Starting phenix.real_space_refine on Tue Mar 3 19:18:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nur_12600/03_2026/7nur_12600.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nur_12600/03_2026/7nur_12600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.125 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nur_12600/03_2026/7nur_12600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nur_12600/03_2026/7nur_12600.map" model { file = "/net/cci-nas-00/data/ceres_data/7nur_12600/03_2026/7nur_12600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nur_12600/03_2026/7nur_12600.cif" } resolution = 3.125 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= 0.003 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5307 2.51 5 N 1417 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8245 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8245 Classifications: {'peptide': 1044} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 61, 'TRANS': 982} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 1.95, per 1000 atoms: 0.24 Number of scatterers: 8245 At special positions: 0 Unit cell: (89.712, 98.256, 120.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1490 8.00 N 1417 7.00 C 5307 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 688 " - pdb=" SG CYS A 727 " distance=2.03 Simple disulfide: pdb=" SG CYS A1301 " - pdb=" SG CYS A1359 " distance=2.03 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: 0.64 Conformation dependent library (CDL) restraints added in 288.2 milliseconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 54.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 308 through 317 removed outlier: 4.288A pdb=" N GLN A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.610A pdb=" N GLY A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 removed outlier: 4.007A pdb=" N ARG A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 421 removed outlier: 3.810A pdb=" N ARG A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 4.000A pdb=" N ILE A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLY A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 436 " --> pdb=" O MET A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 479 removed outlier: 4.058A pdb=" N THR A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN A 470 " --> pdb=" O THR A 466 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA A 477 " --> pdb=" O LYS A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.671A pdb=" N SER A 484 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 505 removed outlier: 3.969A pdb=" N TYR A 498 " --> pdb=" O GLN A 494 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 removed outlier: 4.193A pdb=" N LEU A 561 " --> pdb=" O GLY A 557 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 578 removed outlier: 3.697A pdb=" N LEU A 571 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 576 " --> pdb=" O ILE A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 588 Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.674A pdb=" N GLU A 647 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 removed outlier: 3.969A pdb=" N TYR A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 663 " --> pdb=" O TYR A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 Processing helix chain 'A' and resid 689 through 694 Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 718 through 729 removed outlier: 3.884A pdb=" N TYR A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 743 through 754 Processing helix chain 'A' and resid 763 through 783 Processing helix chain 'A' and resid 792 through 802 Processing helix chain 'A' and resid 804 through 813 Processing helix chain 'A' and resid 824 through 834 removed outlier: 3.561A pdb=" N LEU A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 849 removed outlier: 3.582A pdb=" N TYR A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 860 removed outlier: 3.521A pdb=" N PHE A 860 " --> pdb=" O TYR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 891 Processing helix chain 'A' and resid 896 through 908 Processing helix chain 'A' and resid 914 through 928 removed outlier: 3.890A pdb=" N VAL A 918 " --> pdb=" O GLY A 914 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 920 " --> pdb=" O ARG A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 939 Processing helix chain 'A' and resid 941 through 950 removed outlier: 3.562A pdb=" N TYR A 947 " --> pdb=" O VAL A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 982 through 1012 removed outlier: 3.814A pdb=" N SER A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 996 " --> pdb=" O LYS A 992 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1028 removed outlier: 3.738A pdb=" N GLY A1028 " --> pdb=" O GLN A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1052 removed outlier: 4.123A pdb=" N SER A1048 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1074 Processing helix chain 'A' and resid 1075 through 1082 removed outlier: 3.879A pdb=" N LYS A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1086 Processing helix chain 'A' and resid 1092 through 1111 removed outlier: 3.655A pdb=" N VAL A1106 " --> pdb=" O ALA A1102 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A1107 " --> pdb=" O ALA A1103 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A1108 " --> pdb=" O VAL A1104 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG A1109 " --> pdb=" O ARG A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1129 through 1134 removed outlier: 3.848A pdb=" N LYS A1133 " --> pdb=" O ALA A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 removed outlier: 3.679A pdb=" N SER A1150 " --> pdb=" O ARG A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1185 removed outlier: 3.576A pdb=" N GLU A1163 " --> pdb=" O PRO A1159 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A1167 " --> pdb=" O GLU A1163 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP A1168 " --> pdb=" O MET A1164 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A1180 " --> pdb=" O ILE A1176 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A1181 " --> pdb=" O ALA A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1240 removed outlier: 4.290A pdb=" N ARG A1228 " --> pdb=" O ALA A1224 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP A1236 " --> pdb=" O ARG A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1294 removed outlier: 3.621A pdb=" N GLN A1287 " --> pdb=" O LEU A1283 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A1288 " --> pdb=" O GLN A1284 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A1289 " --> pdb=" O PHE A1285 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A1294 " --> pdb=" O THR A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1303 removed outlier: 3.772A pdb=" N ARG A1302 " --> pdb=" O PRO A1299 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A1303 " --> pdb=" O GLN A1300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1299 through 1303' Processing helix chain 'A' and resid 1328 through 1332 Processing helix chain 'A' and resid 1363 through 1368 Processing sheet with id=AA1, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.993A pdb=" N LEU A 324 " --> pdb=" O LYS A 518 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TRP A 526 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 366 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 528 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 334 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA3, first strand: chain 'A' and resid 601 through 604 Processing sheet with id=AA4, first strand: chain 'A' and resid 1246 through 1256 removed outlier: 5.011A pdb=" N GLU A1268 " --> pdb=" O GLY A1254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1307 through 1309 348 hydrogen bonds defined for protein. 999 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: 1.25 Time building geometry restraints manager: 0.88 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: 2649 1.34 - 1.46: 1638 1.46 - 1.58: 4093 1.58 - 1.70: 0 1.70 - 1.81: 55 Bond restraints: 8435 Sorted by residual: bond pdb=" CA GLU A 858 " pdb=" C GLU A 858 " ideal model delta sigma weight residual 1.523 1.481 0.043 1.80e-02 3.09e+03 5.59e+00 bond pdb=" CA ARG A 916 " pdb=" C ARG A 916 " ideal model delta sigma weight residual 1.522 1.489 0.032 1.72e-02 3.38e+03 3.55e+00 bond pdb=" CB THR A 881 " pdb=" CG2 THR A 881 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.10e+00 bond pdb=" CB VAL A 919 " pdb=" CG1 VAL A 919 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.77e+00 bond pdb=" N LYS A 940 " pdb=" CA LYS A 940 " ideal model delta sigma weight residual 1.456 1.472 -0.016 1.23e-02 6.61e+03 1.77e+00 ... (remaining 8430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 10984 1.72 - 3.43: 371 3.43 - 5.15: 52 5.15 - 6.86: 11 6.86 - 8.58: 5 Bond angle restraints: 11423 Sorted by residual: angle pdb=" CA PHE A1062 " pdb=" C PHE A1062 " pdb=" N PRO A1063 " ideal model delta sigma weight residual 117.82 120.83 -3.01 7.80e-01 1.64e+00 1.49e+01 angle pdb=" CA ALA A1206 " pdb=" C ALA A1206 " pdb=" N HIS A1207 " ideal model delta sigma weight residual 118.43 123.29 -4.86 1.33e+00 5.65e-01 1.34e+01 angle pdb=" C THR A 953 " pdb=" N GLN A 954 " pdb=" CA GLN A 954 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 angle pdb=" N GLY A 621 " pdb=" CA GLY A 621 " pdb=" C GLY A 621 " ideal model delta sigma weight residual 113.18 120.70 -7.52 2.37e+00 1.78e-01 1.01e+01 angle pdb=" N GLU A 958 " pdb=" CA GLU A 958 " pdb=" C GLU A 958 " ideal model delta sigma weight residual 110.80 117.38 -6.58 2.13e+00 2.20e-01 9.55e+00 ... (remaining 11418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4598 17.84 - 35.67: 414 35.67 - 53.51: 85 53.51 - 71.35: 7 71.35 - 89.19: 7 Dihedral angle restraints: 5111 sinusoidal: 2066 harmonic: 3045 Sorted by residual: dihedral pdb=" CA PRO A 817 " pdb=" C PRO A 817 " pdb=" N LEU A 818 " pdb=" CA LEU A 818 " ideal model delta harmonic sigma weight residual -180.00 -149.40 -30.60 0 5.00e+00 4.00e-02 3.74e+01 dihedral pdb=" CA THR A 391 " pdb=" C THR A 391 " pdb=" N ASP A 392 " pdb=" CA ASP A 392 " ideal model delta harmonic sigma weight residual -180.00 -149.59 -30.41 0 5.00e+00 4.00e-02 3.70e+01 dihedral pdb=" CA CYS A1359 " pdb=" C CYS A1359 " pdb=" N PHE A1360 " pdb=" CA PHE A1360 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 5108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 658 0.031 - 0.062: 423 0.062 - 0.094: 133 0.094 - 0.125: 59 0.125 - 0.156: 8 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA VAL A 649 " pdb=" N VAL A 649 " pdb=" C VAL A 649 " pdb=" CB VAL A 649 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA ILE A1274 " pdb=" N ILE A1274 " pdb=" C ILE A1274 " pdb=" CB ILE A1274 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ASP A 392 " pdb=" N ASP A 392 " pdb=" C ASP A 392 " pdb=" CB ASP A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 1278 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 855 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 856 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 856 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 856 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 606 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 607 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1204 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A1205 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A1205 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1205 " 0.023 5.00e-02 4.00e+02 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 413 2.72 - 3.26: 7972 3.26 - 3.81: 11714 3.81 - 4.35: 15023 4.35 - 4.90: 26119 Nonbonded interactions: 61241 Sorted by model distance: nonbonded pdb=" OH TYR A1022 " pdb=" O MET A1090 " model vdw 2.174 3.040 nonbonded pdb=" OG SER A1150 " pdb=" O ALA A1156 " model vdw 2.217 3.040 nonbonded pdb=" O SER A 975 " pdb=" OG SER A 975 " model vdw 2.300 3.040 nonbonded pdb=" O ALA A 489 " pdb=" OG SER A 490 " model vdw 2.317 3.040 nonbonded pdb=" OD1 ASP A 519 " pdb=" N LYS A 520 " model vdw 2.335 3.120 ... (remaining 61236 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: 2.200 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.630 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.007 0.058 8437 Z= 0.275 Angle : 0.768 8.580 11427 Z= 0.435 Chirality : 0.045 0.156 1281 Planarity : 0.005 0.057 1456 Dihedral : 14.307 89.187 3125 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.68 % Favored : 92.02 % Rotamer: Outliers : 0.11 % Allowed : 9.81 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.11 (0.21), residues: 1028 helix: -2.15 (0.19), residues: 520 sheet: -2.95 (0.48), residues: 74 loop : -3.34 (0.24), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 648 TYR 0.016 0.002 TYR A 774 PHE 0.016 0.002 PHE A 457 TRP 0.020 0.002 TRP A 326 HIS 0.007 0.001 HIS A 804 Details of bonding type rmsd covalent geometry : bond 0.00667 ( 8435) covalent geometry : angle 0.76788 (11423) SS BOND : bond 0.00269 ( 2) SS BOND : angle 1.72728 ( 4) hydrogen bonds : bond 0.19256 ( 348) hydrogen bonds : angle 6.04438 ( 999) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.313 Fit side-chains REVERT: A 399 ILE cc_start: 0.6268 (OUTLIER) cc_final: 0.6013 (mt) REVERT: A 846 GLN cc_start: 0.7513 (tp-100) cc_final: 0.7218 (mt0) REVERT: A 1232 ARG cc_start: 0.7297 (ttm-80) cc_final: 0.7068 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.1417 time to fit residues: 18.7397 Evaluate side-chains 77 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.0670 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.0570 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 ASN A 766 HIS A 801 GLN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 ASN A 954 GLN A 994 HIS A1054 ASN A1083 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.103608 restraints weight = 10596.387| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.15 r_work: 0.3075 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8437 Z= 0.110 Angle : 0.551 6.906 11427 Z= 0.289 Chirality : 0.040 0.143 1281 Planarity : 0.005 0.051 1456 Dihedral : 5.283 33.671 1134 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.84 % Favored : 94.07 % Rotamer: Outliers : 0.80 % Allowed : 12.31 % Favored : 86.89 % 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: -2.44 (0.24), residues: 1028 helix: -0.68 (0.22), residues: 522 sheet: -2.14 (0.54), residues: 74 loop : -2.69 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 648 TYR 0.012 0.001 TYR A 774 PHE 0.012 0.001 PHE A 808 TRP 0.011 0.001 TRP A1218 HIS 0.004 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8435) covalent geometry : angle 0.55133 (11423) SS BOND : bond 0.00067 ( 2) SS BOND : angle 0.89654 ( 4) hydrogen bonds : bond 0.04729 ( 348) hydrogen bonds : angle 4.10525 ( 999) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.298 Fit side-chains REVERT: A 1173 GLU cc_start: 0.8702 (tp30) cc_final: 0.8328 (tt0) REVERT: A 1232 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.6833 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6494 (tm-30) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 0.0983 time to fit residues: 12.6688 Evaluate side-chains 84 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1308 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 55 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.0030 chunk 93 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 HIS ** 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 = 0.3457 r_free = 0.3457 target = 0.131163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.101635 restraints weight = 10489.734| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.14 r_work: 0.3023 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8437 Z= 0.130 Angle : 0.545 7.011 11427 Z= 0.282 Chirality : 0.040 0.137 1281 Planarity : 0.005 0.052 1456 Dihedral : 5.002 28.650 1132 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.23 % Favored : 93.68 % Rotamer: Outliers : 1.03 % Allowed : 15.05 % Favored : 83.92 % 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 (0.25), residues: 1028 helix: -0.03 (0.23), residues: 522 sheet: -1.68 (0.57), residues: 74 loop : -2.46 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 648 TYR 0.013 0.001 TYR A 774 PHE 0.014 0.001 PHE A 808 TRP 0.013 0.001 TRP A1218 HIS 0.006 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8435) covalent geometry : angle 0.54468 (11423) SS BOND : bond 0.00694 ( 2) SS BOND : angle 1.32315 ( 4) hydrogen bonds : bond 0.04985 ( 348) hydrogen bonds : angle 3.87797 ( 999) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.317 Fit side-chains REVERT: A 345 ARG cc_start: 0.6712 (ptt180) cc_final: 0.6442 (ptt180) REVERT: A 1173 GLU cc_start: 0.8749 (tp30) cc_final: 0.8386 (tt0) REVERT: A 1218 TRP cc_start: 0.8503 (m100) cc_final: 0.8084 (m-10) REVERT: A 1232 ARG cc_start: 0.7490 (ttm-80) cc_final: 0.6775 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6993 (tm-30) cc_final: 0.6512 (tm-30) REVERT: A 1300 GLN cc_start: 0.8308 (tp-100) cc_final: 0.7926 (mm110) outliers start: 9 outliers final: 9 residues processed: 86 average time/residue: 0.0942 time to fit residues: 11.2819 Evaluate side-chains 83 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1075 MET Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1292 ILE Chi-restraints excluded: chain A residue 1308 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 100 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 56 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 HIS ** 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 = 0.3486 r_free = 0.3486 target = 0.133563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.104189 restraints weight = 10655.559| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.19 r_work: 0.3112 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8437 Z= 0.102 Angle : 0.499 6.421 11427 Z= 0.258 Chirality : 0.039 0.140 1281 Planarity : 0.005 0.049 1456 Dihedral : 4.703 27.962 1132 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 1.60 % Allowed : 15.51 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.26), residues: 1028 helix: 0.49 (0.23), residues: 520 sheet: -1.31 (0.59), residues: 74 loop : -2.24 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 648 TYR 0.011 0.001 TYR A 774 PHE 0.011 0.001 PHE A 808 TRP 0.012 0.001 TRP A1218 HIS 0.005 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8435) covalent geometry : angle 0.49894 (11423) SS BOND : bond 0.00104 ( 2) SS BOND : angle 1.10248 ( 4) hydrogen bonds : bond 0.04018 ( 348) hydrogen bonds : angle 3.68351 ( 999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.332 Fit side-chains REVERT: A 345 ARG cc_start: 0.6823 (ptt180) cc_final: 0.6571 (ptt180) REVERT: A 1173 GLU cc_start: 0.8774 (tp30) cc_final: 0.8411 (tt0) REVERT: A 1218 TRP cc_start: 0.8510 (m100) cc_final: 0.8170 (m-10) REVERT: A 1232 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.6758 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6919 (tm-30) cc_final: 0.6537 (tm-30) REVERT: A 1300 GLN cc_start: 0.8312 (tp-100) cc_final: 0.7953 (mm110) outliers start: 14 outliers final: 11 residues processed: 89 average time/residue: 0.0928 time to fit residues: 11.5381 Evaluate side-chains 86 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1292 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1325 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 80 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.103064 restraints weight = 10627.528| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.17 r_work: 0.3066 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8437 Z= 0.115 Angle : 0.512 6.535 11427 Z= 0.263 Chirality : 0.039 0.136 1281 Planarity : 0.005 0.049 1456 Dihedral : 4.681 27.181 1132 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.36 % Rotamer: Outliers : 1.82 % Allowed : 15.51 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.26), residues: 1028 helix: 0.75 (0.23), residues: 515 sheet: -1.09 (0.59), residues: 74 loop : -2.15 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 648 TYR 0.012 0.001 TYR A 774 PHE 0.013 0.001 PHE A 808 TRP 0.012 0.001 TRP A1218 HIS 0.005 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8435) covalent geometry : angle 0.51141 (11423) SS BOND : bond 0.00131 ( 2) SS BOND : angle 1.13784 ( 4) hydrogen bonds : bond 0.04345 ( 348) hydrogen bonds : angle 3.66740 ( 999) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.315 Fit side-chains REVERT: A 345 ARG cc_start: 0.6802 (ptt180) cc_final: 0.6585 (ptt180) REVERT: A 686 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8232 (mm-30) REVERT: A 1173 GLU cc_start: 0.8794 (tp30) cc_final: 0.8422 (tt0) REVERT: A 1218 TRP cc_start: 0.8509 (m100) cc_final: 0.8211 (m-10) REVERT: A 1232 ARG cc_start: 0.7465 (ttm-80) cc_final: 0.6761 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6538 (tm-30) REVERT: A 1300 GLN cc_start: 0.8315 (tp-100) cc_final: 0.7955 (mm110) outliers start: 16 outliers final: 13 residues processed: 87 average time/residue: 0.0893 time to fit residues: 10.8938 Evaluate side-chains 86 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1292 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1325 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 47 optimal weight: 0.0020 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.104132 restraints weight = 10552.804| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.16 r_work: 0.3108 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8437 Z= 0.105 Angle : 0.496 6.422 11427 Z= 0.256 Chirality : 0.039 0.136 1281 Planarity : 0.004 0.051 1456 Dihedral : 4.575 26.813 1132 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.16 % Favored : 94.75 % Rotamer: Outliers : 1.71 % Allowed : 16.19 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.26), residues: 1028 helix: 0.94 (0.23), residues: 518 sheet: -0.89 (0.61), residues: 74 loop : -2.03 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 648 TYR 0.011 0.001 TYR A 774 PHE 0.012 0.001 PHE A 808 TRP 0.011 0.001 TRP A1218 HIS 0.005 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8435) covalent geometry : angle 0.49586 (11423) SS BOND : bond 0.00123 ( 2) SS BOND : angle 1.10073 ( 4) hydrogen bonds : bond 0.04062 ( 348) hydrogen bonds : angle 3.61651 ( 999) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.327 Fit side-chains REVERT: A 345 ARG cc_start: 0.6825 (ptt180) cc_final: 0.6577 (ptt180) REVERT: A 1173 GLU cc_start: 0.8796 (tp30) cc_final: 0.8424 (tt0) REVERT: A 1218 TRP cc_start: 0.8471 (m100) cc_final: 0.8236 (m-10) REVERT: A 1232 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.6728 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6534 (tm-30) REVERT: A 1271 ARG cc_start: 0.8347 (ptp-110) cc_final: 0.8043 (mtp85) REVERT: A 1300 GLN cc_start: 0.8324 (tp-100) cc_final: 0.7971 (mm110) outliers start: 15 outliers final: 13 residues processed: 89 average time/residue: 0.0913 time to fit residues: 11.4328 Evaluate side-chains 87 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1292 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1325 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 80 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.102561 restraints weight = 10651.085| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.16 r_work: 0.3087 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8437 Z= 0.123 Angle : 0.521 6.652 11427 Z= 0.266 Chirality : 0.040 0.134 1281 Planarity : 0.005 0.049 1456 Dihedral : 4.642 26.223 1132 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 1.94 % Allowed : 15.96 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.26), residues: 1028 helix: 0.98 (0.23), residues: 517 sheet: -0.84 (0.61), residues: 74 loop : -1.98 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 648 TYR 0.012 0.001 TYR A 774 PHE 0.013 0.001 PHE A 808 TRP 0.011 0.001 TRP A1218 HIS 0.005 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8435) covalent geometry : angle 0.52055 (11423) SS BOND : bond 0.00133 ( 2) SS BOND : angle 1.14727 ( 4) hydrogen bonds : bond 0.04450 ( 348) hydrogen bonds : angle 3.66161 ( 999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.307 Fit side-chains REVERT: A 345 ARG cc_start: 0.6806 (ptt180) cc_final: 0.6567 (ptt180) REVERT: A 1173 GLU cc_start: 0.8810 (tp30) cc_final: 0.8428 (tt0) REVERT: A 1218 TRP cc_start: 0.8490 (m100) cc_final: 0.8258 (m-10) REVERT: A 1232 ARG cc_start: 0.7439 (ttm-80) cc_final: 0.6704 (tpp-160) REVERT: A 1237 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6509 (tm-30) REVERT: A 1251 ARG cc_start: 0.8580 (mtm110) cc_final: 0.8363 (mtm110) REVERT: A 1271 ARG cc_start: 0.8403 (ptp-110) cc_final: 0.8131 (mtp85) REVERT: A 1300 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7935 (mm110) outliers start: 17 outliers final: 14 residues processed: 89 average time/residue: 0.0858 time to fit residues: 10.6472 Evaluate side-chains 89 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1292 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1325 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.102160 restraints weight = 10579.996| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.16 r_work: 0.3085 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8437 Z= 0.126 Angle : 0.523 6.926 11427 Z= 0.268 Chirality : 0.040 0.134 1281 Planarity : 0.005 0.050 1456 Dihedral : 4.673 26.277 1132 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 1.82 % Allowed : 16.53 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.26), residues: 1028 helix: 1.00 (0.23), residues: 518 sheet: -0.87 (0.60), residues: 72 loop : -1.92 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 648 TYR 0.012 0.001 TYR A 774 PHE 0.013 0.001 PHE A 808 TRP 0.011 0.001 TRP A1218 HIS 0.005 0.001 HIS A 988 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8435) covalent geometry : angle 0.52228 (11423) SS BOND : bond 0.00130 ( 2) SS BOND : angle 1.19137 ( 4) hydrogen bonds : bond 0.04496 ( 348) hydrogen bonds : angle 3.68414 ( 999) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.301 Fit side-chains REVERT: A 345 ARG cc_start: 0.6802 (ptt180) cc_final: 0.6560 (ptt180) REVERT: A 1173 GLU cc_start: 0.8818 (tp30) cc_final: 0.8432 (tt0) REVERT: A 1218 TRP cc_start: 0.8490 (m100) cc_final: 0.8279 (m-10) REVERT: A 1232 ARG cc_start: 0.7413 (ttm-80) cc_final: 0.6688 (tpp-160) REVERT: A 1237 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6525 (tm-30) REVERT: A 1271 ARG cc_start: 0.8413 (ptp-110) cc_final: 0.8139 (mtp85) REVERT: A 1300 GLN cc_start: 0.8298 (tp-100) cc_final: 0.7933 (mm110) outliers start: 16 outliers final: 15 residues processed: 88 average time/residue: 0.0903 time to fit residues: 11.1460 Evaluate side-chains 89 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1292 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1325 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 55 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.106448 restraints weight = 10507.311| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.14 r_work: 0.3107 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8437 Z= 0.109 Angle : 0.501 6.655 11427 Z= 0.258 Chirality : 0.039 0.139 1281 Planarity : 0.004 0.049 1456 Dihedral : 4.555 26.107 1132 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.82 % Allowed : 16.76 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.26), residues: 1028 helix: 1.09 (0.23), residues: 523 sheet: -0.73 (0.61), residues: 74 loop : -1.86 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 648 TYR 0.011 0.001 TYR A 458 PHE 0.013 0.001 PHE A 808 TRP 0.011 0.001 TRP A1218 HIS 0.004 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8435) covalent geometry : angle 0.50095 (11423) SS BOND : bond 0.00113 ( 2) SS BOND : angle 1.11132 ( 4) hydrogen bonds : bond 0.04085 ( 348) hydrogen bonds : angle 3.61832 ( 999) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.271 Fit side-chains REVERT: A 345 ARG cc_start: 0.6833 (ptt180) cc_final: 0.6594 (ptt180) REVERT: A 1173 GLU cc_start: 0.8806 (tp30) cc_final: 0.8433 (tt0) REVERT: A 1232 ARG cc_start: 0.7415 (ttm-80) cc_final: 0.6703 (tpp-160) REVERT: A 1237 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6539 (tm-30) REVERT: A 1271 ARG cc_start: 0.8376 (ptp-110) cc_final: 0.8120 (mtp85) REVERT: A 1300 GLN cc_start: 0.8296 (tp-100) cc_final: 0.7939 (mm110) outliers start: 16 outliers final: 15 residues processed: 91 average time/residue: 0.0894 time to fit residues: 11.3817 Evaluate side-chains 91 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1292 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1325 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 0.0370 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 HIS A1226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.136133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.107848 restraints weight = 10382.109| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.06 r_work: 0.3113 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8437 Z= 0.126 Angle : 0.527 6.864 11427 Z= 0.270 Chirality : 0.040 0.136 1281 Planarity : 0.005 0.050 1456 Dihedral : 4.623 26.037 1132 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.74 % Favored : 94.16 % Rotamer: Outliers : 1.71 % Allowed : 17.33 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.26), residues: 1028 helix: 0.94 (0.23), residues: 530 sheet: -0.73 (0.61), residues: 72 loop : -1.83 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 648 TYR 0.012 0.001 TYR A 774 PHE 0.013 0.001 PHE A 808 TRP 0.009 0.001 TRP A 997 HIS 0.005 0.001 HIS A 593 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8435) covalent geometry : angle 0.52694 (11423) SS BOND : bond 0.00123 ( 2) SS BOND : angle 1.19033 ( 4) hydrogen bonds : bond 0.04477 ( 348) hydrogen bonds : angle 3.67461 ( 999) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.226 Fit side-chains REVERT: A 345 ARG cc_start: 0.6849 (ptt180) cc_final: 0.6602 (ptt180) REVERT: A 1173 GLU cc_start: 0.8816 (tp30) cc_final: 0.8442 (tt0) REVERT: A 1232 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.6729 (tpp-160) REVERT: A 1237 GLU cc_start: 0.7049 (tm-30) cc_final: 0.6554 (tm-30) REVERT: A 1271 ARG cc_start: 0.8428 (ptp-110) cc_final: 0.8175 (mtp85) REVERT: A 1300 GLN cc_start: 0.8313 (tp-100) cc_final: 0.7957 (mm110) outliers start: 15 outliers final: 15 residues processed: 88 average time/residue: 0.0869 time to fit residues: 10.6642 Evaluate side-chains 90 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 322 CYS Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 481 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1292 ILE Chi-restraints excluded: chain A residue 1308 VAL Chi-restraints excluded: chain A residue 1325 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 100 optimal weight: 0.0170 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.131155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.101870 restraints weight = 10578.913| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.16 r_work: 0.3095 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8437 Z= 0.136 Angle : 0.532 7.061 11427 Z= 0.272 Chirality : 0.040 0.137 1281 Planarity : 0.005 0.050 1456 Dihedral : 4.686 26.083 1132 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.26 % Rotamer: Outliers : 1.94 % Allowed : 16.99 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.26), residues: 1028 helix: 0.95 (0.23), residues: 525 sheet: -0.72 (0.61), residues: 72 loop : -1.81 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 648 TYR 0.013 0.001 TYR A 774 PHE 0.013 0.001 PHE A 808 TRP 0.009 0.001 TRP A1218 HIS 0.005 0.001 HIS A 988 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8435) covalent geometry : angle 0.53110 (11423) SS BOND : bond 0.00125 ( 2) SS BOND : angle 1.22326 ( 4) hydrogen bonds : bond 0.04639 ( 348) hydrogen bonds : angle 3.70135 ( 999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.27 seconds wall clock time: 36 minutes 56.15 seconds (2216.15 seconds total)