Starting phenix.real_space_refine on Wed Mar 4 14:13:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ynb_33957/03_2026/7ynb_33957.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynb_33957/03_2026/7ynb_33957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ynb_33957/03_2026/7ynb_33957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynb_33957/03_2026/7ynb_33957.map" model { file = "/net/cci-nas-00/data/ceres_data/7ynb_33957/03_2026/7ynb_33957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynb_33957/03_2026/7ynb_33957.cif" } resolution = 3.46 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= 0.004 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: 5 Type Number sf(0) Gaussians P 66 5.49 5 S 57 5.16 5 C 8496 2.51 5 N 2463 2.21 5 O 2765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13847 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1536, 12447 Classifications: {'peptide': 1536} Link IDs: {'PTRANS': 84, 'TRANS': 1451} Chain breaks: 4 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 810 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 5, 'rna3p_pur': 7, 'rna3p_pyr': 12} Link IDs: {'rna2p': 19, 'rna3p': 18} Chain: "C" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 590 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 14} Link IDs: {'rna2p': 4, 'rna3p': 23} Time building chain proxies: 3.14, per 1000 atoms: 0.23 Number of scatterers: 13847 At special positions: 0 Unit cell: (93.09, 171.2, 132.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 P 66 15.00 O 2765 8.00 N 2463 7.00 C 8496 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: 1.34 Conformation dependent library (CDL) restraints added in 535.0 milliseconds 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2858 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 18 sheets defined 21.5% alpha, 19.6% beta 14 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 57 through 74 removed outlier: 4.170A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 261 through 276 removed outlier: 3.547A pdb=" N ASN A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 291 through 295 removed outlier: 4.106A pdb=" N ARG A 294 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 295 " --> pdb=" O LEU A 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 291 through 295' Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.804A pdb=" N LEU A 302 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 344 through 365 removed outlier: 4.010A pdb=" N ASP A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.659A pdb=" N VAL A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.675A pdb=" N GLY A 566 " --> pdb=" O ALA A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.219A pdb=" N ASN A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 675 through 689 removed outlier: 3.720A pdb=" N PHE A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.630A pdb=" N ILE A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 removed outlier: 3.774A pdb=" N GLU A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 780 through 784' Processing helix chain 'A' and resid 787 through 801 removed outlier: 3.727A pdb=" N ALA A 791 " --> pdb=" O GLU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.623A pdb=" N ILE A 812 " --> pdb=" O LYS A 809 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 813 " --> pdb=" O SER A 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 809 through 813' Processing helix chain 'A' and resid 946 through 962 removed outlier: 4.257A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1109 removed outlier: 3.976A pdb=" N GLU A1106 " --> pdb=" O ASN A1102 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1247 removed outlier: 3.912A pdb=" N ARG A1235 " --> pdb=" O PRO A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 3.631A pdb=" N LYS A1303 " --> pdb=" O MET A1300 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A1304 " --> pdb=" O ILE A1301 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1300 through 1305' Processing helix chain 'A' and resid 1420 through 1427 removed outlier: 3.880A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP A1426 " --> pdb=" O LYS A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1476 Processing helix chain 'A' and resid 1515 through 1517 No H-bonds generated for 'chain 'A' and resid 1515 through 1517' Processing helix chain 'A' and resid 1518 through 1534 Processing helix chain 'A' and resid 1538 through 1548 Processing helix chain 'A' and resid 1575 through 1580 Processing helix chain 'A' and resid 1588 through 1595 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.689A pdb=" N PHE A 187 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 189 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 191 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 169 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 484 removed outlier: 3.520A pdb=" N GLY A 408 " --> pdb=" O PHE A 530 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 403 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 576 " --> pdb=" O CYS A 407 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 497 through 504 removed outlier: 3.769A pdb=" N GLU A 497 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG A 503 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 723 through 724 removed outlier: 6.766A pdb=" N ASN A 629 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE A 822 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 659 through 663 Processing sheet with id=AA8, first strand: chain 'A' and resid 739 through 744 removed outlier: 3.637A pdb=" N PHE A 757 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS A 755 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB1, first strand: chain 'A' and resid 944 through 945 removed outlier: 5.446A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 944 through 945 Processing sheet with id=AB3, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AB4, first strand: chain 'A' and resid 1001 through 1012 removed outlier: 42.247A pdb=" N ILE A1002 " --> pdb=" O VAL A1121 " (cutoff:3.500A) removed outlier: 35.571A pdb=" N ASP A1123 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 30.308A pdb=" N LYS A1004 " --> pdb=" O ASP A1123 " (cutoff:3.500A) removed outlier: 24.624A pdb=" N ARG A1125 " --> pdb=" O LYS A1004 " (cutoff:3.500A) removed outlier: 19.697A pdb=" N SER A1006 " --> pdb=" O ARG A1125 " (cutoff:3.500A) removed outlier: 14.161A pdb=" N GLN A1127 " --> pdb=" O SER A1006 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N THR A1008 " --> pdb=" O GLN A1127 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA A1129 " --> pdb=" O THR A1008 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG A1010 " --> pdb=" O ALA A1129 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A1047 " --> pdb=" O TRP A1120 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A1122 " --> pdb=" O ARG A1045 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A1041 " --> pdb=" O TYR A1126 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS A1128 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL A1039 " --> pdb=" O LYS A1128 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE A1130 " --> pdb=" O MET A1037 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N MET A1037 " --> pdb=" O PHE A1130 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A1037 " --> pdb=" O LYS A1144 " (cutoff:3.500A) removed outlier: 19.248A pdb=" N CYS A1143 " --> pdb=" O LYS A1223 " (cutoff:3.500A) removed outlier: 14.076A pdb=" N LYS A1223 " --> pdb=" O CYS A1143 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N GLU A1145 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS A1149 " --> pdb=" O THR A1217 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR A1217 " --> pdb=" O HIS A1149 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A1220 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU A1007 " --> pdb=" O PHE A1220 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU A1222 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE A1005 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU A1224 " --> pdb=" O GLN A1003 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N GLN A1003 " --> pdb=" O GLU A1224 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N GLU A1226 " --> pdb=" O HIS A1001 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N HIS A1001 " --> pdb=" O GLU A1226 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A1283 " --> pdb=" O ASN A1280 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL A1284 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N GLU A1229 " --> pdb=" O VAL A1284 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ASP A1286 " --> pdb=" O GLU A1229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1070 through 1071 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1086 removed outlier: 3.601A pdb=" N PHE A1083 " --> pdb=" O LEU A1096 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A1096 " --> pdb=" O PHE A1083 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A1085 " --> pdb=" O PHE A1094 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A1094 " --> pdb=" O VAL A1085 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1187 through 1188 removed outlier: 3.556A pdb=" N ASP A1187 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1200 through 1202 Processing sheet with id=AB9, first strand: chain 'A' and resid 1385 through 1387 310 hydrogen bonds defined for protein. 882 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4107 1.33 - 1.45: 2769 1.45 - 1.57: 7219 1.57 - 1.70: 130 1.70 - 1.82: 82 Bond restraints: 14307 Sorted by residual: bond pdb=" N CYS A 965 " pdb=" CA CYS A 965 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.53e+00 bond pdb=" N CYS A 86 " pdb=" CA CYS A 86 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.41e-02 5.03e+03 6.98e+00 bond pdb=" N CYS A1342 " pdb=" CA CYS A1342 " ideal model delta sigma weight residual 1.452 1.489 -0.036 1.41e-02 5.03e+03 6.69e+00 bond pdb=" N CYS A1345 " pdb=" CA CYS A1345 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.26e-02 6.30e+03 6.22e+00 bond pdb=" N CYS A 708 " pdb=" CA CYS A 708 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.37e-02 5.33e+03 5.70e+00 ... (remaining 14302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 18953 1.78 - 3.55: 562 3.55 - 5.33: 62 5.33 - 7.11: 12 7.11 - 8.88: 4 Bond angle restraints: 19593 Sorted by residual: angle pdb=" N ARG A1346 " pdb=" CA ARG A1346 " pdb=" C ARG A1346 " ideal model delta sigma weight residual 113.88 108.17 5.71 1.23e+00 6.61e-01 2.15e+01 angle pdb=" N TYR A 866 " pdb=" CA TYR A 866 " pdb=" C TYR A 866 " ideal model delta sigma weight residual 111.02 116.25 -5.23 1.25e+00 6.40e-01 1.75e+01 angle pdb=" C LYS A1107 " pdb=" N LEU A1108 " pdb=" CA LEU A1108 " ideal model delta sigma weight residual 120.44 125.26 -4.82 1.30e+00 5.92e-01 1.38e+01 angle pdb=" N CYS A 123 " pdb=" CA CYS A 123 " pdb=" C CYS A 123 " ideal model delta sigma weight residual 110.07 105.83 4.24 1.26e+00 6.30e-01 1.13e+01 angle pdb=" C LEU A1108 " pdb=" N GLU A1109 " pdb=" CA GLU A1109 " ideal model delta sigma weight residual 121.54 127.84 -6.30 1.91e+00 2.74e-01 1.09e+01 ... (remaining 19588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.68: 8264 31.68 - 63.36: 424 63.36 - 95.05: 58 95.05 - 126.73: 5 126.73 - 158.41: 2 Dihedral angle restraints: 8753 sinusoidal: 4322 harmonic: 4431 Sorted by residual: dihedral pdb=" C4' A C -2 " pdb=" C3' A C -2 " pdb=" C2' A C -2 " pdb=" C1' A C -2 " ideal model delta sinusoidal sigma weight residual -35.00 32.58 -67.58 1 8.00e+00 1.56e-02 9.28e+01 dihedral pdb=" C5' A C -2 " pdb=" C4' A C -2 " pdb=" C3' A C -2 " pdb=" O3' A C -2 " ideal model delta sinusoidal sigma weight residual 147.00 82.03 64.97 1 8.00e+00 1.56e-02 8.65e+01 dihedral pdb=" O4' A C -2 " pdb=" C4' A C -2 " pdb=" C3' A C -2 " pdb=" C2' A C -2 " ideal model delta sinusoidal sigma weight residual 24.00 -33.84 57.84 1 8.00e+00 1.56e-02 7.02e+01 ... (remaining 8750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1683 0.055 - 0.110: 350 0.110 - 0.165: 61 0.165 - 0.220: 4 0.220 - 0.275: 1 Chirality restraints: 2099 Sorted by residual: chirality pdb=" C3' A C -2 " pdb=" C4' A C -2 " pdb=" O3' A C -2 " pdb=" C2' A C -2 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C2' A C -2 " pdb=" C3' A C -2 " pdb=" O2' A C -2 " pdb=" C1' A C -2 " both_signs ideal model delta sigma weight residual False -2.52 -2.74 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA CYS A 123 " pdb=" N CYS A 123 " pdb=" C CYS A 123 " pdb=" CB CYS A 123 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2096 not shown) Planarity restraints: 2318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 435 " 0.049 5.00e-02 4.00e+02 7.40e-02 8.75e+00 pdb=" N PRO A 436 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 863 " -0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO A 864 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 636 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO A 637 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 637 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 637 " -0.034 5.00e-02 4.00e+02 ... (remaining 2315 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 433 2.68 - 3.24: 12020 3.24 - 3.79: 20015 3.79 - 4.35: 26513 4.35 - 4.90: 44920 Nonbonded interactions: 103901 Sorted by model distance: nonbonded pdb=" O2' A B 11 " pdb=" O4' C B 12 " model vdw 2.127 3.040 nonbonded pdb=" OE1 GLU A 70 " pdb=" NH2 ARG A 104 " model vdw 2.254 3.120 nonbonded pdb=" OG SER A1006 " pdb=" OD1 ASP A1221 " model vdw 2.257 3.040 nonbonded pdb=" NH2 ARG A 917 " pdb=" O GLU A 922 " model vdw 2.274 3.120 nonbonded pdb=" N ASP A1404 " pdb=" OD1 ASP A1404 " model vdw 2.286 3.120 ... (remaining 103896 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.210 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 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 0.046 14307 Z= 0.225 Angle : 0.719 8.885 19593 Z= 0.423 Chirality : 0.047 0.275 2099 Planarity : 0.006 0.074 2318 Dihedral : 18.406 158.408 5895 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.01 % Favored : 88.79 % Rotamer: Outliers : 1.26 % Allowed : 11.38 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.17), residues: 1526 helix: -1.93 (0.25), residues: 306 sheet: -2.04 (0.28), residues: 282 loop : -3.94 (0.14), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 967 TYR 0.010 0.001 TYR A1147 PHE 0.014 0.002 PHE A 528 TRP 0.024 0.001 TRP A1600 HIS 0.006 0.001 HIS A1279 Details of bonding type rmsd covalent geometry : bond 0.00483 (14307) covalent geometry : angle 0.71859 (19593) hydrogen bonds : bond 0.21250 ( 339) hydrogen bonds : angle 6.99251 ( 952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 120 average time/residue: 0.1709 time to fit residues: 27.6982 Evaluate side-chains 77 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 913 ASP Chi-restraints excluded: chain A residue 1105 GLN Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1312 CYS Chi-restraints excluded: chain A residue 1404 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN A 464 ASN A 531 GLN A 985 ASN A1095 HIS A1127 GLN A1417 HIS A1483 HIS A1514 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.104048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.077390 restraints weight = 26261.864| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.45 r_work: 0.2845 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14307 Z= 0.123 Angle : 0.604 10.277 19593 Z= 0.317 Chirality : 0.043 0.195 2099 Planarity : 0.006 0.064 2318 Dihedral : 16.438 165.415 2698 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 1.41 % Allowed : 14.06 % Favored : 84.52 % 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: -3.44 (0.19), residues: 1526 helix: -0.18 (0.30), residues: 308 sheet: -1.42 (0.29), residues: 270 loop : -3.53 (0.15), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 924 TYR 0.007 0.001 TYR A1209 PHE 0.027 0.001 PHE A1073 TRP 0.015 0.001 TRP A1600 HIS 0.005 0.001 HIS A1279 Details of bonding type rmsd covalent geometry : bond 0.00277 (14307) covalent geometry : angle 0.60430 (19593) hydrogen bonds : bond 0.04057 ( 339) hydrogen bonds : angle 4.66591 ( 952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1097 TRP cc_start: 0.8911 (m-10) cc_final: 0.8262 (m100) REVERT: A 1211 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7429 (tmm) outliers start: 19 outliers final: 10 residues processed: 91 average time/residue: 0.1154 time to fit residues: 15.8638 Evaluate side-chains 75 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1022 ASP Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1500 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 118 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A1248 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.099245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.072414 restraints weight = 26550.118| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.53 r_work: 0.2747 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14307 Z= 0.206 Angle : 0.648 10.166 19593 Z= 0.341 Chirality : 0.045 0.190 2099 Planarity : 0.005 0.063 2318 Dihedral : 16.265 161.717 2687 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.71 % Favored : 87.29 % Rotamer: Outliers : 1.86 % Allowed : 16.44 % Favored : 81.70 % 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: -2.97 (0.19), residues: 1526 helix: 0.72 (0.32), residues: 304 sheet: -1.31 (0.29), residues: 288 loop : -3.36 (0.16), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 470 TYR 0.012 0.001 TYR A1276 PHE 0.018 0.002 PHE A1083 TRP 0.018 0.001 TRP A1600 HIS 0.005 0.001 HIS A1149 Details of bonding type rmsd covalent geometry : bond 0.00490 (14307) covalent geometry : angle 0.64813 (19593) hydrogen bonds : bond 0.04955 ( 339) hydrogen bonds : angle 4.42978 ( 952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8821 (mm) REVERT: A 393 ARG cc_start: 0.7689 (mpt180) cc_final: 0.7361 (mpt180) REVERT: A 1211 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7758 (tmm) outliers start: 25 outliers final: 15 residues processed: 81 average time/residue: 0.1065 time to fit residues: 13.3505 Evaluate side-chains 73 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1022 ASP Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1500 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 148 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.0570 chunk 62 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 112 optimal weight: 3.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A1280 ASN A1418 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.103197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.076664 restraints weight = 26264.626| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.54 r_work: 0.2828 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14307 Z= 0.104 Angle : 0.547 11.229 19593 Z= 0.284 Chirality : 0.041 0.199 2099 Planarity : 0.005 0.062 2318 Dihedral : 16.147 165.218 2687 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 2.31 % Allowed : 16.67 % Favored : 81.03 % 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: -2.49 (0.20), residues: 1526 helix: 1.41 (0.33), residues: 295 sheet: -0.80 (0.30), residues: 270 loop : -3.16 (0.16), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 917 TYR 0.007 0.001 TYR A1126 PHE 0.018 0.001 PHE A1073 TRP 0.015 0.001 TRP A1600 HIS 0.005 0.001 HIS A1149 Details of bonding type rmsd covalent geometry : bond 0.00236 (14307) covalent geometry : angle 0.54731 (19593) hydrogen bonds : bond 0.03135 ( 339) hydrogen bonds : angle 4.04526 ( 952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8712 (mm) REVERT: A 621 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7543 (tpp80) REVERT: A 1211 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.7640 (tmm) REVERT: A 1280 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7900 (p0) outliers start: 31 outliers final: 14 residues processed: 83 average time/residue: 0.1092 time to fit residues: 14.1854 Evaluate side-chains 76 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1280 ASN Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1491 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 57 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 0.0060 chunk 20 optimal weight: 0.0050 chunk 143 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.099504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.072769 restraints weight = 26632.509| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.53 r_work: 0.2765 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14307 Z= 0.189 Angle : 0.608 10.341 19593 Z= 0.317 Chirality : 0.044 0.192 2099 Planarity : 0.005 0.063 2318 Dihedral : 16.109 162.330 2687 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 2.01 % Allowed : 17.63 % Favored : 80.36 % 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: -2.41 (0.20), residues: 1526 helix: 1.47 (0.33), residues: 302 sheet: -0.76 (0.31), residues: 268 loop : -3.13 (0.16), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 393 TYR 0.011 0.001 TYR A 866 PHE 0.017 0.002 PHE A1073 TRP 0.015 0.001 TRP A1600 HIS 0.006 0.001 HIS A1279 Details of bonding type rmsd covalent geometry : bond 0.00449 (14307) covalent geometry : angle 0.60759 (19593) hydrogen bonds : bond 0.04303 ( 339) hydrogen bonds : angle 4.15596 ( 952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8724 (mm) REVERT: A 1211 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.7865 (tmm) outliers start: 27 outliers final: 17 residues processed: 75 average time/residue: 0.0996 time to fit residues: 12.1949 Evaluate side-chains 73 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 382 PHE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1491 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1428 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.097583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.070921 restraints weight = 26665.447| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.51 r_work: 0.2739 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 14307 Z= 0.231 Angle : 0.646 9.652 19593 Z= 0.340 Chirality : 0.046 0.192 2099 Planarity : 0.005 0.065 2318 Dihedral : 16.166 160.795 2687 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.98 % Favored : 87.02 % Rotamer: Outliers : 2.08 % Allowed : 18.01 % Favored : 79.91 % 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: -2.48 (0.20), residues: 1526 helix: 1.39 (0.33), residues: 302 sheet: -1.19 (0.30), residues: 295 loop : -3.06 (0.17), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.015 0.002 TYR A1081 PHE 0.017 0.002 PHE A1073 TRP 0.018 0.001 TRP A1600 HIS 0.006 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00551 (14307) covalent geometry : angle 0.64632 (19593) hydrogen bonds : bond 0.04774 ( 339) hydrogen bonds : angle 4.30145 ( 952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8618 (mm) REVERT: A 1211 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.7974 (tmm) REVERT: A 1269 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8549 (tt) outliers start: 28 outliers final: 18 residues processed: 79 average time/residue: 0.0936 time to fit residues: 12.0106 Evaluate side-chains 75 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1298 ASP Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1491 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 99 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 127 optimal weight: 0.0980 chunk 118 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.074688 restraints weight = 26393.720| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.52 r_work: 0.2804 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14307 Z= 0.107 Angle : 0.549 10.426 19593 Z= 0.285 Chirality : 0.041 0.196 2099 Planarity : 0.005 0.064 2318 Dihedral : 16.077 164.184 2687 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 1.93 % Allowed : 18.38 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.13 (0.21), residues: 1526 helix: 1.68 (0.33), residues: 301 sheet: -0.56 (0.31), residues: 263 loop : -2.92 (0.17), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 917 TYR 0.010 0.001 TYR A1081 PHE 0.016 0.001 PHE A1073 TRP 0.016 0.001 TRP A1600 HIS 0.006 0.001 HIS A1149 Details of bonding type rmsd covalent geometry : bond 0.00246 (14307) covalent geometry : angle 0.54876 (19593) hydrogen bonds : bond 0.03126 ( 339) hydrogen bonds : angle 3.98001 ( 952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8547 (mm) REVERT: A 621 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.6970 (tpp80) REVERT: A 1211 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.7879 (tmm) REVERT: A 1269 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8594 (tt) outliers start: 26 outliers final: 15 residues processed: 75 average time/residue: 0.1040 time to fit residues: 12.4858 Evaluate side-chains 73 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1280 ASN Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1491 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 3 optimal weight: 3.9990 chunk 109 optimal weight: 0.0060 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 78 optimal weight: 0.2980 overall best weight: 2.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.098184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.071133 restraints weight = 26745.639| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.55 r_work: 0.2719 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 14307 Z= 0.250 Angle : 0.649 9.312 19593 Z= 0.339 Chirality : 0.046 0.188 2099 Planarity : 0.005 0.065 2318 Dihedral : 16.098 160.771 2687 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.37 % Favored : 86.63 % Rotamer: Outliers : 2.31 % Allowed : 18.60 % Favored : 79.09 % 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: -2.30 (0.21), residues: 1526 helix: 1.49 (0.33), residues: 305 sheet: -1.12 (0.30), residues: 294 loop : -2.92 (0.17), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.014 0.002 TYR A1081 PHE 0.017 0.002 PHE A 528 TRP 0.016 0.001 TRP A1600 HIS 0.007 0.001 HIS A1279 Details of bonding type rmsd covalent geometry : bond 0.00600 (14307) covalent geometry : angle 0.64912 (19593) hydrogen bonds : bond 0.04863 ( 339) hydrogen bonds : angle 4.25206 ( 952) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8599 (mm) REVERT: A 1115 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: A 1211 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8011 (tmm) REVERT: A 1269 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8613 (tt) outliers start: 31 outliers final: 20 residues processed: 81 average time/residue: 0.1075 time to fit residues: 13.9498 Evaluate side-chains 79 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 913 ASP Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1491 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 16 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1280 ASN A1419 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.099388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.072482 restraints weight = 26772.713| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.55 r_work: 0.2754 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14307 Z= 0.177 Angle : 0.599 9.642 19593 Z= 0.313 Chirality : 0.044 0.190 2099 Planarity : 0.005 0.065 2318 Dihedral : 16.097 161.686 2687 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 1.86 % Allowed : 19.12 % Favored : 79.02 % 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: -2.17 (0.21), residues: 1526 helix: 1.53 (0.33), residues: 306 sheet: -0.74 (0.31), residues: 267 loop : -2.88 (0.17), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 444 TYR 0.014 0.001 TYR A1081 PHE 0.015 0.001 PHE A 747 TRP 0.017 0.001 TRP A1600 HIS 0.006 0.001 HIS A1149 Details of bonding type rmsd covalent geometry : bond 0.00421 (14307) covalent geometry : angle 0.59920 (19593) hydrogen bonds : bond 0.04070 ( 339) hydrogen bonds : angle 4.14548 ( 952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8564 (mm) REVERT: A 1115 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: A 1211 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.7974 (tmm) REVERT: A 1269 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8581 (tt) outliers start: 25 outliers final: 19 residues processed: 75 average time/residue: 0.1150 time to fit residues: 13.7329 Evaluate side-chains 78 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1280 ASN Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1510 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.098213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.071659 restraints weight = 26585.366| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.52 r_work: 0.2751 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14307 Z= 0.179 Angle : 0.602 9.550 19593 Z= 0.315 Chirality : 0.044 0.190 2099 Planarity : 0.005 0.065 2318 Dihedral : 16.088 161.422 2686 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer: Outliers : 1.86 % Allowed : 19.05 % Favored : 79.09 % 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: -2.14 (0.21), residues: 1526 helix: 1.59 (0.33), residues: 305 sheet: -0.73 (0.31), residues: 267 loop : -2.87 (0.17), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 444 TYR 0.014 0.001 TYR A1081 PHE 0.015 0.001 PHE A 747 TRP 0.017 0.001 TRP A1600 HIS 0.005 0.001 HIS A1149 Details of bonding type rmsd covalent geometry : bond 0.00428 (14307) covalent geometry : angle 0.60165 (19593) hydrogen bonds : bond 0.04122 ( 339) hydrogen bonds : angle 4.14244 ( 952) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8544 (mm) REVERT: A 621 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7166 (tpp80) REVERT: A 1115 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: A 1211 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.7924 (tmm) REVERT: A 1269 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8580 (tt) outliers start: 25 outliers final: 20 residues processed: 75 average time/residue: 0.1148 time to fit residues: 13.5196 Evaluate side-chains 80 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 913 ASP Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1115 GLU Chi-restraints excluded: chain A residue 1133 ILE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1211 MET Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1280 ASN Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1510 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 87 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 44 optimal weight: 0.0670 chunk 135 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.101395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.074978 restraints weight = 26653.179| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.44 r_work: 0.2806 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14307 Z= 0.119 Angle : 0.554 10.030 19593 Z= 0.288 Chirality : 0.042 0.193 2099 Planarity : 0.005 0.064 2318 Dihedral : 16.053 162.543 2686 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 1.71 % Allowed : 19.27 % Favored : 79.02 % 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: -2.01 (0.21), residues: 1526 helix: 1.71 (0.33), residues: 307 sheet: -0.52 (0.32), residues: 256 loop : -2.81 (0.17), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1193 TYR 0.012 0.001 TYR A1081 PHE 0.015 0.001 PHE A1073 TRP 0.017 0.001 TRP A1600 HIS 0.006 0.001 HIS A1149 Details of bonding type rmsd covalent geometry : bond 0.00276 (14307) covalent geometry : angle 0.55382 (19593) hydrogen bonds : bond 0.03338 ( 339) hydrogen bonds : angle 3.98914 ( 952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.08 seconds wall clock time: 55 minutes 54.48 seconds (3354.48 seconds total)