411: 0 0.411 - 0.514: 5 Chirality restraints: 2262 Sorted by residual: chirality pdb=" P C B 67 " pdb=" OP1 C B 67 " pdb=" OP2 C B 67 " pdb=" O5' C B 67 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" P A B 69 " pdb=" OP1 A B 69 " pdb=" OP2 A B 69 " pdb=" O5' A B 69 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.41e+00 chirality pdb=" P A B 68 " pdb=" OP1 A B 68 " pdb=" OP2 A B 68 " pdb=" O5' A B 68 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.26e+00 ... (remaining 2259 not shown) Planarity restraints: 1893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 951 " -0.335 9.50e-02 1.11e+02 1.50e-01 1.39e+01 pdb=" NE ARG A 951 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 951 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 951 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 951 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 549 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C VAL A 549 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL A 549 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP A 550 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 566 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.53e+00 pdb=" CD GLU A 566 " 0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU A 566 " -0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU A 566 " -0.019 2.00e-02 2.50e+03 ... (remaining 1890 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2024 2.76 - 3.30: 11761 3.30 - 3.83: 23259 3.83 - 4.37: 26961 4.37 - 4.90: 42016 Nonbonded interactions: 106021 Sorted by model distance: nonbonded pdb=" OE2 GLU A 762 " pdb=" OG SER A 960 " model vdw 2.229 3.040 nonbonded pdb=" O2' A B 47 " pdb=" O LEU A 101 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR A 5 " pdb=" O HIS A 754 " model vdw 2.273 3.040 nonbonded pdb=" O ILE A1273 " pdb=" OG SER A1277 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 517 " pdb=" NZ LYS A 554 " model vdw 2.295 3.120 ... (remaining 106016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.060 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 40.580 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 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 : 0.005 0.068 13430 Z= 0.259 Angle : 0.804 10.468 18922 Z= 0.457 Chirality : 0.052 0.514 2262 Planarity : 0.007 0.150 1893 Dihedral : 20.181 174.133 5389 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.61 % Allowed : 21.19 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.21), residues: 1350 helix: -0.13 (0.19), residues: 641 sheet: 0.14 (0.45), residues: 119 loop : -1.28 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 476 HIS 0.009 0.001 HIS A 328 PHE 0.050 0.002 PHE A 897 TYR 0.032 0.002 TYR A 594 ARG 0.016 0.001 ARG A 400 Details of bonding type rmsd hydrogen bonds : bond 0.13050 ( 620) hydrogen bonds : angle 6.49412 ( 1717) covalent geometry : bond 0.00478 (13430) covalent geometry : angle 0.80359 (18922) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 1.104 Fit side-chains REVERT: A 84 GLU cc_start: 0.8781 (pp20) cc_final: 0.8560 (tm-30) REVERT: A 397 ASP cc_start: 0.7885 (t0) cc_final: 0.7434 (t0) REVERT: A 424 ARG cc_start: 0.8587 (mmm-85) cc_final: 0.8051 (mmt-90) REVERT: A 506 LYS cc_start: 0.7786 (mtmt) cc_final: 0.7057 (mmmt) REVERT: A 517 TYR cc_start: 0.8409 (m-80) cc_final: 0.8188 (m-10) REVERT: A 649 LYS cc_start: 0.8884 (tttm) cc_final: 0.8517 (tptt) REVERT: A 663 SER cc_start: 0.8890 (t) cc_final: 0.8659 (p) REVERT: A 721 HIS cc_start: 0.8225 (m90) cc_final: 0.7793 (t-170) REVERT: A 757 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8398 (mt-10) REVERT: A 933 GLN cc_start: 0.8621 (tt0) cc_final: 0.8264 (tm-30) REVERT: A 1124 LYS cc_start: 0.8562 (tppt) cc_final: 0.8068 (tmtm) REVERT: A 1160 VAL cc_start: 0.8536 (p) cc_final: 0.8218 (m) outliers start: 5 outliers final: 3 residues processed: 116 average time/residue: 1.2439 time to fit residues: 158.4972 Evaluate side-chains 103 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1092 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 116 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 ASN A 758 ASN A 844 GLN ** A 920 GLN ** 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 = 0.3785 r_free = 0.3785 target = 0.127012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.082551 restraints weight = 21544.723| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.94 r_work: 0.2915 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13430 Z= 0.177 Angle : 0.554 7.783 18922 Z= 0.303 Chirality : 0.039 0.281 2262 Planarity : 0.004 0.050 1893 Dihedral : 21.043 176.801 3477 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.60 % Allowed : 16.59 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.22), residues: 1350 helix: 0.84 (0.20), residues: 648 sheet: 0.10 (0.45), residues: 124 loop : -0.88 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 476 HIS 0.004 0.001 HIS A 328 PHE 0.017 0.001 PHE A 916 TYR 0.015 0.001 TYR A 362 ARG 0.004 0.000 ARG A1078 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 620) hydrogen bonds : angle 4.63068 ( 1717) covalent geometry : bond 0.00389 (13430) covalent geometry : angle 0.55389 (18922) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 1.112 Fit side-chains REVERT: A 383 MET cc_start: 0.8048 (ttm) cc_final: 0.7820 (mtm) REVERT: A 390 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8643 (mm) REVERT: A 397 ASP cc_start: 0.8340 (t0) cc_final: 0.7914 (t0) REVERT: A 424 ARG cc_start: 0.8613 (mmm-85) cc_final: 0.8103 (mmt-90) REVERT: A 649 LYS cc_start: 0.8831 (tttm) cc_final: 0.8454 (tptt) REVERT: A 653 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7899 (mmp-170) REVERT: A 721 HIS cc_start: 0.8271 (m90) cc_final: 0.7868 (t-170) REVERT: A 933 GLN cc_start: 0.8665 (tt0) cc_final: 0.8317 (tm130) REVERT: A 1124 LYS cc_start: 0.8668 (tppt) cc_final: 0.8202 (tmtm) outliers start: 38 outliers final: 15 residues processed: 132 average time/residue: 1.0874 time to fit residues: 159.1321 Evaluate side-chains 106 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 653 ARG Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 63 optimal weight: 1.9990 chunk 118 optimal weight: 0.0980 chunk 35 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 ASN A 899 ASN ** A 920 GLN ** 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 = 0.3809 r_free = 0.3809 target = 0.129385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.086327 restraints weight = 22058.388| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.93 r_work: 0.2908 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13430 Z= 0.164 Angle : 0.529 8.036 18922 Z= 0.289 Chirality : 0.039 0.273 2262 Planarity : 0.003 0.051 1893 Dihedral : 21.031 175.756 3477 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.00 % Allowed : 17.55 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1350 helix: 1.28 (0.21), residues: 646 sheet: 0.10 (0.45), residues: 124 loop : -0.73 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 PHE 0.012 0.001 PHE A 446 TYR 0.027 0.001 TYR A 515 ARG 0.004 0.000 ARG A1078 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 620) hydrogen bonds : angle 4.32558 ( 1717) covalent geometry : bond 0.00359 (13430) covalent geometry : angle 0.52940 (18922) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 1.144 Fit side-chains REVERT: A 383 MET cc_start: 0.8264 (ttm) cc_final: 0.8029 (mtm) REVERT: A 390 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8799 (mm) REVERT: A 397 ASP cc_start: 0.8473 (t0) cc_final: 0.8020 (t0) REVERT: A 424 ARG cc_start: 0.8766 (mmm-85) cc_final: 0.8210 (mmt-90) REVERT: A 506 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7407 (mmmt) REVERT: A 595 HIS cc_start: 0.6381 (m170) cc_final: 0.6011 (m170) REVERT: A 649 LYS cc_start: 0.8883 (tttm) cc_final: 0.8489 (tptt) REVERT: A 653 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8021 (mmp-170) REVERT: A 664 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8409 (tpp80) REVERT: A 721 HIS cc_start: 0.8318 (m90) cc_final: 0.8079 (t-170) REVERT: A 917 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7513 (pp) REVERT: A 933 GLN cc_start: 0.8801 (tt0) cc_final: 0.8452 (tm130) REVERT: A 952 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8372 (mt-10) REVERT: A 1124 LYS cc_start: 0.8729 (tppt) cc_final: 0.8307 (tmtm) outliers start: 33 outliers final: 12 residues processed: 122 average time/residue: 1.1849 time to fit residues: 159.1543 Evaluate side-chains 103 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 653 ARG Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 82 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 ASN ** A 920 GLN ** 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 = 0.3702 r_free = 0.3702 target = 0.121446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.076440 restraints weight = 21410.697| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.95 r_work: 0.2787 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13430 Z= 0.271 Angle : 0.592 8.516 18922 Z= 0.325 Chirality : 0.042 0.306 2262 Planarity : 0.004 0.054 1893 Dihedral : 21.283 174.813 3477 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.36 % Allowed : 16.95 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.23), residues: 1350 helix: 1.23 (0.21), residues: 648 sheet: -0.09 (0.44), residues: 124 loop : -0.72 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 476 HIS 0.006 0.001 HIS A1241 PHE 0.018 0.002 PHE A 446 TYR 0.021 0.002 TYR A 362 ARG 0.005 0.001 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.04442 ( 620) hydrogen bonds : angle 4.45273 ( 1717) covalent geometry : bond 0.00604 (13430) covalent geometry : angle 0.59185 (18922) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 1.306 Fit side-chains REVERT: A 40 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7586 (ttt-90) REVERT: A 390 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8625 (mm) REVERT: A 397 ASP cc_start: 0.8316 (t0) cc_final: 0.7808 (t0) REVERT: A 424 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8158 (mmt-90) REVERT: A 457 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8231 (mmm-85) REVERT: A 506 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7352 (mmmt) REVERT: A 649 LYS cc_start: 0.8803 (tttm) cc_final: 0.8186 (tptt) REVERT: A 653 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.8021 (mmp-170) REVERT: A 661 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.6723 (mtp85) REVERT: A 721 HIS cc_start: 0.8397 (m90) cc_final: 0.8162 (t-170) REVERT: A 897 PHE cc_start: 0.8041 (t80) cc_final: 0.7796 (t80) REVERT: A 1124 LYS cc_start: 0.8673 (tppt) cc_final: 0.8222 (tmtm) outliers start: 36 outliers final: 15 residues processed: 114 average time/residue: 1.1755 time to fit residues: 148.1061 Evaluate side-chains 98 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 653 ARG Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 82 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 68 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.123819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.079264 restraints weight = 21731.220| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.93 r_work: 0.2843 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13430 Z= 0.163 Angle : 0.516 6.459 18922 Z= 0.283 Chirality : 0.038 0.265 2262 Planarity : 0.003 0.052 1893 Dihedral : 21.153 175.417 3477 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.39 % Allowed : 17.55 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1350 helix: 1.45 (0.21), residues: 647 sheet: -0.09 (0.45), residues: 124 loop : -0.65 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 476 HIS 0.004 0.001 HIS A 116 PHE 0.013 0.001 PHE A 446 TYR 0.016 0.001 TYR A 515 ARG 0.004 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 620) hydrogen bonds : angle 4.25551 ( 1717) covalent geometry : bond 0.00359 (13430) covalent geometry : angle 0.51638 (18922) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 1.333 Fit side-chains REVERT: A 40 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8194 (tpp-160) REVERT: A 342 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.5913 (mp10) REVERT: A 390 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8632 (mm) REVERT: A 397 ASP cc_start: 0.8270 (t0) cc_final: 0.7736 (t0) REVERT: A 424 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8014 (mmt-90) REVERT: A 506 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7380 (mmmt) REVERT: A 604 LYS cc_start: 0.8865 (tttt) cc_final: 0.8637 (tttt) REVERT: A 649 LYS cc_start: 0.8785 (tttm) cc_final: 0.8146 (tptt) REVERT: A 653 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7939 (mmp-170) REVERT: A 661 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.6803 (mtp85) REVERT: A 721 HIS cc_start: 0.8334 (m90) cc_final: 0.8112 (t-170) REVERT: A 917 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7663 (pp) REVERT: A 952 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8322 (mt-10) REVERT: A 1124 LYS cc_start: 0.8656 (tppt) cc_final: 0.8204 (tmtm) outliers start: 28 outliers final: 15 residues processed: 108 average time/residue: 1.2884 time to fit residues: 153.2028 Evaluate side-chains 97 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 653 ARG Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.124427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.079847 restraints weight = 21941.684| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.95 r_work: 0.2860 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13430 Z= 0.151 Angle : 0.501 6.285 18922 Z= 0.275 Chirality : 0.037 0.262 2262 Planarity : 0.003 0.054 1893 Dihedral : 21.058 176.868 3477 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.36 % Allowed : 16.83 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1350 helix: 1.62 (0.21), residues: 647 sheet: 0.01 (0.45), residues: 122 loop : -0.59 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 476 HIS 0.003 0.001 HIS A 116 PHE 0.011 0.001 PHE A 446 TYR 0.012 0.001 TYR A 155 ARG 0.003 0.000 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 620) hydrogen bonds : angle 4.14209 ( 1717) covalent geometry : bond 0.00331 (13430) covalent geometry : angle 0.50071 (18922) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 1.234 Fit side-chains REVERT: A 40 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7459 (ttt-90) REVERT: A 342 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.5826 (mp10) REVERT: A 390 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8668 (mm) REVERT: A 397 ASP cc_start: 0.8163 (t0) cc_final: 0.7601 (t0) REVERT: A 404 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8971 (p) REVERT: A 424 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8122 (mmt-90) REVERT: A 506 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7431 (mmmt) REVERT: A 604 LYS cc_start: 0.8909 (tttt) cc_final: 0.8649 (tttt) REVERT: A 649 LYS cc_start: 0.8772 (tttm) cc_final: 0.8120 (tptt) REVERT: A 653 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.8005 (mmp-170) REVERT: A 917 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7727 (pp) REVERT: A 952 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8325 (mt-10) REVERT: A 1124 LYS cc_start: 0.8679 (tppt) cc_final: 0.8224 (tmtm) outliers start: 36 outliers final: 12 residues processed: 116 average time/residue: 1.1945 time to fit residues: 152.3084 Evaluate side-chains 97 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 653 ARG Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 126 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 63 optimal weight: 0.1980 chunk 139 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 49 optimal weight: 0.0060 chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.125455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.081295 restraints weight = 21544.846| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.91 r_work: 0.2889 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13430 Z= 0.120 Angle : 0.491 6.332 18922 Z= 0.269 Chirality : 0.037 0.249 2262 Planarity : 0.003 0.053 1893 Dihedral : 21.037 176.731 3477 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.15 % Allowed : 18.40 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1350 helix: 1.72 (0.21), residues: 648 sheet: 0.07 (0.46), residues: 122 loop : -0.60 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 PHE 0.011 0.001 PHE A 446 TYR 0.011 0.001 TYR A 529 ARG 0.002 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 620) hydrogen bonds : angle 4.08829 ( 1717) covalent geometry : bond 0.00256 (13430) covalent geometry : angle 0.49110 (18922) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 1.126 Fit side-chains REVERT: A 65 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8563 (mmpt) REVERT: A 145 SER cc_start: 0.8157 (t) cc_final: 0.7941 (p) REVERT: A 342 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.5581 (mp10) REVERT: A 390 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8620 (mm) REVERT: A 397 ASP cc_start: 0.8134 (t0) cc_final: 0.7570 (t0) REVERT: A 404 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8948 (p) REVERT: A 424 ARG cc_start: 0.8541 (mmm-85) cc_final: 0.8002 (mmt-90) REVERT: A 506 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7389 (mmmt) REVERT: A 604 LYS cc_start: 0.8904 (tttt) cc_final: 0.8648 (tttt) REVERT: A 661 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.6944 (mtp85) REVERT: A 895 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7672 (ptm-80) REVERT: A 917 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7808 (mp) REVERT: A 952 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8300 (mt-10) REVERT: A 1124 LYS cc_start: 0.8657 (tppt) cc_final: 0.8200 (tmtm) outliers start: 26 outliers final: 9 residues processed: 106 average time/residue: 1.2417 time to fit residues: 144.5425 Evaluate side-chains 96 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 895 ARG Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 145 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.123610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.078828 restraints weight = 21857.755| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.94 r_work: 0.2837 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13430 Z= 0.176 Angle : 0.514 5.980 18922 Z= 0.281 Chirality : 0.038 0.269 2262 Planarity : 0.003 0.054 1893 Dihedral : 21.033 176.401 3475 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.27 % Allowed : 17.80 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1350 helix: 1.68 (0.21), residues: 651 sheet: -0.00 (0.46), residues: 122 loop : -0.54 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 476 HIS 0.003 0.001 HIS A 116 PHE 0.013 0.001 PHE A1327 TYR 0.015 0.001 TYR A 155 ARG 0.003 0.000 ARG A 437 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 620) hydrogen bonds : angle 4.13266 ( 1717) covalent geometry : bond 0.00390 (13430) covalent geometry : angle 0.51426 (18922) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 1.438 Fit side-chains revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7586 (ttt-90) REVERT: A 342 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.5854 (mp10) REVERT: A 390 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8669 (mm) REVERT: A 397 ASP cc_start: 0.8178 (t0) cc_final: 0.7632 (t0) REVERT: A 404 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8985 (p) REVERT: A 424 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8200 (mmt-90) REVERT: A 506 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7510 (mmmt) REVERT: A 604 LYS cc_start: 0.8959 (tttt) cc_final: 0.8691 (tttt) REVERT: A 895 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7747 (ptm-80) REVERT: A 948 LYS cc_start: 0.8357 (tppp) cc_final: 0.8008 (tppp) REVERT: A 952 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8331 (mt-10) REVERT: A 1124 LYS cc_start: 0.8708 (tppt) cc_final: 0.8255 (tmtm) outliers start: 27 outliers final: 12 residues processed: 103 average time/residue: 1.2578 time to fit residues: 142.8216 Evaluate side-chains 99 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 895 ARG Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 56 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.124396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.079944 restraints weight = 21693.902| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.91 r_work: 0.2858 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13430 Z= 0.155 Angle : 0.502 5.875 18922 Z= 0.274 Chirality : 0.037 0.258 2262 Planarity : 0.003 0.053 1893 Dihedral : 21.004 176.486 3475 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.54 % Allowed : 19.01 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.23), residues: 1350 helix: 1.75 (0.21), residues: 645 sheet: 0.13 (0.46), residues: 120 loop : -0.59 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS A 116 PHE 0.011 0.001 PHE A 446 TYR 0.012 0.001 TYR A 155 ARG 0.003 0.000 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 620) hydrogen bonds : angle 4.08726 ( 1717) covalent geometry : bond 0.00342 (13430) covalent geometry : angle 0.50214 (18922) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7578 (ttt-90) REVERT: A 342 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.5794 (mp10) REVERT: A 390 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8647 (mm) REVERT: A 397 ASP cc_start: 0.8140 (t0) cc_final: 0.7596 (t0) REVERT: A 404 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8997 (p) REVERT: A 424 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.8126 (mmt-90) REVERT: A 506 LYS cc_start: 0.8254 (mtmt) cc_final: 0.7537 (mmmt) REVERT: A 604 LYS cc_start: 0.8986 (tttt) cc_final: 0.8721 (tttt) REVERT: A 661 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.6981 (mtp85) REVERT: A 917 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7924 (mp) REVERT: A 948 LYS cc_start: 0.8281 (tppp) cc_final: 0.7896 (tppp) REVERT: A 952 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8326 (mt-10) REVERT: A 1124 LYS cc_start: 0.8683 (tppt) cc_final: 0.8231 (tmtm) outliers start: 21 outliers final: 12 residues processed: 96 average time/residue: 1.3428 time to fit residues: 141.1499 Evaluate side-chains 94 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 125 optimal weight: 0.1980 chunk 112 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 135 optimal weight: 0.0470 chunk 91 optimal weight: 20.0000 chunk 44 optimal weight: 0.4980 chunk 113 optimal weight: 0.6980 chunk 98 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 920 GLN ** 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 = 0.3753 r_free = 0.3753 target = 0.125020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.080731 restraints weight = 21533.033| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.90 r_work: 0.2877 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13430 Z= 0.125 Angle : 0.498 6.047 18922 Z= 0.272 Chirality : 0.037 0.254 2262 Planarity : 0.003 0.053 1893 Dihedral : 21.007 176.600 3475 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.06 % Allowed : 19.37 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1350 helix: 1.75 (0.21), residues: 650 sheet: 0.13 (0.46), residues: 120 loop : -0.54 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS A 116 PHE 0.014 0.001 PHE A 587 TYR 0.034 0.001 TYR A1001 ARG 0.002 0.000 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 620) hydrogen bonds : angle 4.07968 ( 1717) covalent geometry : bond 0.00270 (13430) covalent geometry : angle 0.49827 (18922) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7552 (ttt-90) REVERT: A 342 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.5778 (mp10) REVERT: A 390 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8665 (mm) REVERT: A 397 ASP cc_start: 0.8097 (t0) cc_final: 0.7552 (t0) REVERT: A 404 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8970 (p) REVERT: A 424 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.8110 (mmt-90) REVERT: A 506 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7531 (mmmt) REVERT: A 604 LYS cc_start: 0.9004 (tttt) cc_final: 0.8739 (tttt) REVERT: A 661 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.6974 (mtp85) REVERT: A 917 ILE cc_start: 0.8165 (pp) cc_final: 0.7910 (mp) REVERT: A 948 LYS cc_start: 0.8264 (tppp) cc_final: 0.7881 (tppp) REVERT: A 952 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8330 (mt-10) REVERT: A 1124 LYS cc_start: 0.8665 (tppt) cc_final: 0.8212 (tmtm) outliers start: 17 outliers final: 10 residues processed: 93 average time/residue: 1.3464 time to fit residues: 136.8281 Evaluate side-chains 93 residues out of total 1217 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 661 ARG Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 42 optimal weight: 4.9990 chunk 53 optimal weight: 0.0070 chunk 96 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.123248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.078543 restraints weight = 21624.959| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.93 r_work: 0.2827 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13430 Z= 0.194 Angle : 0.527 7.299 18922 Z= 0.288 Chirality : 0.039 0.269 2262 Planarity : 0.003 0.054 1893 Dihedral : 21.020 176.283 3475 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.54 % Allowed : 18.64 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1350 helix: 1.72 (0.21), residues: 651 sheet: 0.01 (0.46), residues: 122 loop : -0.53 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 476 HIS 0.004 0.001 HIS A1241 PHE 0.013 0.001 PHE A1327 TYR 0.015 0.001 TYR A 155 ARG 0.004 0.000 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 620) hydrogen bonds : angle 4.12939 ( 1717) covalent geometry : bond 0.00432 (13430) covalent geometry : angle 0.52730 (18922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11216.74 seconds wall clock time: 192 minutes 23.02 seconds (11543.02 seconds total)