Starting phenix.real_space_refine on Wed Feb 12 19:43:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nur_12600/02_2025/7nur_12600.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nur_12600/02_2025/7nur_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_12600/02_2025/7nur_12600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nur_12600/02_2025/7nur_12600.map" model { file = "/net/cci-nas-00/data/ceres_data/7nur_12600/02_2025/7nur_12600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nur_12600/02_2025/7nur_12600.cif" } resolution = 3.125 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= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 5.15, per 1000 atoms: 0.62 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: 2.07 Conformation dependent library (CDL) restraints added in 940.3 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: 0.91 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: 2.42 Time building geometry restraints manager: 2.40 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: 1.960 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 21.770 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- 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 8435 Z= 0.434 Angle : 0.768 8.580 11423 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 (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: -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 TRP 0.020 0.002 TRP A 326 HIS 0.007 0.001 HIS A 804 PHE 0.016 0.002 PHE A 457 TYR 0.016 0.002 TYR A 774 ARG 0.008 0.001 ARG A 648 *********************** 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 : 0.957 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: 0.3200 time to fit residues: 42.5887 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 : 0.883 ------------------------------------------------------------------------------- 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 87 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 43 optimal weight: 0.0970 chunk 26 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.0470 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.132812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.105078 restraints weight = 10470.420| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.95 r_work: 0.3149 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8435 Z= 0.151 Angle : 0.556 6.904 11423 Z= 0.292 Chirality : 0.040 0.143 1281 Planarity : 0.005 0.051 1456 Dihedral : 5.303 33.289 1134 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.26 % Rotamer: Outliers : 0.80 % Allowed : 12.54 % Favored : 86.66 % 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: -2.47 (0.24), residues: 1028 helix: -0.70 (0.22), residues: 522 sheet: -2.18 (0.53), residues: 74 loop : -2.71 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1218 HIS 0.005 0.001 HIS A 988 PHE 0.012 0.001 PHE A 808 TYR 0.012 0.001 TYR A 774 ARG 0.003 0.000 ARG A 648 *********************** 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 : 0.923 Fit side-chains REVERT: A 1173 GLU cc_start: 0.8724 (tp30) cc_final: 0.8346 (tt0) REVERT: A 1232 ARG cc_start: 0.7583 (ttm-80) cc_final: 0.6881 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6507 (tm-30) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 0.2247 time to fit residues: 29.1378 Evaluate side-chains 83 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.0670 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.141500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.116687 restraints weight = 10405.952| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.63 r_work: 0.3107 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8435 Z= 0.184 Angle : 0.533 6.827 11423 Z= 0.276 Chirality : 0.040 0.139 1281 Planarity : 0.005 0.052 1456 Dihedral : 4.960 28.661 1132 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.13 % Favored : 93.77 % Rotamer: Outliers : 1.03 % Allowed : 14.82 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.74 (0.25), residues: 1028 helix: -0.03 (0.23), residues: 521 sheet: -1.70 (0.56), residues: 74 loop : -2.47 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1218 HIS 0.005 0.001 HIS A 988 PHE 0.013 0.001 PHE A 808 TYR 0.012 0.001 TYR A 774 ARG 0.003 0.000 ARG A 648 *********************** 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 : 0.910 Fit side-chains REVERT: A 345 ARG cc_start: 0.6728 (ptt180) cc_final: 0.6465 (ptt180) REVERT: A 1173 GLU cc_start: 0.8606 (tp30) cc_final: 0.8290 (tt0) REVERT: A 1218 TRP cc_start: 0.8492 (m100) cc_final: 0.8095 (m-10) REVERT: A 1232 ARG cc_start: 0.7419 (ttm-80) cc_final: 0.6770 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6464 (tm-30) REVERT: A 1300 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7895 (mm110) outliers start: 9 outliers final: 9 residues processed: 86 average time/residue: 0.2241 time to fit residues: 26.7135 Evaluate side-chains 84 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 86 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 4 optimal weight: 0.0670 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.135257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.106212 restraints weight = 10457.656| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.15 r_work: 0.3097 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8435 Z= 0.138 Angle : 0.493 6.238 11423 Z= 0.255 Chirality : 0.038 0.141 1281 Planarity : 0.004 0.049 1456 Dihedral : 4.646 27.833 1132 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 1.48 % Allowed : 15.39 % Favored : 83.12 % 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: -1.08 (0.26), residues: 1028 helix: 0.55 (0.23), residues: 520 sheet: -1.28 (0.59), residues: 74 loop : -2.23 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1218 HIS 0.004 0.001 HIS A 593 PHE 0.011 0.001 PHE A 808 TYR 0.011 0.001 TYR A 458 ARG 0.003 0.000 ARG A 648 *********************** 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: 13 poor density : 79 time to evaluate : 0.955 Fit side-chains REVERT: A 345 ARG cc_start: 0.6839 (ptt180) cc_final: 0.6592 (ptt180) REVERT: A 1173 GLU cc_start: 0.8767 (tp30) cc_final: 0.8411 (tt0) REVERT: A 1218 TRP cc_start: 0.8492 (m100) cc_final: 0.8173 (m-10) REVERT: A 1232 ARG cc_start: 0.7449 (ttm-80) cc_final: 0.6786 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6534 (tm-30) REVERT: A 1300 GLN cc_start: 0.8293 (tp-100) cc_final: 0.7923 (mm110) outliers start: 13 outliers final: 9 residues processed: 89 average time/residue: 0.2238 time to fit residues: 27.4249 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 : 0.938 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.132872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103814 restraints weight = 10477.829| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.15 r_work: 0.3102 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8435 Z= 0.177 Angle : 0.512 6.433 11423 Z= 0.264 Chirality : 0.039 0.135 1281 Planarity : 0.005 0.051 1456 Dihedral : 4.647 27.103 1132 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.26 % Rotamer: Outliers : 1.71 % Allowed : 15.96 % Favored : 82.33 % 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: -0.83 (0.26), residues: 1028 helix: 0.79 (0.23), residues: 515 sheet: -1.08 (0.60), residues: 74 loop : -2.14 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1218 HIS 0.005 0.001 HIS A 593 PHE 0.013 0.001 PHE A 808 TYR 0.012 0.001 TYR A 774 ARG 0.003 0.000 ARG A 648 *********************** 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: 15 poor density : 75 time to evaluate : 0.965 Fit side-chains REVERT: A 345 ARG cc_start: 0.6802 (ptt180) cc_final: 0.6598 (ptt180) REVERT: A 686 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8205 (mm-30) REVERT: A 1173 GLU cc_start: 0.8782 (tp30) cc_final: 0.8423 (tt0) REVERT: A 1218 TRP cc_start: 0.8524 (m100) cc_final: 0.8220 (m-10) REVERT: A 1232 ARG cc_start: 0.7481 (ttm-80) cc_final: 0.6762 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6532 (tm-30) REVERT: A 1300 GLN cc_start: 0.8312 (tp-100) cc_final: 0.7951 (mm110) outliers start: 15 outliers final: 13 residues processed: 87 average time/residue: 0.2203 time to fit residues: 27.0555 Evaluate side-chains 85 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 chunk 99 optimal weight: 0.0870 chunk 66 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.133838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104659 restraints weight = 10525.585| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.16 r_work: 0.3105 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8435 Z= 0.148 Angle : 0.489 6.245 11423 Z= 0.252 Chirality : 0.038 0.136 1281 Planarity : 0.004 0.049 1456 Dihedral : 4.511 26.567 1132 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 1.82 % Allowed : 16.08 % 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 (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: -0.52 (0.26), residues: 1028 helix: 1.02 (0.23), residues: 518 sheet: -0.85 (0.61), residues: 74 loop : -2.00 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1218 HIS 0.005 0.001 HIS A 593 PHE 0.011 0.001 PHE A 808 TYR 0.011 0.001 TYR A 458 ARG 0.002 0.000 ARG A 648 *********************** 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 91 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.935 Fit side-chains REVERT: A 345 ARG cc_start: 0.6808 (ptt180) cc_final: 0.6600 (ptt180) REVERT: A 1173 GLU cc_start: 0.8792 (tp30) cc_final: 0.8423 (tt0) REVERT: A 1232 ARG cc_start: 0.7406 (ttm-80) cc_final: 0.6692 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6526 (tm-30) REVERT: A 1271 ARG cc_start: 0.8353 (ptp-110) cc_final: 0.8078 (mtp85) REVERT: A 1300 GLN cc_start: 0.8288 (tp-100) cc_final: 0.7926 (mm110) outliers start: 16 outliers final: 12 residues processed: 88 average time/residue: 0.2337 time to fit residues: 28.1444 Evaluate side-chains 85 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 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 6 optimal weight: 5.9990 chunk 36 optimal weight: 0.0170 chunk 56 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.138291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111048 restraints weight = 10360.192| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.94 r_work: 0.3131 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8435 Z= 0.170 Angle : 0.504 6.322 11423 Z= 0.257 Chirality : 0.039 0.135 1281 Planarity : 0.004 0.049 1456 Dihedral : 4.520 25.931 1132 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.16 % Favored : 94.75 % 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 (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: -0.43 (0.26), residues: 1028 helix: 1.10 (0.23), residues: 517 sheet: -0.79 (0.61), residues: 74 loop : -1.95 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 997 HIS 0.005 0.001 HIS A 593 PHE 0.012 0.001 PHE A 808 TYR 0.012 0.001 TYR A 774 ARG 0.002 0.000 ARG A 648 *********************** 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 94 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.881 Fit side-chains REVERT: A 345 ARG cc_start: 0.6702 (ptt180) cc_final: 0.6466 (ptt180) REVERT: A 799 GLN cc_start: 0.7668 (mt0) cc_final: 0.7383 (tt0) REVERT: A 1173 GLU cc_start: 0.8674 (tp30) cc_final: 0.8280 (tt0) REVERT: A 1232 ARG cc_start: 0.7170 (ttm-80) cc_final: 0.6450 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6818 (tm-30) cc_final: 0.6365 (tm-30) REVERT: A 1251 ARG cc_start: 0.8474 (mtm110) cc_final: 0.8229 (mtm110) REVERT: A 1271 ARG cc_start: 0.8274 (ptp-110) cc_final: 0.8032 (mtp85) REVERT: A 1300 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7820 (mm110) outliers start: 16 outliers final: 14 residues processed: 90 average time/residue: 0.2115 time to fit residues: 26.6468 Evaluate side-chains 90 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 41 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 101 optimal weight: 0.0570 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1226 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.103584 restraints weight = 10559.512| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.15 r_work: 0.3103 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8435 Z= 0.180 Angle : 0.511 6.613 11423 Z= 0.262 Chirality : 0.039 0.134 1281 Planarity : 0.004 0.049 1456 Dihedral : 4.549 25.636 1132 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % 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 (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: -0.39 (0.26), residues: 1028 helix: 1.06 (0.23), residues: 524 sheet: -0.75 (0.61), residues: 74 loop : -1.88 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 997 HIS 0.005 0.001 HIS A 593 PHE 0.012 0.001 PHE A 808 TYR 0.012 0.001 TYR A 774 ARG 0.002 0.000 ARG A 648 *********************** 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 : 0.833 Fit side-chains REVERT: A 345 ARG cc_start: 0.6829 (ptt180) cc_final: 0.6589 (ptt180) REVERT: A 799 GLN cc_start: 0.7755 (mt0) cc_final: 0.7500 (tt0) REVERT: A 1173 GLU cc_start: 0.8815 (tp30) cc_final: 0.8436 (tt0) REVERT: A 1232 ARG cc_start: 0.7343 (ttm-80) cc_final: 0.6628 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6997 (tm-30) cc_final: 0.6517 (tm-30) REVERT: A 1271 ARG cc_start: 0.8408 (ptp-110) cc_final: 0.8167 (mtp85) REVERT: A 1300 GLN cc_start: 0.8311 (tp-100) cc_final: 0.7930 (mm110) outliers start: 16 outliers final: 14 residues processed: 89 average time/residue: 0.2259 time to fit residues: 27.8916 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 : 0.949 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 0.0670 chunk 88 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 86 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 = 0.135662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.106462 restraints weight = 10634.054| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.18 r_work: 0.3087 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8435 Z= 0.127 Angle : 0.478 5.997 11423 Z= 0.245 Chirality : 0.038 0.137 1281 Planarity : 0.004 0.049 1456 Dihedral : 4.334 25.420 1132 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.60 % Allowed : 16.88 % Favored : 81.53 % 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: -0.14 (0.27), residues: 1028 helix: 1.31 (0.23), residues: 522 sheet: -0.65 (0.63), residues: 74 loop : -1.82 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 997 HIS 0.004 0.001 HIS A 593 PHE 0.011 0.001 PHE A 808 TYR 0.010 0.001 TYR A 458 ARG 0.002 0.000 ARG A 648 *********************** 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: 14 poor density : 80 time to evaluate : 0.934 Fit side-chains REVERT: A 345 ARG cc_start: 0.6866 (ptt180) cc_final: 0.6642 (ptt180) REVERT: A 799 GLN cc_start: 0.7776 (mt0) cc_final: 0.7508 (tt0) REVERT: A 1173 GLU cc_start: 0.8807 (tp30) cc_final: 0.8415 (tt0) REVERT: A 1232 ARG cc_start: 0.7248 (ttm-80) cc_final: 0.6530 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6916 (tm-30) cc_final: 0.6507 (tm-30) REVERT: A 1300 GLN cc_start: 0.8241 (tp-100) cc_final: 0.7868 (mm110) outliers start: 14 outliers final: 13 residues processed: 90 average time/residue: 0.2252 time to fit residues: 27.9355 Evaluate side-chains 88 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 59 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 77 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.138359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.110074 restraints weight = 10375.741| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.07 r_work: 0.3137 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8435 Z= 0.175 Angle : 0.506 6.263 11423 Z= 0.259 Chirality : 0.039 0.133 1281 Planarity : 0.004 0.050 1456 Dihedral : 4.424 24.707 1132 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 1.71 % Allowed : 16.76 % Favored : 81.53 % 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: -0.19 (0.27), residues: 1028 helix: 1.19 (0.23), residues: 530 sheet: -0.66 (0.62), residues: 72 loop : -1.78 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 997 HIS 0.005 0.001 HIS A 593 PHE 0.013 0.001 PHE A 808 TYR 0.011 0.001 TYR A 774 ARG 0.002 0.000 ARG A 648 ********************** 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 93 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.915 Fit side-chains REVERT: A 345 ARG cc_start: 0.6842 (ptt180) cc_final: 0.6604 (ptt180) REVERT: A 799 GLN cc_start: 0.7730 (mt0) cc_final: 0.7505 (tt0) REVERT: A 1173 GLU cc_start: 0.8811 (tp30) cc_final: 0.8443 (tt0) REVERT: A 1232 ARG cc_start: 0.7291 (ttm-80) cc_final: 0.6579 (tpp-160) REVERT: A 1237 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6530 (tm-30) REVERT: A 1300 GLN cc_start: 0.8290 (tp-100) cc_final: 0.7939 (mm110) outliers start: 15 outliers final: 15 residues processed: 88 average time/residue: 0.1987 time to fit residues: 24.9798 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 : 0.954 ------------------------------------------------------------------------------- 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 680 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 0.0670 chunk 2 optimal weight: 0.0980 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 92 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.106504 restraints weight = 10617.076| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.17 r_work: 0.3149 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8435 Z= 0.143 Angle : 0.484 6.048 11423 Z= 0.249 Chirality : 0.038 0.136 1281 Planarity : 0.004 0.049 1456 Dihedral : 4.334 24.690 1132 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % 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 (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 (0.27), residues: 1028 helix: 1.33 (0.23), residues: 529 sheet: -0.61 (0.63), residues: 72 loop : -1.73 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 997 HIS 0.004 0.001 HIS A 593 PHE 0.011 0.001 PHE A 808 TYR 0.010 0.001 TYR A 458 ARG 0.002 0.000 ARG A 648 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4681.00 seconds wall clock time: 83 minutes 29.15 seconds (5009.15 seconds total)