Starting phenix.real_space_refine on Sat Jul 26 02:30:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nur_12600/07_2025/7nur_12600.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nur_12600/07_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_12600/07_2025/7nur_12600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nur_12600/07_2025/7nur_12600.map" model { file = "/net/cci-nas-00/data/ceres_data/7nur_12600/07_2025/7nur_12600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nur_12600/07_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-5711/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: 6.13, per 1000 atoms: 0.74 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: 1.90 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 0.85 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: 2.83 Time building geometry restraints manager: 2.34 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.630 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.600 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.19256 ( 348) hydrogen bonds : angle 6.04438 ( 999) SS BOND : bond 0.00269 ( 2) SS BOND : angle 1.72728 ( 4) covalent geometry : bond 0.00667 ( 8435) covalent geometry : angle 0.76788 (11423) *********************** 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 : 0.904 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: 0.3273 time to fit residues: 43.8619 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 : 0.917 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 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: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.133609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.106727 restraints weight = 10469.788| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.86 r_work: 0.3048 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8437 Z= 0.118 Angle : 0.562 7.039 11427 Z= 0.294 Chirality : 0.040 0.143 1281 Planarity : 0.005 0.052 1456 Dihedral : 5.346 33.125 1134 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.84 % Favored : 94.07 % 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: -2.48 (0.24), residues: 1028 helix: -0.71 (0.22), residues: 522 sheet: -2.20 (0.53), residues: 74 loop : -2.72 (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 593 PHE 0.012 0.001 PHE A 808 TYR 0.013 0.001 TYR A 774 ARG 0.003 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.05002 ( 348) hydrogen bonds : angle 4.13804 ( 999) SS BOND : bond 0.00075 ( 2) SS BOND : angle 0.97798 ( 4) covalent geometry : bond 0.00260 ( 8435) covalent geometry : angle 0.56196 (11423) *********************** 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 : 0.959 Fit side-chains REVERT: A 1173 GLU cc_start: 0.8682 (tp30) cc_final: 0.8284 (tt0) REVERT: A 1232 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.6788 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6877 (tm-30) cc_final: 0.6435 (tm-30) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 0.2223 time to fit residues: 28.8463 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 : 0.832 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.0970 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.140581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.115812 restraints weight = 10406.975| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.62 r_work: 0.3046 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1471 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= 0.132 Angle : 0.547 7.096 11427 Z= 0.283 Chirality : 0.040 0.139 1281 Planarity : 0.005 0.053 1456 Dihedral : 5.034 28.809 1132 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.13 % Favored : 93.77 % Rotamer: Outliers : 1.03 % Allowed : 15.17 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.25), residues: 1028 helix: -0.05 (0.23), residues: 521 sheet: -1.73 (0.56), residues: 74 loop : -2.45 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1218 HIS 0.006 0.001 HIS A 988 PHE 0.013 0.001 PHE A 808 TYR 0.013 0.001 TYR A 774 ARG 0.003 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.04974 ( 348) hydrogen bonds : angle 3.89131 ( 999) SS BOND : bond 0.00265 ( 2) SS BOND : angle 1.13477 ( 4) covalent geometry : bond 0.00315 ( 8435) covalent geometry : angle 0.54651 (11423) *********************** 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 86 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.951 Fit side-chains REVERT: A 345 ARG cc_start: 0.6565 (ptt180) cc_final: 0.6276 (ptt180) REVERT: A 1173 GLU cc_start: 0.8570 (tp30) cc_final: 0.8174 (tt0) REVERT: A 1218 TRP cc_start: 0.8466 (m100) cc_final: 0.7939 (m-10) REVERT: A 1232 ARG cc_start: 0.7300 (ttm-80) cc_final: 0.6604 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6793 (tm-30) cc_final: 0.6303 (tm-30) REVERT: A 1300 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7726 (mm110) outliers start: 9 outliers final: 9 residues processed: 85 average time/residue: 0.2192 time to fit residues: 25.9761 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 : 0.944 ------------------------------------------------------------------------------- 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: 0.8980 chunk 68 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.131140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.101804 restraints weight = 10525.824| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.15 r_work: 0.3077 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1613 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= 0.129 Angle : 0.536 7.036 11427 Z= 0.276 Chirality : 0.040 0.138 1281 Planarity : 0.005 0.052 1456 Dihedral : 4.934 28.467 1132 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.26 % Rotamer: Outliers : 1.71 % Allowed : 15.39 % 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 (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: -1.31 (0.25), residues: 1028 helix: 0.31 (0.23), residues: 521 sheet: -1.47 (0.57), residues: 74 loop : -2.26 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1218 HIS 0.005 0.001 HIS A 593 PHE 0.013 0.001 PHE A 808 TYR 0.013 0.001 TYR A 774 ARG 0.003 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 348) hydrogen bonds : angle 3.80692 ( 999) SS BOND : bond 0.00167 ( 2) SS BOND : angle 1.32952 ( 4) covalent geometry : bond 0.00310 ( 8435) covalent geometry : angle 0.53554 (11423) *********************** 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 91 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.887 Fit side-chains REVERT: A 345 ARG cc_start: 0.6757 (ptt180) cc_final: 0.6475 (ptt180) REVERT: A 1173 GLU cc_start: 0.8794 (tp30) cc_final: 0.8422 (tt0) REVERT: A 1218 TRP cc_start: 0.8513 (m100) cc_final: 0.8118 (m-10) REVERT: A 1232 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.6761 (tpp-160) REVERT: A 1237 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6507 (tm-30) REVERT: A 1300 GLN cc_start: 0.8193 (tp-100) cc_final: 0.7826 (mm110) outliers start: 15 outliers final: 13 residues processed: 87 average time/residue: 0.2076 time to fit residues: 25.3401 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 : 0.867 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.130030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.100866 restraints weight = 10518.905| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.15 r_work: 0.3063 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8437 Z= 0.143 Angle : 0.546 7.382 11427 Z= 0.281 Chirality : 0.040 0.136 1281 Planarity : 0.005 0.050 1456 Dihedral : 4.934 27.792 1132 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.23 % Favored : 93.68 % Rotamer: Outliers : 2.05 % Allowed : 15.39 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.09 (0.26), residues: 1028 helix: 0.49 (0.23), residues: 521 sheet: -1.26 (0.58), residues: 74 loop : -2.17 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1218 HIS 0.006 0.001 HIS A 593 PHE 0.014 0.001 PHE A 808 TYR 0.014 0.001 TYR A 774 ARG 0.003 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.04965 ( 348) hydrogen bonds : angle 3.81203 ( 999) SS BOND : bond 0.00135 ( 2) SS BOND : angle 1.18844 ( 4) covalent geometry : bond 0.00350 ( 8435) covalent geometry : angle 0.54609 (11423) *********************** 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 97 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.878 Fit side-chains REVERT: A 345 ARG cc_start: 0.6815 (ptt180) cc_final: 0.6534 (ptt180) REVERT: A 1173 GLU cc_start: 0.8792 (tp30) cc_final: 0.8412 (tt0) REVERT: A 1218 TRP cc_start: 0.8526 (m100) cc_final: 0.8147 (m-10) REVERT: A 1232 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.6814 (tpp-160) REVERT: A 1237 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6567 (tm-30) REVERT: A 1300 GLN cc_start: 0.8182 (tp-100) cc_final: 0.7847 (mm110) outliers start: 18 outliers final: 14 residues processed: 94 average time/residue: 0.2059 time to fit residues: 27.4318 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 : 0.879 ------------------------------------------------------------------------------- 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 382 GLN 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 53 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 96 optimal weight: 0.0670 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.0570 chunk 99 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.133322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104133 restraints weight = 10513.990| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.16 r_work: 0.3017 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1935 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= 0.096 Angle : 0.494 6.402 11427 Z= 0.255 Chirality : 0.039 0.143 1281 Planarity : 0.004 0.049 1456 Dihedral : 4.652 27.423 1132 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.71 % Allowed : 16.42 % Favored : 81.87 % 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: -0.66 (0.26), residues: 1028 helix: 0.89 (0.23), residues: 518 sheet: -0.94 (0.61), residues: 74 loop : -2.04 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.002 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 348) hydrogen bonds : angle 3.65141 ( 999) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.73268 ( 4) covalent geometry : bond 0.00212 ( 8435) covalent geometry : angle 0.49363 (11423) *********************** 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: 15 poor density : 76 time to evaluate : 0.900 Fit side-chains REVERT: A 345 ARG cc_start: 0.6738 (ptt180) cc_final: 0.6457 (ptt180) REVERT: A 1173 GLU cc_start: 0.8762 (tp30) cc_final: 0.8362 (tt0) REVERT: A 1218 TRP cc_start: 0.8449 (m100) cc_final: 0.8149 (m-10) REVERT: A 1232 ARG cc_start: 0.7337 (ttm-80) cc_final: 0.6660 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6487 (tm-30) REVERT: A 1271 ARG cc_start: 0.8313 (ptp-110) cc_final: 0.8000 (mtp85) REVERT: A 1300 GLN cc_start: 0.8121 (tp-100) cc_final: 0.7818 (mm110) outliers start: 15 outliers final: 13 residues processed: 88 average time/residue: 0.2095 time to fit residues: 26.0979 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 : 0.856 ------------------------------------------------------------------------------- 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 6 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 62 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.131543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102462 restraints weight = 10524.793| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.13 r_work: 0.3089 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1894 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= 0.124 Angle : 0.522 7.016 11427 Z= 0.268 Chirality : 0.040 0.138 1281 Planarity : 0.005 0.050 1456 Dihedral : 4.700 26.672 1132 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.74 % Favored : 94.16 % Rotamer: Outliers : 2.05 % Allowed : 16.76 % Favored : 81.19 % 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: -0.58 (0.26), residues: 1028 helix: 0.94 (0.23), residues: 518 sheet: -0.84 (0.60), residues: 74 loop : -1.99 (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 0.013 0.001 PHE A 808 TYR 0.013 0.001 TYR A 774 ARG 0.002 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.04490 ( 348) hydrogen bonds : angle 3.68350 ( 999) SS BOND : bond 0.00128 ( 2) SS BOND : angle 1.31404 ( 4) covalent geometry : bond 0.00299 ( 8435) covalent geometry : angle 0.52185 (11423) *********************** 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 91 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 1.038 Fit side-chains REVERT: A 345 ARG cc_start: 0.6792 (ptt180) cc_final: 0.6532 (ptt180) REVERT: A 686 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8171 (mm-30) REVERT: A 1173 GLU cc_start: 0.8802 (tp30) cc_final: 0.8429 (tt0) REVERT: A 1218 TRP cc_start: 0.8522 (m100) cc_final: 0.8244 (m-10) REVERT: A 1232 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.6686 (tpp-160) REVERT: A 1237 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6545 (tm-30) REVERT: A 1251 ARG cc_start: 0.8585 (mtm110) cc_final: 0.8358 (mtm110) REVERT: A 1271 ARG cc_start: 0.8407 (ptp-110) cc_final: 0.8122 (mtp85) REVERT: A 1300 GLN cc_start: 0.8073 (tp-100) cc_final: 0.7792 (mm110) outliers start: 18 outliers final: 15 residues processed: 88 average time/residue: 0.2159 time to fit residues: 26.5511 Evaluate side-chains 87 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 0.0270 chunk 7 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.133437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.104185 restraints weight = 10539.358| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.17 r_work: 0.3110 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2043 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= 0.102 Angle : 0.499 6.599 11427 Z= 0.256 Chirality : 0.039 0.141 1281 Planarity : 0.004 0.049 1456 Dihedral : 4.563 26.433 1132 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.94 % Allowed : 16.88 % Favored : 81.19 % 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: -0.37 (0.26), residues: 1028 helix: 1.12 (0.23), residues: 518 sheet: -0.77 (0.61), residues: 74 loop : -1.90 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1218 HIS 0.004 0.001 HIS A 593 PHE 0.012 0.001 PHE A 808 TYR 0.011 0.001 TYR A 458 ARG 0.003 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 348) hydrogen bonds : angle 3.60684 ( 999) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.97591 ( 4) covalent geometry : bond 0.00233 ( 8435) covalent geometry : angle 0.49855 (11423) *********************** 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 90 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.867 Fit side-chains REVERT: A 345 ARG cc_start: 0.6798 (ptt180) cc_final: 0.6547 (ptt180) REVERT: A 1173 GLU cc_start: 0.8802 (tp30) cc_final: 0.8424 (tt0) REVERT: A 1232 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.6677 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6531 (tm-30) REVERT: A 1271 ARG cc_start: 0.8370 (ptp-110) cc_final: 0.8137 (mtp85) REVERT: A 1300 GLN cc_start: 0.8029 (tp-100) cc_final: 0.7713 (mm110) outliers start: 17 outliers final: 15 residues processed: 87 average time/residue: 0.2175 time to fit residues: 26.0907 Evaluate side-chains 87 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 1360 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.131699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.102188 restraints weight = 10672.898| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.18 r_work: 0.3085 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8437 Z= 0.129 Angle : 0.534 9.858 11427 Z= 0.271 Chirality : 0.040 0.137 1281 Planarity : 0.005 0.050 1456 Dihedral : 4.645 26.225 1132 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.74 % Favored : 94.16 % Rotamer: Outliers : 2.05 % Allowed : 16.99 % 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 (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: -0.44 (0.26), residues: 1028 helix: 0.97 (0.23), residues: 525 sheet: -0.80 (0.61), residues: 72 loop : -1.84 (0.28), residues: 431 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 0.012 0.001 TYR A 774 ARG 0.002 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 348) hydrogen bonds : angle 3.66749 ( 999) SS BOND : bond 0.00115 ( 2) SS BOND : angle 1.16750 ( 4) covalent geometry : bond 0.00315 ( 8435) covalent geometry : angle 0.53370 (11423) *********************** 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 91 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.852 Fit side-chains REVERT: A 345 ARG cc_start: 0.6834 (ptt180) cc_final: 0.6569 (ptt180) REVERT: A 1173 GLU cc_start: 0.8827 (tp30) cc_final: 0.8435 (tt0) REVERT: A 1232 ARG cc_start: 0.7347 (ttm-80) cc_final: 0.6669 (tpp-160) REVERT: A 1237 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6522 (tm-30) REVERT: A 1271 ARG cc_start: 0.8380 (ptp-110) cc_final: 0.8115 (mtp85) REVERT: A 1300 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7715 (mm110) outliers start: 18 outliers final: 16 residues processed: 88 average time/residue: 0.2079 time to fit residues: 25.3503 Evaluate side-chains 88 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 740 THR 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 59 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 77 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.136314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.107260 restraints weight = 10452.247| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.16 r_work: 0.3135 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 8437 Z= 0.088 Angle : 0.487 8.572 11427 Z= 0.246 Chirality : 0.038 0.143 1281 Planarity : 0.004 0.049 1456 Dihedral : 4.357 25.678 1132 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.60 % Allowed : 17.33 % 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 (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: -0.08 (0.27), residues: 1028 helix: 1.34 (0.23), residues: 523 sheet: -0.61 (0.63), residues: 74 loop : -1.77 (0.29), residues: 431 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 0.010 0.001 PHE A 808 TYR 0.010 0.001 TYR A 458 ARG 0.002 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 348) hydrogen bonds : angle 3.51449 ( 999) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.86231 ( 4) covalent geometry : bond 0.00195 ( 8435) covalent geometry : angle 0.48659 (11423) ********************** 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 90 residues out of total 890 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.876 Fit side-chains REVERT: A 345 ARG cc_start: 0.6844 (ptt180) cc_final: 0.6594 (ptt180) REVERT: A 1173 GLU cc_start: 0.8800 (tp30) cc_final: 0.8411 (tt0) REVERT: A 1232 ARG cc_start: 0.7286 (ttm-80) cc_final: 0.6573 (tpp-160) REVERT: A 1237 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6502 (tm-30) REVERT: A 1300 GLN cc_start: 0.7969 (tp-100) cc_final: 0.7703 (mm110) outliers start: 14 outliers final: 11 residues processed: 87 average time/residue: 0.2100 time to fit residues: 25.6712 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 : 0.831 ------------------------------------------------------------------------------- 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 740 THR Chi-restraints excluded: chain A residue 881 THR 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 82 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 89 optimal weight: 0.0670 overall best weight: 0.7920 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.134019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.104802 restraints weight = 10615.679| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.15 r_work: 0.3105 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8437 Z= 0.120 Angle : 0.527 8.598 11427 Z= 0.266 Chirality : 0.040 0.135 1281 Planarity : 0.004 0.050 1456 Dihedral : 4.472 25.126 1132 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.26 % Rotamer: Outliers : 1.71 % Allowed : 17.56 % Favored : 80.73 % 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: -0.18 (0.27), residues: 1028 helix: 1.16 (0.23), residues: 531 sheet: -0.57 (0.63), residues: 74 loop : -1.73 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 997 HIS 0.005 0.001 HIS A 988 PHE 0.013 0.001 PHE A 808 TYR 0.013 0.001 TYR A 774 ARG 0.002 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 348) hydrogen bonds : angle 3.57395 ( 999) SS BOND : bond 0.00081 ( 2) SS BOND : angle 1.04485 ( 4) covalent geometry : bond 0.00291 ( 8435) covalent geometry : angle 0.52673 (11423) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4976.73 seconds wall clock time: 86 minutes 39.87 seconds (5199.87 seconds total)