Starting phenix.real_space_refine on Thu Jul 2 18:27:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oe1_70383/07_2026/9oe1_70383.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oe1_70383/07_2026/9oe1_70383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oe1_70383/07_2026/9oe1_70383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oe1_70383/07_2026/9oe1_70383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oe1_70383/07_2026/9oe1_70383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oe1_70383/07_2026/9oe1_70383.map" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 49 5.16 5 C 5944 2.51 5 N 1564 2.21 5 O 1757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9322 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9129 Classifications: {'peptide': 1178} Link IDs: {'PTRANS': 27, 'TRANS': 1150} Chain breaks: 2 Chain: "A" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 193 Unusual residues: {' MG': 2, 'AGS': 2, 'R1H': 2} Classifications: {'undetermined': 6, 'water': 33} Link IDs: {None: 38} Time building chain proxies: 1.76, per 1000 atoms: 0.19 Number of scatterers: 9322 At special positions: 0 Unit cell: (75.53, 116.2, 148.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 49 16.00 P 6 15.00 Mg 2 11.99 O 1757 8.00 N 1564 7.00 C 5944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 375.4 milliseconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 70.5% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 49 through 98 removed outlier: 4.022A pdb=" N LEU A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) Proline residue: A 71 - end of helix removed outlier: 4.193A pdb=" N VAL A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 162 Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 172 through 190 Processing helix chain 'A' and resid 192 through 216 removed outlier: 3.585A pdb=" N GLY A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 246 through 265 removed outlier: 3.598A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 272 Processing helix chain 'A' and resid 274 through 328 removed outlier: 3.545A pdb=" N ASN A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 376 removed outlier: 3.528A pdb=" N THR A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Proline residue: A 355 - end of helix removed outlier: 3.503A pdb=" N HIS A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 446 removed outlier: 3.616A pdb=" N GLN A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 514 through 519 removed outlier: 3.521A pdb=" N ILE A 518 " --> pdb=" O ALA A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 552 removed outlier: 3.921A pdb=" N ARG A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 616 through 624 removed outlier: 3.749A pdb=" N LYS A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 638 Processing helix chain 'A' and resid 695 through 703 removed outlier: 3.806A pdb=" N LEU A 702 " --> pdb=" O THR A 698 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN A 703 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 722 Processing helix chain 'A' and resid 722 through 737 removed outlier: 3.551A pdb=" N ALA A 726 " --> pdb=" O GLY A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 742 through 795 Processing helix chain 'A' and resid 798 through 804 removed outlier: 3.611A pdb=" N ASP A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.750A pdb=" N THR A 827 " --> pdb=" O GLN A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 852 Processing helix chain 'A' and resid 852 through 888 Proline residue: A 864 - end of helix removed outlier: 4.089A pdb=" N ALA A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS A 885 " --> pdb=" O ALA A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 901 removed outlier: 3.883A pdb=" N ILE A 894 " --> pdb=" O GLN A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 910 through 922 Processing helix chain 'A' and resid 923 through 964 removed outlier: 4.695A pdb=" N ILE A 947 " --> pdb=" O SER A 943 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TYR A 948 " --> pdb=" O GLN A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 993 Processing helix chain 'A' and resid 995 through 1012 Processing helix chain 'A' and resid 1073 through 1082 Processing helix chain 'A' and resid 1103 through 1110 removed outlier: 3.575A pdb=" N GLN A1110 " --> pdb=" O TRP A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1129 removed outlier: 3.842A pdb=" N ILE A1129 " --> pdb=" O LEU A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1133 removed outlier: 3.534A pdb=" N ASP A1133 " --> pdb=" O ALA A1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1130 through 1133' Processing helix chain 'A' and resid 1139 through 1149 removed outlier: 3.532A pdb=" N ILE A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1158 removed outlier: 4.359A pdb=" N PHE A1155 " --> pdb=" O ASN A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1190 removed outlier: 4.229A pdb=" N ARG A1190 " --> pdb=" O ARG A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1220 removed outlier: 3.512A pdb=" N GLU A1209 " --> pdb=" O ASP A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1236 Processing helix chain 'A' and resid 1254 through 1261 Processing helix chain 'A' and resid 1262 through 1273 removed outlier: 3.518A pdb=" N TYR A1266 " --> pdb=" O GLN A1262 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 422 Processing sheet with id=AA2, first strand: chain 'A' and resid 404 through 405 Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.858A pdb=" N ILE A 428 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR A 427 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ALA A 604 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA A 429 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N PHE A 606 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 431 " --> pdb=" O PHE A 606 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU A 613 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN A 607 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE A 611 " --> pdb=" O GLN A 607 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1057 through 1058 Processing sheet with id=AA5, first strand: chain 'A' and resid 1038 through 1040 removed outlier: 5.394A pdb=" N VAL A1038 " --> pdb=" O GLY A1053 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1111 through 1114 removed outlier: 6.074A pdb=" N ALA A1065 " --> pdb=" O ALA A1242 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A1244 " --> pdb=" O ALA A1065 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A1067 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A1241 " --> pdb=" O GLN A1252 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLN A1252 " --> pdb=" O ILE A1241 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A1243 " --> pdb=" O VAL A1250 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.82 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 3014 1.35 - 1.50: 2452 1.50 - 1.65: 3903 1.65 - 1.80: 55 1.80 - 1.95: 32 Bond restraints: 9456 Sorted by residual: bond pdb=" O3B AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" O3A AGS A1303 " pdb=" PA AGS A1303 " ideal model delta sigma weight residual 1.664 1.586 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O3A AGS A1304 " pdb=" PA AGS A1304 " ideal model delta sigma weight residual 1.664 1.586 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" N VAL A 414 " pdb=" CA VAL A 414 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.04e+01 ... (remaining 9451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 12585 2.58 - 5.17: 166 5.17 - 7.75: 31 7.75 - 10.34: 16 10.34 - 12.92: 1 Bond angle restraints: 12799 Sorted by residual: angle pdb=" C GLN A1272 " pdb=" N MET A1273 " pdb=" CA MET A1273 " ideal model delta sigma weight residual 121.94 113.25 8.69 2.00e+00 2.50e-01 1.89e+01 angle pdb=" C31 R1H A1305 " pdb=" C33 R1H A1305 " pdb=" C42 R1H A1305 " ideal model delta sigma weight residual 123.25 110.33 12.92 3.00e+00 1.11e-01 1.85e+01 angle pdb=" C ASN A 416 " pdb=" CA ASN A 416 " pdb=" CB ASN A 416 " ideal model delta sigma weight residual 111.17 104.75 6.42 1.54e+00 4.22e-01 1.74e+01 angle pdb=" N LEU A 415 " pdb=" CA LEU A 415 " pdb=" CB LEU A 415 " ideal model delta sigma weight residual 110.59 117.37 -6.78 1.65e+00 3.67e-01 1.69e+01 angle pdb=" CA VAL A 414 " pdb=" C VAL A 414 " pdb=" O VAL A 414 " ideal model delta sigma weight residual 120.78 116.13 4.65 1.25e+00 6.40e-01 1.38e+01 ... (remaining 12794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.28: 5302 30.28 - 60.56: 308 60.56 - 90.84: 71 90.84 - 121.12: 11 121.12 - 151.40: 7 Dihedral angle restraints: 5699 sinusoidal: 2317 harmonic: 3382 Sorted by residual: dihedral pdb=" O2A AGS A1303 " pdb=" O3A AGS A1303 " pdb=" PA AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sinusoidal sigma weight residual -52.28 99.12 -151.40 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" O2B AGS A1304 " pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " pdb=" PG AGS A1304 " ideal model delta sinusoidal sigma weight residual 7.37 149.93 -142.56 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" O3A AGS A1304 " pdb=" O3B AGS A1304 " pdb=" PB AGS A1304 " pdb=" PG AGS A1304 " ideal model delta sinusoidal sigma weight residual -107.39 34.68 -142.07 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 5696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1171 0.050 - 0.100: 241 0.100 - 0.151: 41 0.151 - 0.201: 12 0.201 - 0.251: 2 Chirality restraints: 1467 Sorted by residual: chirality pdb=" C3' AGS A1303 " pdb=" C2' AGS A1303 " pdb=" C4' AGS A1303 " pdb=" O3' AGS A1303 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C3' AGS A1304 " pdb=" C2' AGS A1304 " pdb=" C4' AGS A1304 " pdb=" O3' AGS A1304 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA VAL A 986 " pdb=" N VAL A 986 " pdb=" C VAL A 986 " pdb=" CB VAL A 986 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.79e-01 ... (remaining 1464 not shown) Planarity restraints: 1610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 R1H A1305 " 0.307 2.00e-02 2.50e+03 2.49e-01 7.73e+02 pdb=" C31 R1H A1305 " -0.097 2.00e-02 2.50e+03 pdb=" C33 R1H A1305 " 0.204 2.00e-02 2.50e+03 pdb=" N30 R1H A1305 " -0.405 2.00e-02 2.50e+03 pdb=" O32 R1H A1305 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 R1H A1305 " -0.119 2.00e-02 2.50e+03 1.02e-01 1.31e+02 pdb=" C22 R1H A1305 " 0.001 2.00e-02 2.50e+03 pdb=" C24 R1H A1305 " -0.075 2.00e-02 2.50e+03 pdb=" N21 R1H A1305 " 0.180 2.00e-02 2.50e+03 pdb=" O23 R1H A1305 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C29 R1H A1306 " -0.079 2.00e-02 2.50e+03 6.80e-02 5.79e+01 pdb=" C31 R1H A1306 " -0.007 2.00e-02 2.50e+03 pdb=" C33 R1H A1306 " -0.049 2.00e-02 2.50e+03 pdb=" N30 R1H A1306 " 0.119 2.00e-02 2.50e+03 pdb=" O32 R1H A1306 " 0.016 2.00e-02 2.50e+03 ... (remaining 1607 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 88 2.55 - 3.14: 7430 3.14 - 3.72: 14880 3.72 - 4.31: 20713 4.31 - 4.90: 34996 Nonbonded interactions: 78107 Sorted by model distance: nonbonded pdb=" OG SER A1075 " pdb="MG MG A1301 " model vdw 1.962 2.170 nonbonded pdb="MG MG A1301 " pdb=" O3G AGS A1304 " model vdw 2.007 2.170 nonbonded pdb=" OD2 ASP A 169 " pdb=" OH TYR A 449 " model vdw 2.209 3.040 nonbonded pdb=" NE2 GLN A 542 " pdb=" O ALA A 562 " model vdw 2.221 3.120 nonbonded pdb=" O MET A 794 " pdb=" OH TYR A 802 " model vdw 2.237 3.040 ... (remaining 78102 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: 4.670 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.360 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 9456 Z= 0.281 Angle : 0.786 12.919 12799 Z= 0.413 Chirality : 0.045 0.251 1467 Planarity : 0.008 0.249 1610 Dihedral : 21.401 151.401 3527 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.86 % Favored : 94.80 % Rotamer: Outliers : 3.07 % Allowed : 20.45 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1172 helix: 1.25 (0.19), residues: 794 sheet: -2.09 (0.63), residues: 53 loop : -1.93 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1136 TYR 0.024 0.001 TYR A 252 PHE 0.045 0.002 PHE A 525 TRP 0.005 0.001 TRP A 853 HIS 0.007 0.001 HIS A 880 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.28 ( 9456) covalent geometry : angle 0.78569 / 0.41 (12799) hydrogen bonds : bond 0.14493 / 9.48 ( 628) hydrogen bonds : angle 5.55305 / 4.07 ( 1851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8039 (mt0) REVERT: A 910 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.6197 (mpp-170) outliers start: 30 outliers final: 16 residues processed: 88 average time/residue: 0.0768 time to fit residues: 10.6221 Evaluate side-chains 69 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 452 GLN Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 720 ASN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 902 VAL Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1152 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 542 GLN A 608 ASN ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 ASN A1272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.082166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.058713 restraints weight = 24949.834| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.21 r_work: 0.2941 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9456 Z= 0.152 Angle : 0.632 14.902 12799 Z= 0.312 Chirality : 0.041 0.239 1467 Planarity : 0.004 0.042 1610 Dihedral : 17.082 141.701 1427 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer: Outliers : 3.48 % Allowed : 22.09 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.25), residues: 1172 helix: 1.70 (0.19), residues: 799 sheet: -1.72 (0.66), residues: 53 loop : -1.49 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1136 TYR 0.019 0.001 TYR A 252 PHE 0.024 0.002 PHE A 731 TRP 0.006 0.001 TRP A 141 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 9456) covalent geometry : angle 0.63191 / 0.31 (12799) hydrogen bonds : bond 0.05052 / 3.25 ( 628) hydrogen bonds : angle 4.28320 / 3.16 ( 1851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 161 MET cc_start: 0.9521 (mmp) cc_final: 0.9213 (tpp) REVERT: A 519 MET cc_start: 0.8817 (mtm) cc_final: 0.8572 (mtm) REVERT: A 598 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8296 (tpt90) REVERT: A 613 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8368 (pt0) REVERT: A 910 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.5656 (mpp-170) outliers start: 34 outliers final: 15 residues processed: 88 average time/residue: 0.0828 time to fit residues: 11.1332 Evaluate side-chains 68 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 598 ARG Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 68 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.081689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.058719 restraints weight = 24218.358| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.18 r_work: 0.2909 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9456 Z= 0.132 Angle : 0.567 11.713 12799 Z= 0.283 Chirality : 0.039 0.143 1467 Planarity : 0.003 0.042 1610 Dihedral : 14.221 150.664 1409 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.90 % Rotamer: Outliers : 3.78 % Allowed : 21.47 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.25), residues: 1172 helix: 1.99 (0.19), residues: 799 sheet: -1.38 (0.67), residues: 53 loop : -1.43 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 543 TYR 0.018 0.001 TYR A 252 PHE 0.019 0.001 PHE A 731 TRP 0.007 0.001 TRP A 853 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9456) covalent geometry : angle 0.56690 / 0.28 (12799) hydrogen bonds : bond 0.04793 / 3.09 ( 628) hydrogen bonds : angle 3.99350 / 2.93 ( 1851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 55 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9510 (mmp) cc_final: 0.9178 (tpp) REVERT: A 423 MET cc_start: 0.8164 (tmm) cc_final: 0.7881 (tmm) REVERT: A 613 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8494 (pt0) REVERT: A 1017 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8127 (t70) REVERT: A 1055 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8501 (tppt) outliers start: 37 outliers final: 17 residues processed: 86 average time/residue: 0.0786 time to fit residues: 10.6055 Evaluate side-chains 70 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1055 LYS Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.081104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.058077 restraints weight = 24656.261| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.22 r_work: 0.2896 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9456 Z= 0.134 Angle : 0.557 11.325 12799 Z= 0.280 Chirality : 0.039 0.203 1467 Planarity : 0.003 0.041 1610 Dihedral : 13.303 152.158 1400 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.75 % Favored : 96.08 % Rotamer: Outliers : 3.07 % Allowed : 22.39 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.25), residues: 1172 helix: 2.16 (0.19), residues: 793 sheet: -1.31 (0.63), residues: 58 loop : -1.21 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1136 TYR 0.015 0.001 TYR A 252 PHE 0.017 0.001 PHE A 731 TRP 0.006 0.001 TRP A 853 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9456) covalent geometry : angle 0.55671 / 0.28 (12799) hydrogen bonds : bond 0.04598 / 2.97 ( 628) hydrogen bonds : angle 3.89697 / 2.85 ( 1851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 51 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8662 (mmm) cc_final: 0.8434 (mmm) REVERT: A 423 MET cc_start: 0.8240 (tmm) cc_final: 0.7943 (tmm) REVERT: A 1017 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8147 (t70) REVERT: A 1055 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8466 (tppt) outliers start: 30 outliers final: 16 residues processed: 75 average time/residue: 0.0859 time to fit residues: 9.7663 Evaluate side-chains 67 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1055 LYS Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 22 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 921 ASN A1256 GLN A1262 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.080340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.056647 restraints weight = 24943.882| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.32 r_work: 0.2868 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9456 Z= 0.152 Angle : 0.565 10.637 12799 Z= 0.282 Chirality : 0.041 0.327 1467 Planarity : 0.003 0.040 1610 Dihedral : 13.043 166.343 1398 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer: Outliers : 2.97 % Allowed : 22.70 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.25), residues: 1172 helix: 2.21 (0.18), residues: 787 sheet: -1.08 (0.64), residues: 58 loop : -1.12 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 582 TYR 0.015 0.001 TYR A 252 PHE 0.015 0.001 PHE A 731 TRP 0.007 0.001 TRP A 853 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 9456) covalent geometry : angle 0.56525 / 0.28 (12799) hydrogen bonds : bond 0.04702 / 3.05 ( 628) hydrogen bonds : angle 3.89424 / 2.85 ( 1851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 51 time to evaluate : 0.365 Fit side-chains REVERT: A 197 MET cc_start: 0.8679 (mmm) cc_final: 0.8458 (mmm) REVERT: A 423 MET cc_start: 0.8355 (tmm) cc_final: 0.8058 (tmm) REVERT: A 519 MET cc_start: 0.9420 (mmt) cc_final: 0.8988 (mmm) REVERT: A 621 MET cc_start: 0.9261 (mmm) cc_final: 0.8891 (mmm) REVERT: A 910 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.5553 (mpp-170) REVERT: A 1017 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8207 (t70) REVERT: A 1055 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8464 (tppt) outliers start: 29 outliers final: 15 residues processed: 75 average time/residue: 0.0801 time to fit residues: 9.3834 Evaluate side-chains 67 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1055 LYS Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 48 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 HIS A 921 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.081044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.058064 restraints weight = 24476.013| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.23 r_work: 0.2885 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9456 Z= 0.119 Angle : 0.538 10.535 12799 Z= 0.270 Chirality : 0.039 0.144 1467 Planarity : 0.003 0.037 1610 Dihedral : 12.617 160.973 1395 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 2.25 % Allowed : 23.31 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.25), residues: 1172 helix: 2.32 (0.19), residues: 791 sheet: -0.91 (0.65), residues: 58 loop : -1.25 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1136 TYR 0.016 0.001 TYR A 252 PHE 0.016 0.001 PHE A 731 TRP 0.007 0.001 TRP A 853 HIS 0.002 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 9456) covalent geometry : angle 0.53834 / 0.27 (12799) hydrogen bonds : bond 0.04430 / 2.87 ( 628) hydrogen bonds : angle 3.81405 / 2.80 ( 1851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8631 (mmm) cc_final: 0.8407 (mmm) REVERT: A 519 MET cc_start: 0.9453 (mmt) cc_final: 0.9095 (mmm) REVERT: A 560 ASP cc_start: 0.8489 (t0) cc_final: 0.8259 (t70) REVERT: A 1017 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8207 (t70) REVERT: A 1055 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8446 (tppt) REVERT: A 1093 MET cc_start: 0.8347 (mmp) cc_final: 0.8094 (mmp) outliers start: 22 outliers final: 11 residues processed: 70 average time/residue: 0.0742 time to fit residues: 7.7504 Evaluate side-chains 63 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1055 LYS Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1113 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 ASN ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.078338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.055184 restraints weight = 24872.606| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.23 r_work: 0.2833 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9456 Z= 0.227 Angle : 0.605 10.109 12799 Z= 0.305 Chirality : 0.041 0.148 1467 Planarity : 0.003 0.035 1610 Dihedral : 12.710 162.978 1395 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.82 % Rotamer: Outliers : 2.35 % Allowed : 23.42 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.25), residues: 1172 helix: 2.11 (0.18), residues: 792 sheet: -0.91 (0.65), residues: 58 loop : -1.27 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 179 TYR 0.015 0.001 TYR A 252 PHE 0.016 0.002 PHE A1029 TRP 0.008 0.001 TRP A 853 HIS 0.011 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 ( 9456) covalent geometry : angle 0.60523 / 0.30 (12799) hydrogen bonds : bond 0.05046 / 3.28 ( 628) hydrogen bonds : angle 4.00857 / 2.94 ( 1851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8715 (mmm) cc_final: 0.8489 (mmm) REVERT: A 1017 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8213 (t70) REVERT: A 1093 MET cc_start: 0.8393 (mmp) cc_final: 0.8135 (mmp) outliers start: 23 outliers final: 15 residues processed: 68 average time/residue: 0.0601 time to fit residues: 6.6582 Evaluate side-chains 64 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 880 HIS Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 69 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.080441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.056961 restraints weight = 24969.728| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.28 r_work: 0.2906 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9456 Z= 0.127 Angle : 0.552 10.382 12799 Z= 0.276 Chirality : 0.039 0.160 1467 Planarity : 0.003 0.036 1610 Dihedral : 12.535 160.254 1395 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.99 % Rotamer: Outliers : 1.43 % Allowed : 23.72 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.25), residues: 1172 helix: 2.27 (0.19), residues: 794 sheet: -0.78 (0.65), residues: 58 loop : -1.28 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 179 TYR 0.016 0.001 TYR A 252 PHE 0.015 0.001 PHE A 731 TRP 0.008 0.001 TRP A 853 HIS 0.012 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 9456) covalent geometry : angle 0.55169 / 0.28 (12799) hydrogen bonds : bond 0.04562 / 2.95 ( 628) hydrogen bonds : angle 3.83423 / 2.81 ( 1851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8675 (mmm) cc_final: 0.8466 (mmm) REVERT: A 1017 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8256 (t70) REVERT: A 1093 MET cc_start: 0.8360 (mmp) cc_final: 0.8014 (mmm) outliers start: 14 outliers final: 10 residues processed: 60 average time/residue: 0.0663 time to fit residues: 6.4619 Evaluate side-chains 58 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1113 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.079073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.055462 restraints weight = 25248.460| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.29 r_work: 0.2869 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9456 Z= 0.184 Angle : 0.590 12.025 12799 Z= 0.294 Chirality : 0.040 0.147 1467 Planarity : 0.003 0.035 1610 Dihedral : 12.433 159.535 1395 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.01 % Favored : 95.82 % Rotamer: Outliers : 1.43 % Allowed : 23.72 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.25), residues: 1172 helix: 2.19 (0.18), residues: 793 sheet: -0.75 (0.66), residues: 58 loop : -1.29 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 179 TYR 0.016 0.001 TYR A 252 PHE 0.015 0.002 PHE A1029 TRP 0.007 0.001 TRP A 853 HIS 0.010 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 9456) covalent geometry : angle 0.59027 / 0.29 (12799) hydrogen bonds : bond 0.04870 / 3.17 ( 628) hydrogen bonds : angle 3.91412 / 2.88 ( 1851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8710 (mmm) cc_final: 0.8496 (mmm) REVERT: A 388 TYR cc_start: 0.8298 (t80) cc_final: 0.8030 (t80) REVERT: A 1017 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8321 (t70) REVERT: A 1093 MET cc_start: 0.8368 (mmp) cc_final: 0.8031 (mmm) outliers start: 14 outliers final: 9 residues processed: 58 average time/residue: 0.0632 time to fit residues: 6.1086 Evaluate side-chains 57 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.080301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.056918 restraints weight = 25083.153| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.29 r_work: 0.2905 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9456 Z= 0.121 Angle : 0.560 11.724 12799 Z= 0.275 Chirality : 0.039 0.144 1467 Planarity : 0.003 0.035 1610 Dihedral : 12.089 156.797 1395 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.92 % Favored : 95.99 % Rotamer: Outliers : 0.92 % Allowed : 23.93 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.25), residues: 1172 helix: 2.35 (0.19), residues: 788 sheet: -0.66 (0.66), residues: 58 loop : -1.10 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 179 TYR 0.016 0.001 TYR A 252 PHE 0.015 0.001 PHE A 731 TRP 0.007 0.001 TRP A 853 HIS 0.010 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 9456) covalent geometry : angle 0.55963 / 0.28 (12799) hydrogen bonds : bond 0.04497 / 2.92 ( 628) hydrogen bonds : angle 3.78442 / 2.78 ( 1851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8686 (mmm) cc_final: 0.8479 (mmm) REVERT: A 388 TYR cc_start: 0.8303 (t80) cc_final: 0.8032 (t80) REVERT: A 621 MET cc_start: 0.8987 (mmm) cc_final: 0.8651 (mmm) REVERT: A 1017 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8308 (t70) REVERT: A 1093 MET cc_start: 0.8336 (mmp) cc_final: 0.7995 (mmm) outliers start: 9 outliers final: 8 residues processed: 54 average time/residue: 0.0694 time to fit residues: 6.1190 Evaluate side-chains 56 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1081 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 48 optimal weight: 0.0170 chunk 32 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.081434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.058804 restraints weight = 24728.892| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.21 r_work: 0.2927 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9456 Z= 0.113 Angle : 0.542 11.358 12799 Z= 0.266 Chirality : 0.039 0.152 1467 Planarity : 0.003 0.035 1610 Dihedral : 11.373 149.896 1395 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.92 % Allowed : 23.93 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.25), residues: 1172 helix: 2.42 (0.19), residues: 794 sheet: -0.49 (0.68), residues: 58 loop : -1.09 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 179 TYR 0.014 0.001 TYR A 252 PHE 0.015 0.001 PHE A 731 TRP 0.007 0.001 TRP A 853 HIS 0.009 0.001 HIS A 628 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 9456) covalent geometry : angle 0.54234 / 0.27 (12799) hydrogen bonds : bond 0.04188 / 2.71 ( 628) hydrogen bonds : angle 3.66024 / 2.70 ( 1851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1996.59 seconds wall clock time: 35 minutes 6.65 seconds (2106.65 seconds total)