Starting phenix.real_space_refine on Thu Oct 22 23:49:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/32um_59181/10_2026/32um_59181.cif Found real_map, /net/cci-nas-00/data/ceres_data/32um_59181/10_2026/32um_59181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/32um_59181/10_2026/32um_59181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/32um_59181/10_2026/32um_59181.map" model { file = "/net/cci-nas-00/data/ceres_data/32um_59181/10_2026/32um_59181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/32um_59181/10_2026/32um_59181.cif" } resolution = 3.1 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= 0.001 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 11 5.49 5 S 48 5.16 5 C 4202 2.51 5 N 1164 2.21 5 O 1268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6693 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6473 Classifications: {'peptide': 796} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Chain: "G" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 220 Classifications: {'RNA': 11} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 9} Time building chain proxies: 1.34, per 1000 atoms: 0.20 Number of scatterers: 6693 At special positions: 0 Unit cell: (80.997, 99.617, 119.168, 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 48 16.00 P 11 15.00 O 1268 8.00 N 1164 7.00 C 4202 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: 0.61 Conformation dependent library (CDL) restraints added in 348.4 milliseconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1520 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 46.6% alpha, 13.4% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 332 through 336 Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 364 through 393 Proline residue: A 383 - end of helix Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 434 through 438 removed outlier: 4.015A pdb=" N LYS A 438 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.750A pdb=" N ALA A 495 " --> pdb=" O GLN A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 523 removed outlier: 4.484A pdb=" N HIS A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL A 518 " --> pdb=" O ALA A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 525 No H-bonds generated for 'chain 'A' and resid 524 through 525' Processing helix chain 'A' and resid 526 through 530 removed outlier: 3.725A pdb=" N VAL A 530 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 548 through 553 removed outlier: 4.185A pdb=" N GLY A 552 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 548 through 553' Processing helix chain 'A' and resid 586 through 590 removed outlier: 3.798A pdb=" N TRP A 590 " --> pdb=" O PRO A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 597 removed outlier: 3.648A pdb=" N LEU A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 612 Processing helix chain 'A' and resid 624 through 639 Processing helix chain 'A' and resid 639 through 644 removed outlier: 4.254A pdb=" N TRP A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 Processing helix chain 'A' and resid 689 through 692 Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 710 through 739 removed outlier: 3.914A pdb=" N TYR A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N MET A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU A 724 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 958 Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.714A pdb=" N GLU A 965 " --> pdb=" O GLU A 961 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 961 through 966' Processing helix chain 'A' and resid 967 through 976 removed outlier: 3.672A pdb=" N ILE A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 991 Processing helix chain 'A' and resid 991 through 999 removed outlier: 4.191A pdb=" N LYS A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1011 Processing helix chain 'A' and resid 1012 through 1018 Processing helix chain 'A' and resid 1042 through 1049 Processing helix chain 'A' and resid 1054 through 1062 Processing helix chain 'A' and resid 1076 through 1084 removed outlier: 4.203A pdb=" N LEU A1082 " --> pdb=" O GLU A1078 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU A1083 " --> pdb=" O ILE A1079 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A1084 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1099 Processing helix chain 'A' and resid 1130 through 1147 removed outlier: 3.505A pdb=" N GLN A1147 " --> pdb=" O TYR A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1152 No H-bonds generated for 'chain 'A' and resid 1150 through 1152' Processing helix chain 'A' and resid 1160 through 1169 Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1208 through 1212 removed outlier: 3.698A pdb=" N GLN A1212 " --> pdb=" O GLY A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1222 Processing helix chain 'A' and resid 1233 through 1238 Processing helix chain 'A' and resid 1240 through 1253 Processing helix chain 'A' and resid 1276 through 1283 removed outlier: 3.607A pdb=" N GLN A1281 " --> pdb=" O SER A1278 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 420 removed outlier: 5.553A pdb=" N ILE A 416 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN A 431 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 418 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 427 " --> pdb=" O MET A 420 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN A 483 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 453 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 508 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE A 503 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP A 413 " --> pdb=" O PHE A 503 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 677 through 679 removed outlier: 6.754A pdb=" N VAL A 678 " --> pdb=" O GLY A 982 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N THR A 984 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS A 656 " --> pdb=" O MET A 983 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 653 " --> pdb=" O ILE A1004 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA A 615 " --> pdb=" O LEU A1029 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLY A1031 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE A 617 " --> pdb=" O GLY A1031 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1071 through 1072 Processing sheet with id=AA4, first strand: chain 'A' and resid 1180 through 1183 removed outlier: 3.581A pdb=" N ARG A1180 " --> pdb=" O ILE A1154 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ASN A1192 " --> pdb=" O LYS A1225 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLY A1227 " --> pdb=" O ASN A1192 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE A1194 " --> pdb=" O GLY A1227 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR A1229 " --> pdb=" O ILE A1194 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU A1196 " --> pdb=" O TYR A1229 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ILE A1231 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER A1198 " --> pdb=" O ILE A1231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA6, first strand: chain 'A' and resid 1260 through 1263 241 hydrogen bonds defined for protein. 651 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1862 1.34 - 1.46: 1208 1.46 - 1.58: 3688 1.58 - 1.71: 21 1.71 - 1.83: 67 Bond restraints: 6846 Sorted by residual: bond pdb=" C5' U G 6 " pdb=" C4' U G 6 " ideal model delta sigma weight residual 1.508 1.539 -0.031 7.00e-03 2.04e+04 1.98e+01 bond pdb=" C5' U G 7 " pdb=" C4' U G 7 " ideal model delta sigma weight residual 1.508 1.538 -0.030 7.00e-03 2.04e+04 1.82e+01 bond pdb=" C4' U G 4 " pdb=" O4' U G 4 " ideal model delta sigma weight residual 1.454 1.416 0.038 1.00e-02 1.00e+04 1.46e+01 bond pdb=" C5' U G 11 " pdb=" C4' U G 11 " ideal model delta sigma weight residual 1.508 1.534 -0.026 7.00e-03 2.04e+04 1.43e+01 bond pdb=" C5' U G 12 " pdb=" C4' U G 12 " ideal model delta sigma weight residual 1.508 1.534 -0.026 7.00e-03 2.04e+04 1.36e+01 ... (remaining 6841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 6931 2.12 - 4.23: 2061 4.23 - 6.35: 254 6.35 - 8.47: 37 8.47 - 10.59: 4 Bond angle restraints: 9287 Sorted by residual: angle pdb=" C LEU A1150 " pdb=" CA LEU A1150 " pdb=" CB LEU A1150 " ideal model delta sigma weight residual 108.86 119.45 -10.59 1.44e+00 4.82e-01 5.40e+01 angle pdb=" CA PHE A1210 " pdb=" CB PHE A1210 " pdb=" CG PHE A1210 " ideal model delta sigma weight residual 113.80 120.53 -6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" O4' U G 11 " pdb=" C1' U G 11 " pdb=" N1 U G 11 " ideal model delta sigma weight residual 108.50 112.83 -4.33 7.00e-01 2.04e+00 3.83e+01 angle pdb=" O2 U G 6 " pdb=" C2 U G 6 " pdb=" N3 U G 6 " ideal model delta sigma weight residual 122.20 117.92 4.28 7.00e-01 2.04e+00 3.75e+01 angle pdb=" C GLU A 965 " pdb=" N LEU A 966 " pdb=" CA LEU A 966 " ideal model delta sigma weight residual 120.82 129.85 -9.03 1.50e+00 4.44e-01 3.63e+01 ... (remaining 9282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.64: 3745 18.64 - 37.28: 344 37.28 - 55.91: 91 55.91 - 74.55: 29 74.55 - 93.19: 13 Dihedral angle restraints: 4222 sinusoidal: 1879 harmonic: 2343 Sorted by residual: dihedral pdb=" C ARG A 701 " pdb=" N ARG A 701 " pdb=" CA ARG A 701 " pdb=" CB ARG A 701 " ideal model delta harmonic sigma weight residual -122.60 -142.37 19.77 0 2.50e+00 1.60e-01 6.26e+01 dihedral pdb=" N ARG A 701 " pdb=" C ARG A 701 " pdb=" CA ARG A 701 " pdb=" CB ARG A 701 " ideal model delta harmonic sigma weight residual 122.80 141.92 -19.12 0 2.50e+00 1.60e-01 5.85e+01 dihedral pdb=" C LEU A 666 " pdb=" N LEU A 666 " pdb=" CA LEU A 666 " pdb=" CB LEU A 666 " ideal model delta harmonic sigma weight residual -122.60 -141.55 18.95 0 2.50e+00 1.60e-01 5.75e+01 ... (remaining 4219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 899 0.152 - 0.303: 127 0.303 - 0.455: 10 0.455 - 0.606: 2 0.606 - 0.758: 3 Chirality restraints: 1041 Sorted by residual: chirality pdb=" CA ARG A 701 " pdb=" N ARG A 701 " pdb=" C ARG A 701 " pdb=" CB ARG A 701 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CA LEU A 666 " pdb=" N LEU A 666 " pdb=" C LEU A 666 " pdb=" CB LEU A 666 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CA LYS A 631 " pdb=" N LYS A 631 " pdb=" C LYS A 631 " pdb=" CB LYS A 631 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 ... (remaining 1038 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U G 10 " -0.215 2.00e-02 2.50e+03 1.01e-01 2.28e+02 pdb=" N1 U G 10 " 0.119 2.00e-02 2.50e+03 pdb=" C2 U G 10 " 0.077 2.00e-02 2.50e+03 pdb=" O2 U G 10 " 0.015 2.00e-02 2.50e+03 pdb=" N3 U G 10 " 0.023 2.00e-02 2.50e+03 pdb=" C4 U G 10 " -0.028 2.00e-02 2.50e+03 pdb=" O4 U G 10 " -0.113 2.00e-02 2.50e+03 pdb=" C5 U G 10 " 0.024 2.00e-02 2.50e+03 pdb=" C6 U G 10 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U G 11 " -0.168 2.00e-02 2.50e+03 7.95e-02 1.42e+02 pdb=" N1 U G 11 " 0.078 2.00e-02 2.50e+03 pdb=" C2 U G 11 " 0.061 2.00e-02 2.50e+03 pdb=" O2 U G 11 " 0.015 2.00e-02 2.50e+03 pdb=" N3 U G 11 " 0.031 2.00e-02 2.50e+03 pdb=" C4 U G 11 " -0.021 2.00e-02 2.50e+03 pdb=" O4 U G 11 " -0.103 2.00e-02 2.50e+03 pdb=" C5 U G 11 " 0.033 2.00e-02 2.50e+03 pdb=" C6 U G 11 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1229 " 0.157 2.00e-02 2.50e+03 8.12e-02 1.32e+02 pdb=" CG TYR A1229 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR A1229 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR A1229 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR A1229 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR A1229 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A1229 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR A1229 " 0.103 2.00e-02 2.50e+03 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 3132 3.00 - 3.47: 6751 3.47 - 3.95: 11157 3.95 - 4.42: 12474 4.42 - 4.90: 20067 Nonbonded interactions: 53581 Sorted by model distance: nonbonded pdb=" OG1 THR A 984 " pdb=" OP1 U G 10 " model vdw 2.520 3.040 nonbonded pdb=" OE1 GLU A1133 " pdb=" OG SER A1198 " model vdw 2.530 3.040 nonbonded pdb=" OH TYR A 368 " pdb=" OE2 GLU A1013 " model vdw 2.548 3.040 nonbonded pdb=" O LYS A1174 " pdb=" OG1 THR A1175 " model vdw 2.554 3.040 nonbonded pdb=" OE2 GLU A1124 " pdb=" OG1 THR A1161 " model vdw 2.575 3.040 ... (remaining 53576 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: 4.030 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.160 Find NCS groups from input model: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 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 : 0.012 0.055 6846 Z= 0.793 Angle : 1.934 10.587 9287 Z= 1.336 Chirality : 0.115 0.758 1041 Planarity : 0.018 0.226 1167 Dihedral : 16.856 93.191 2702 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.43 % Favored : 95.32 % Rotamer: Outliers : 6.21 % Allowed : 9.38 % Favored : 84.41 % Cbeta Deviations : 1.84 % Peptide Plane: Cis-proline : 2.86 % 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: -1.58 (0.28), residues: 790 helix: -2.49 (0.21), residues: 288 sheet: -0.01 (0.53), residues: 101 loop : 0.02 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 698 TYR 0.157 0.020 TYR A1229 PHE 0.106 0.015 PHE A1210 TRP 0.057 0.021 TRP A 442 HIS 0.011 0.003 HIS A1307 Details of bonding type rmsd/Z covalent geometry : bond 0.01247 / 0.79 ( 6846) covalent geometry : angle 1.93391 / 1.34 ( 9287) hydrogen bonds : bond 0.20423 / 13.69 ( 241) hydrogen bonds : angle 7.94110 / 5.50 ( 651) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 TYR cc_start: 0.8920 (m-80) cc_final: 0.8409 (m-80) REVERT: A 428 TYR cc_start: 0.8095 (m-80) cc_final: 0.7828 (m-80) REVERT: A 452 SER cc_start: 0.8795 (m) cc_final: 0.8471 (t) REVERT: A 462 GLU cc_start: 0.7801 (tp30) cc_final: 0.7593 (mm-30) REVERT: A 493 LEU cc_start: 0.7979 (mm) cc_final: 0.7360 (mp) REVERT: A 529 ASP cc_start: 0.7249 (m-30) cc_final: 0.6882 (t0) REVERT: A 545 GLU cc_start: 0.6847 (mp0) cc_final: 0.6530 (pm20) REVERT: A 603 MET cc_start: 0.8752 (tpt) cc_final: 0.8263 (tpt) REVERT: A 686 SER cc_start: 0.8775 (m) cc_final: 0.8163 (p) REVERT: A 734 LYS cc_start: 0.5150 (OUTLIER) cc_final: 0.4884 (ttpp) REVERT: A 1010 GLU cc_start: 0.7982 (tt0) cc_final: 0.7354 (mt-10) REVERT: A 1068 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7490 (tmm-80) REVERT: A 1102 LYS cc_start: 0.7898 (ptpp) cc_final: 0.7691 (ptmm) REVERT: A 1116 ASN cc_start: 0.8079 (p0) cc_final: 0.7743 (m-40) REVERT: A 1228 MET cc_start: 0.8749 (ttt) cc_final: 0.8436 (ttp) REVERT: A 1282 LYS cc_start: 0.8392 (mttt) cc_final: 0.8189 (mtpt) outliers start: 45 outliers final: 8 residues processed: 181 average time/residue: 0.1219 time to fit residues: 26.8568 Evaluate side-chains 100 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 1068 ARG Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1181 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN A 526 GLN A 727 GLN A1015 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.142306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.105510 restraints weight = 9286.158| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.24 r_work: 0.3102 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6846 Z= 0.181 Angle : 0.785 14.144 9287 Z= 0.404 Chirality : 0.052 0.204 1041 Planarity : 0.005 0.085 1167 Dihedral : 12.191 67.239 1076 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.41 % Allowed : 11.72 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.62 (0.29), residues: 790 helix: -1.07 (0.27), residues: 301 sheet: -0.05 (0.47), residues: 125 loop : 0.30 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 946 TYR 0.018 0.002 TYR A 715 PHE 0.020 0.002 PHE A1210 TRP 0.006 0.002 TRP A 590 HIS 0.007 0.001 HIS A1026 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 6846) covalent geometry : angle 0.78497 / 0.40 ( 9287) hydrogen bonds : bond 0.05178 / 3.59 ( 241) hydrogen bonds : angle 5.52187 / 3.92 ( 651) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.257 Fit side-chains REVERT: A 343 ASN cc_start: 0.8425 (p0) cc_final: 0.8198 (m110) REVERT: A 428 TYR cc_start: 0.8366 (m-80) cc_final: 0.8084 (m-80) REVERT: A 431 GLN cc_start: 0.8493 (tt0) cc_final: 0.8283 (tt0) REVERT: A 462 GLU cc_start: 0.8451 (tp30) cc_final: 0.8242 (mm-30) REVERT: A 529 ASP cc_start: 0.7753 (m-30) cc_final: 0.7522 (t0) REVERT: A 545 GLU cc_start: 0.7230 (mp0) cc_final: 0.6993 (pm20) REVERT: A 603 MET cc_start: 0.9089 (tpt) cc_final: 0.8860 (tpt) REVERT: A 677 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8600 (mt) REVERT: A 719 MET cc_start: 0.6066 (tpp) cc_final: 0.5764 (tpt) REVERT: A 734 LYS cc_start: 0.5068 (OUTLIER) cc_final: 0.4786 (pttp) REVERT: A 969 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: A 1010 GLU cc_start: 0.8774 (tt0) cc_final: 0.8517 (mt-10) REVERT: A 1059 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9044 (mp) REVERT: A 1068 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.7245 (tmm-80) REVERT: A 1104 LYS cc_start: 0.8710 (mptm) cc_final: 0.8340 (mmmt) REVERT: A 1116 ASN cc_start: 0.8419 (p0) cc_final: 0.8027 (m-40) REVERT: A 1210 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7449 (t80) outliers start: 32 outliers final: 10 residues processed: 118 average time/residue: 0.0985 time to fit residues: 14.9497 Evaluate side-chains 94 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1068 ARG Chi-restraints excluded: chain A residue 1131 GLN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1210 PHE Chi-restraints excluded: chain A residue 1320 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [42, 24, 64, 30, 72, 75, 4, 62, 31, 26, 35] chunk 42 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 64 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 474 GLN A 487 ASN A1026 HIS A1307 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.141551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104982 restraints weight = 9376.551| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.23 r_work: 0.3106 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6846 Z= 0.144 Angle : 0.667 12.462 9287 Z= 0.338 Chirality : 0.047 0.193 1041 Planarity : 0.004 0.039 1167 Dihedral : 10.860 60.818 1061 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.72 % Allowed : 12.97 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.39 (0.29), residues: 790 helix: -0.59 (0.28), residues: 311 sheet: -0.16 (0.46), residues: 127 loop : 0.28 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1001 TYR 0.011 0.002 TYR A1229 PHE 0.018 0.002 PHE A1210 TRP 0.005 0.001 TRP A 590 HIS 0.004 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6846) covalent geometry : angle 0.66736 / 0.34 ( 9287) hydrogen bonds : bond 0.04472 / 3.09 ( 241) hydrogen bonds : angle 4.96744 / 3.51 ( 651) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.255 Fit side-chains REVERT: A 428 TYR cc_start: 0.8383 (m-80) cc_final: 0.8130 (m-80) REVERT: A 431 GLN cc_start: 0.8485 (tt0) cc_final: 0.8277 (tt0) REVERT: A 462 GLU cc_start: 0.8541 (tp30) cc_final: 0.8316 (mm-30) REVERT: A 529 ASP cc_start: 0.7789 (m-30) cc_final: 0.7455 (t0) REVERT: A 545 GLU cc_start: 0.7244 (mp0) cc_final: 0.7010 (pm20) REVERT: A 631 LYS cc_start: 0.8426 (ptpt) cc_final: 0.8168 (mtpp) REVERT: A 719 MET cc_start: 0.5965 (tpp) cc_final: 0.5660 (tpt) REVERT: A 722 MET cc_start: 0.4860 (mtm) cc_final: 0.4651 (mmm) REVERT: A 723 LYS cc_start: 0.5165 (mmpt) cc_final: 0.4721 (mttt) REVERT: A 734 LYS cc_start: 0.5169 (OUTLIER) cc_final: 0.4858 (ptmt) REVERT: A 969 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: A 1001 ARG cc_start: 0.8639 (ttm170) cc_final: 0.7992 (ttm-80) REVERT: A 1010 GLU cc_start: 0.8777 (tt0) cc_final: 0.8537 (mt-10) REVERT: A 1104 LYS cc_start: 0.8723 (mptm) cc_final: 0.8327 (mmmt) REVERT: A 1116 ASN cc_start: 0.8413 (p0) cc_final: 0.8124 (m-40) REVERT: A 1188 GLN cc_start: 0.8179 (tt0) cc_final: 0.7944 (tt0) REVERT: A 1207 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8142 (mttp) REVERT: A 1210 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7503 (t80) outliers start: 27 outliers final: 12 residues processed: 107 average time/residue: 0.0886 time to fit residues: 12.3963 Evaluate side-chains 90 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1210 PHE Chi-restraints excluded: chain A residue 1320 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [37, 70, 61, 15, 74, 2, 3, 25, 77, 44, 7] chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN A1048 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.137286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.100665 restraints weight = 9384.091| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.27 r_work: 0.3030 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 6846 Z= 0.231 Angle : 0.708 12.844 9287 Z= 0.357 Chirality : 0.050 0.197 1041 Planarity : 0.005 0.035 1167 Dihedral : 10.859 60.804 1057 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.59 % Allowed : 14.21 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.29 (0.29), residues: 790 helix: -0.44 (0.29), residues: 298 sheet: -0.25 (0.46), residues: 125 loop : 0.29 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 701 TYR 0.015 0.002 TYR A1229 PHE 0.027 0.002 PHE A1210 TRP 0.006 0.001 TRP A1243 HIS 0.006 0.001 HIS A1248 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.23 ( 6846) covalent geometry : angle 0.70774 / 0.36 ( 9287) hydrogen bonds : bond 0.04870 / 3.33 ( 241) hydrogen bonds : angle 5.11645 / 3.59 ( 651) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.274 Fit side-chains REVERT: A 428 TYR cc_start: 0.8450 (m-80) cc_final: 0.8197 (m-80) REVERT: A 462 GLU cc_start: 0.8524 (tp30) cc_final: 0.8309 (mm-30) REVERT: A 529 ASP cc_start: 0.7778 (m-30) cc_final: 0.7391 (t0) REVERT: A 722 MET cc_start: 0.5051 (mtm) cc_final: 0.4683 (mmm) REVERT: A 734 LYS cc_start: 0.5184 (OUTLIER) cc_final: 0.4874 (pttp) REVERT: A 969 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: A 1001 ARG cc_start: 0.8599 (ttm170) cc_final: 0.7991 (ttm-80) REVERT: A 1010 GLU cc_start: 0.8919 (tt0) cc_final: 0.8693 (mt-10) REVERT: A 1104 LYS cc_start: 0.8808 (mptm) cc_final: 0.8381 (mmmt) REVERT: A 1139 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: A 1207 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8112 (mttp) REVERT: A 1210 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7655 (t80) outliers start: 26 outliers final: 15 residues processed: 95 average time/residue: 0.1026 time to fit residues: 12.6376 Evaluate side-chains 84 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1210 PHE Chi-restraints excluded: chain A residue 1320 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [26, 62, 20, 12, 16, 71, 76, 13, 3, 75, 36] chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 GLN A1255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.100758 restraints weight = 9449.031| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.29 r_work: 0.3026 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6846 Z= 0.200 Angle : 0.665 11.699 9287 Z= 0.335 Chirality : 0.048 0.182 1041 Planarity : 0.004 0.039 1167 Dihedral : 10.511 60.815 1057 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.72 % Allowed : 15.03 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.28 (0.29), residues: 790 helix: -0.28 (0.29), residues: 298 sheet: -0.46 (0.45), residues: 125 loop : 0.23 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 701 TYR 0.013 0.002 TYR A1229 PHE 0.022 0.002 PHE A1210 TRP 0.005 0.001 TRP A1243 HIS 0.005 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 ( 6846) covalent geometry : angle 0.66545 / 0.34 ( 9287) hydrogen bonds : bond 0.04527 / 3.10 ( 241) hydrogen bonds : angle 4.95620 / 3.48 ( 651) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.154 Fit side-chains REVERT: A 462 GLU cc_start: 0.8526 (tp30) cc_final: 0.8304 (mm-30) REVERT: A 529 ASP cc_start: 0.7782 (m-30) cc_final: 0.7322 (t0) REVERT: A 722 MET cc_start: 0.5121 (mtm) cc_final: 0.4599 (mmm) REVERT: A 723 LYS cc_start: 0.5414 (mmpt) cc_final: 0.5059 (mttt) REVERT: A 734 LYS cc_start: 0.5145 (OUTLIER) cc_final: 0.4883 (ptmt) REVERT: A 969 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: A 1001 ARG cc_start: 0.8688 (ttm170) cc_final: 0.8061 (ttm-80) REVERT: A 1007 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8208 (mm-30) REVERT: A 1010 GLU cc_start: 0.8930 (tt0) cc_final: 0.8464 (mt-10) REVERT: A 1104 LYS cc_start: 0.8831 (mptm) cc_final: 0.8394 (mmmt) REVERT: A 1139 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: A 1188 GLN cc_start: 0.8358 (tt0) cc_final: 0.8149 (tt0) REVERT: A 1207 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8120 (mttp) REVERT: A 1210 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7630 (t80) outliers start: 27 outliers final: 15 residues processed: 90 average time/residue: 0.0878 time to fit residues: 10.3480 Evaluate side-chains 82 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1210 PHE Chi-restraints excluded: chain A residue 1320 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [32, 20, 29, 4, 69, 48, 38, 35, 40, 24, 66] chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.0030 chunk 4 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.138205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.101719 restraints weight = 9359.892| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.24 r_work: 0.3045 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6846 Z= 0.172 Angle : 0.630 11.100 9287 Z= 0.319 Chirality : 0.046 0.171 1041 Planarity : 0.004 0.039 1167 Dihedral : 10.289 60.739 1056 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.72 % Allowed : 14.90 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.08 (0.29), residues: 790 helix: 0.01 (0.29), residues: 295 sheet: -0.46 (0.45), residues: 125 loop : 0.26 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 713 TYR 0.012 0.001 TYR A1229 PHE 0.020 0.002 PHE A1210 TRP 0.005 0.001 TRP A1243 HIS 0.004 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 6846) covalent geometry : angle 0.63043 / 0.32 ( 9287) hydrogen bonds : bond 0.04314 / 2.97 ( 241) hydrogen bonds : angle 4.86781 / 3.41 ( 651) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.257 Fit side-chains REVERT: A 428 TYR cc_start: 0.8429 (m-80) cc_final: 0.8214 (m-80) REVERT: A 462 GLU cc_start: 0.8533 (tp30) cc_final: 0.8280 (mm-30) REVERT: A 529 ASP cc_start: 0.7710 (m-30) cc_final: 0.7233 (t0) REVERT: A 722 MET cc_start: 0.4862 (mtm) cc_final: 0.4575 (mmm) REVERT: A 723 LYS cc_start: 0.5557 (mmpt) cc_final: 0.5231 (mttt) REVERT: A 734 LYS cc_start: 0.5179 (OUTLIER) cc_final: 0.4939 (ptmt) REVERT: A 736 LEU cc_start: 0.4570 (OUTLIER) cc_final: 0.4238 (tm) REVERT: A 969 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7637 (mp10) REVERT: A 1001 ARG cc_start: 0.8604 (ttm170) cc_final: 0.8016 (ttm-80) REVERT: A 1007 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8168 (mm-30) REVERT: A 1010 GLU cc_start: 0.8896 (tt0) cc_final: 0.8382 (mt-10) REVERT: A 1104 LYS cc_start: 0.8795 (mptm) cc_final: 0.8338 (mmmt) REVERT: A 1139 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: A 1207 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8102 (mttp) REVERT: A 1210 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7635 (t80) outliers start: 27 outliers final: 14 residues processed: 90 average time/residue: 0.0949 time to fit residues: 11.2160 Evaluate side-chains 78 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1210 PHE Chi-restraints excluded: chain A residue 1320 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [7, 64, 56, 68, 66, 65, 1, 25, 67, 10, 5] chunk 7 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 1 optimal weight: 0.0370 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 10 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 overall best weight: 0.2256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1035 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.140549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.104620 restraints weight = 9320.548| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.22 r_work: 0.3090 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6846 Z= 0.110 Angle : 0.575 10.861 9287 Z= 0.290 Chirality : 0.044 0.190 1041 Planarity : 0.004 0.041 1167 Dihedral : 10.168 60.562 1056 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.62 % Allowed : 15.72 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.19 (0.29), residues: 790 helix: 0.32 (0.30), residues: 295 sheet: -0.34 (0.46), residues: 124 loop : 0.35 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.009 0.001 TYR A1229 PHE 0.012 0.001 PHE A1056 TRP 0.004 0.001 TRP A 590 HIS 0.003 0.001 HIS A 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 6846) covalent geometry : angle 0.57545 / 0.29 ( 9287) hydrogen bonds : bond 0.03664 / 2.53 ( 241) hydrogen bonds : angle 4.60314 / 3.25 ( 651) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.254 Fit side-chains REVERT: A 462 GLU cc_start: 0.8535 (tp30) cc_final: 0.8259 (mm-30) REVERT: A 529 ASP cc_start: 0.7614 (m-30) cc_final: 0.6963 (t0) REVERT: A 687 GLU cc_start: 0.8212 (pm20) cc_final: 0.8008 (mp0) REVERT: A 723 LYS cc_start: 0.5567 (mmpt) cc_final: 0.5227 (mttt) REVERT: A 734 LYS cc_start: 0.5278 (OUTLIER) cc_final: 0.5042 (ptmt) REVERT: A 969 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8083 (mp10) REVERT: A 1001 ARG cc_start: 0.8542 (ttm170) cc_final: 0.8008 (ttm-80) REVERT: A 1007 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8149 (mm-30) REVERT: A 1010 GLU cc_start: 0.8844 (tt0) cc_final: 0.8398 (mt-10) REVERT: A 1104 LYS cc_start: 0.8727 (mptm) cc_final: 0.8301 (mmmt) REVERT: A 1139 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: A 1207 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8049 (mttp) REVERT: A 1210 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7589 (t80) outliers start: 19 outliers final: 9 residues processed: 82 average time/residue: 0.1002 time to fit residues: 10.7693 Evaluate side-chains 73 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1210 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [48, 55, 12, 45, 3, 15, 77, 42, 31, 58, 60] chunk 48 optimal weight: 0.7980 chunk 55 optimal weight: 0.0570 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.138223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.101990 restraints weight = 9386.991| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.22 r_work: 0.3052 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6846 Z= 0.168 Angle : 0.614 10.795 9287 Z= 0.310 Chirality : 0.046 0.173 1041 Planarity : 0.004 0.042 1167 Dihedral : 10.154 60.607 1056 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.76 % Allowed : 15.72 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.18 (0.29), residues: 790 helix: 0.38 (0.30), residues: 292 sheet: -0.42 (0.45), residues: 125 loop : 0.31 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.010 0.001 TYR A1229 PHE 0.020 0.002 PHE A1210 TRP 0.004 0.001 TRP A1243 HIS 0.004 0.001 HIS A1248 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 6846) covalent geometry : angle 0.61365 / 0.31 ( 9287) hydrogen bonds : bond 0.04093 / 2.79 ( 241) hydrogen bonds : angle 4.73650 / 3.33 ( 651) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.249 Fit side-chains REVERT: A 462 GLU cc_start: 0.8557 (tp30) cc_final: 0.8289 (mm-30) REVERT: A 529 ASP cc_start: 0.7648 (m-30) cc_final: 0.7181 (t0) REVERT: A 687 GLU cc_start: 0.8234 (pm20) cc_final: 0.8034 (mp0) REVERT: A 736 LEU cc_start: 0.4583 (OUTLIER) cc_final: 0.4225 (tm) REVERT: A 969 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7722 (mp10) REVERT: A 1001 ARG cc_start: 0.8560 (ttm170) cc_final: 0.8001 (ttm-80) REVERT: A 1007 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8120 (mm-30) REVERT: A 1010 GLU cc_start: 0.8895 (tt0) cc_final: 0.8353 (mt-10) REVERT: A 1104 LYS cc_start: 0.8751 (mptm) cc_final: 0.8297 (mmmt) REVERT: A 1139 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: A 1207 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8049 (mttp) REVERT: A 1210 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7685 (t80) outliers start: 20 outliers final: 10 residues processed: 78 average time/residue: 0.1004 time to fit residues: 10.2128 Evaluate side-chains 74 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 969 GLN Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1210 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [4, 19, 74, 33, 38, 53, 76, 63, 35, 32, 56] chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.137210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.101097 restraints weight = 9411.059| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.21 r_work: 0.3032 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6846 Z= 0.182 Angle : 0.636 10.704 9287 Z= 0.320 Chirality : 0.046 0.173 1041 Planarity : 0.004 0.043 1167 Dihedral : 10.050 60.647 1052 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.48 % Allowed : 16.14 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.08 (0.29), residues: 790 helix: 0.34 (0.30), residues: 291 sheet: -0.43 (0.45), residues: 125 loop : 0.18 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.011 0.001 TYR A1229 PHE 0.020 0.002 PHE A1210 TRP 0.004 0.001 TRP A 643 HIS 0.004 0.001 HIS A1248 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 ( 6846) covalent geometry : angle 0.63630 / 0.32 ( 9287) hydrogen bonds : bond 0.04184 / 2.83 ( 241) hydrogen bonds : angle 4.76344 / 3.35 ( 651) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.265 Fit side-chains REVERT: A 462 GLU cc_start: 0.8546 (tp30) cc_final: 0.8285 (mm-30) REVERT: A 529 ASP cc_start: 0.7710 (m-30) cc_final: 0.7000 (t0) REVERT: A 723 LYS cc_start: 0.5454 (mmpt) cc_final: 0.4945 (mttt) REVERT: A 736 LEU cc_start: 0.4630 (OUTLIER) cc_final: 0.4298 (tm) REVERT: A 1001 ARG cc_start: 0.8567 (ttm170) cc_final: 0.7990 (ttm-80) REVERT: A 1010 GLU cc_start: 0.8915 (tt0) cc_final: 0.8588 (mt-10) REVERT: A 1104 LYS cc_start: 0.8773 (mptm) cc_final: 0.8559 (mmtt) REVERT: A 1139 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: A 1207 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8026 (mttp) REVERT: A 1210 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7686 (t80) outliers start: 18 outliers final: 11 residues processed: 76 average time/residue: 0.0980 time to fit residues: 9.7352 Evaluate side-chains 76 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1210 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [0, 8, 5, 57, 24, 51, 44, 29, 13, 36, 15] chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 0.0050 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.137275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.101045 restraints weight = 9387.110| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.22 r_work: 0.3035 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6846 Z= 0.179 Angle : 0.642 10.607 9287 Z= 0.322 Chirality : 0.046 0.173 1041 Planarity : 0.004 0.044 1167 Dihedral : 9.748 60.721 1052 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.21 % Allowed : 16.14 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.05 (0.29), residues: 790 helix: 0.36 (0.30), residues: 291 sheet: -0.53 (0.44), residues: 132 loop : 0.18 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 962 TYR 0.011 0.001 TYR A1229 PHE 0.020 0.002 PHE A1210 TRP 0.005 0.001 TRP A 643 HIS 0.004 0.001 HIS A1248 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 6846) covalent geometry : angle 0.64208 / 0.32 ( 9287) hydrogen bonds : bond 0.04176 / 2.82 ( 241) hydrogen bonds : angle 4.76082 / 3.36 ( 651) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.316 Fit side-chains REVERT: A 462 GLU cc_start: 0.8557 (tp30) cc_final: 0.8306 (mm-30) REVERT: A 529 ASP cc_start: 0.7722 (m-30) cc_final: 0.6997 (t0) REVERT: A 722 MET cc_start: 0.3472 (mmm) cc_final: 0.3232 (mmm) REVERT: A 723 LYS cc_start: 0.5367 (mmpt) cc_final: 0.5069 (mmpt) REVERT: A 736 LEU cc_start: 0.4575 (OUTLIER) cc_final: 0.4224 (tm) REVERT: A 1001 ARG cc_start: 0.8564 (ttm170) cc_final: 0.7986 (ttm-80) REVERT: A 1010 GLU cc_start: 0.8898 (tt0) cc_final: 0.8559 (mt-10) REVERT: A 1104 LYS cc_start: 0.8772 (mptm) cc_final: 0.8562 (mmtt) REVERT: A 1139 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: A 1207 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7987 (mttp) REVERT: A 1210 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7725 (t80) outliers start: 16 outliers final: 11 residues processed: 77 average time/residue: 0.0918 time to fit residues: 9.5204 Evaluate side-chains 73 residues out of total 725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 421 CYS Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 478 CYS Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1210 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: [73, 38, 57, 27, 42, 65, 40, 32, 33, 76, 23] chunk 73 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 0.0870 chunk 27 optimal weight: 0.0670 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 0.0870 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.1652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1025 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.140641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.104815 restraints weight = 9298.790| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.22 r_work: 0.3085 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6846 Z= 0.110 Angle : 0.582 10.508 9287 Z= 0.291 Chirality : 0.044 0.186 1041 Planarity : 0.004 0.045 1167 Dihedral : 9.567 60.600 1052 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.21 % Allowed : 16.41 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.33 (0.30), residues: 790 helix: 0.61 (0.30), residues: 292 sheet: -0.36 (0.46), residues: 125 loop : 0.30 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 713 TYR 0.009 0.001 TYR A 956 PHE 0.011 0.001 PHE A1056 TRP 0.004 0.001 TRP A1243 HIS 0.003 0.001 HIS A 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 6846) covalent geometry : angle 0.58194 / 0.29 ( 9287) hydrogen bonds : bond 0.03521 / 2.43 ( 241) hydrogen bonds : angle 4.50801 / 3.20 ( 651) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2065.46 seconds wall clock time: 36 minutes 2.38 seconds (2162.38 seconds total)