Starting phenix.real_space_refine on Fri Oct 10 21:43:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pee_17630/10_2025/8pee_17630.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pee_17630/10_2025/8pee_17630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pee_17630/10_2025/8pee_17630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pee_17630/10_2025/8pee_17630.map" model { file = "/net/cci-nas-00/data/ceres_data/8pee_17630/10_2025/8pee_17630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pee_17630/10_2025/8pee_17630.cif" } resolution = 3.8 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= 0.006 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 5960 2.51 5 N 1541 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9217 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 8967 Classifications: {'peptide': 1157} Link IDs: {'PTRANS': 29, 'TRANS': 1127} Chain breaks: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'JJI': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 206 Unusual residues: {'JIZ': 1, 'Y01': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 2.00, per 1000 atoms: 0.22 Number of scatterers: 9217 At special positions: 0 Unit cell: (71.982, 114.669, 147.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1677 8.00 N 1541 7.00 C 5960 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 337.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 67.2% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.589A pdb=" N TYR A 41 " --> pdb=" O MET A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 82 removed outlier: 4.252A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 87 through 92 removed outlier: 4.381A pdb=" N MET A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 92' Processing helix chain 'A' and resid 99 through 152 removed outlier: 3.890A pdb=" N TYR A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.741A pdb=" N PHE A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 207 removed outlier: 4.176A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 256 removed outlier: 3.720A pdb=" N LEU A 212 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 3.877A pdb=" N GLY A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 265 through 319 removed outlier: 3.976A pdb=" N GLU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 344 removed outlier: 3.518A pdb=" N SER A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 365 removed outlier: 3.794A pdb=" N PHE A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 4.053A pdb=" N LYS A 401 " --> pdb=" O PRO A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 437 removed outlier: 4.118A pdb=" N GLN A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 528 through 543 removed outlier: 3.645A pdb=" N ARG A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 584 through 591 removed outlier: 3.993A pdb=" N VAL A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 701 removed outlier: 3.797A pdb=" N LYS A 698 " --> pdb=" O TRP A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 737 removed outlier: 3.932A pdb=" N GLN A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 3.981A pdb=" N PHE A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 743 through 795 Processing helix chain 'A' and resid 796 through 802 Processing helix chain 'A' and resid 806 through 816 Processing helix chain 'A' and resid 821 through 826 removed outlier: 3.579A pdb=" N THR A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 899 removed outlier: 4.084A pdb=" N ILE A 832 " --> pdb=" O ARG A 828 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 833 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLN A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU A 853 " --> pdb=" O TYR A 849 " (cutoff:3.500A) Proline residue: A 862 - end of helix removed outlier: 4.043A pdb=" N ILE A 892 " --> pdb=" O GLY A 888 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 906 Processing helix chain 'A' and resid 909 through 962 removed outlier: 3.716A pdb=" N GLU A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE A 922 " --> pdb=" O GLN A 918 " (cutoff:3.500A) Proline residue: A 923 - end of helix removed outlier: 3.523A pdb=" N MET A 928 " --> pdb=" O TYR A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 990 removed outlier: 3.874A pdb=" N PHE A 979 " --> pdb=" O SER A 975 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 980 " --> pdb=" O ALA A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1010 Processing helix chain 'A' and resid 1068 through 1072 removed outlier: 3.910A pdb=" N LYS A1072 " --> pdb=" O GLY A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1080 removed outlier: 4.142A pdb=" N GLU A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1107 Processing helix chain 'A' and resid 1122 through 1129 Processing helix chain 'A' and resid 1130 through 1132 No H-bonds generated for 'chain 'A' and resid 1130 through 1132' Processing helix chain 'A' and resid 1140 through 1149 Processing helix chain 'A' and resid 1150 through 1155 Processing helix chain 'A' and resid 1165 through 1169 Processing helix chain 'A' and resid 1173 through 1188 removed outlier: 4.000A pdb=" N ARG A1188 " --> pdb=" O ARG A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1203 Processing helix chain 'A' and resid 1206 through 1221 Processing helix chain 'A' and resid 1229 through 1236 removed outlier: 3.605A pdb=" N ILE A1233 " --> pdb=" O ARG A1229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AA3, first strand: chain 'A' and resid 466 through 468 removed outlier: 6.468A pdb=" N VAL A 419 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 3.717A pdb=" N PHE A1091 " --> pdb=" O GLN A1032 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1034 through 1038 removed outlier: 6.784A pdb=" N LEU A1052 " --> pdb=" O GLY A1035 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL A1037 " --> pdb=" O GLN A1050 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLN A1050 " --> pdb=" O VAL A1037 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 6.219A pdb=" N LEU A1193 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE A1226 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU A1195 " --> pdb=" O ILE A1226 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1662 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.24: 764 1.24 - 1.45: 3188 1.45 - 1.66: 5379 1.66 - 1.88: 71 1.88 - 2.09: 1 Bond restraints: 9403 Sorted by residual: bond pdb=" CBD Y01 A1407 " pdb=" CBG Y01 A1407 " ideal model delta sigma weight residual 1.520 1.023 0.497 2.00e-02 2.50e+03 6.18e+02 bond pdb=" C03 JJI A1401 " pdb=" N02 JJI A1401 " ideal model delta sigma weight residual 1.362 1.783 -0.421 2.00e-02 2.50e+03 4.42e+02 bond pdb=" C08 JJI A1401 " pdb=" N04 JJI A1401 " ideal model delta sigma weight residual 1.363 1.769 -0.406 2.00e-02 2.50e+03 4.13e+02 bond pdb=" C13 JJI A1401 " pdb=" N06 JJI A1401 " ideal model delta sigma weight residual 1.363 1.768 -0.405 2.00e-02 2.50e+03 4.11e+02 bond pdb=" CAS Y01 A1407 " pdb=" CAU Y01 A1407 " ideal model delta sigma weight residual 1.530 1.147 0.383 2.00e-02 2.50e+03 3.66e+02 ... (remaining 9398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 12586 3.61 - 7.22: 139 7.22 - 10.83: 12 10.83 - 14.44: 1 14.44 - 18.04: 7 Bond angle restraints: 12745 Sorted by residual: angle pdb=" C02 JJI A1401 " pdb=" S01 JJI A1401 " pdb=" C04 JJI A1401 " ideal model delta sigma weight residual 89.76 107.80 -18.04 3.00e+00 1.11e-01 3.62e+01 angle pdb=" C12 JJI A1401 " pdb=" S03 JJI A1401 " pdb=" C14 JJI A1401 " ideal model delta sigma weight residual 89.85 107.52 -17.67 3.00e+00 1.11e-01 3.47e+01 angle pdb=" C07 JIZ A1402 " pdb=" S02 JIZ A1402 " pdb=" C09 JIZ A1402 " ideal model delta sigma weight residual 89.67 107.31 -17.64 3.00e+00 1.11e-01 3.46e+01 angle pdb=" C07 JJI A1401 " pdb=" S02 JJI A1401 " pdb=" C09 JJI A1401 " ideal model delta sigma weight residual 89.54 107.09 -17.55 3.00e+00 1.11e-01 3.42e+01 angle pdb=" C12 JIZ A1402 " pdb=" S03 JIZ A1402 " pdb=" C14 JIZ A1402 " ideal model delta sigma weight residual 89.68 106.95 -17.27 3.00e+00 1.11e-01 3.31e+01 ... (remaining 12740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.96: 5577 28.96 - 57.92: 229 57.92 - 86.88: 25 86.88 - 115.84: 10 115.84 - 144.80: 5 Dihedral angle restraints: 5846 sinusoidal: 2535 harmonic: 3311 Sorted by residual: dihedral pdb=" CA MET A 99 " pdb=" C MET A 99 " pdb=" N PHE A 100 " pdb=" CA PHE A 100 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" N04 JJI A1401 " pdb=" C08 JJI A1401 " pdb=" C10 JJI A1401 " pdb=" N05 JJI A1401 " ideal model delta sinusoidal sigma weight residual 132.37 -12.43 144.80 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" N04 JJI A1401 " pdb=" C08 JJI A1401 " pdb=" C10 JJI A1401 " pdb=" O02 JJI A1401 " ideal model delta sinusoidal sigma weight residual 309.09 168.02 141.07 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 5843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.318: 1462 0.318 - 0.636: 2 0.636 - 0.954: 1 0.954 - 1.272: 0 1.272 - 1.590: 1 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CBD Y01 A1407 " pdb=" CAK Y01 A1407 " pdb=" CBF Y01 A1407 " pdb=" CBG Y01 A1407 " both_signs ideal model delta sigma weight residual False 2.70 1.11 1.59 2.00e-01 2.50e+01 6.32e+01 chirality pdb=" CBG Y01 A1407 " pdb=" CAQ Y01 A1407 " pdb=" CBD Y01 A1407 " pdb=" CBI Y01 A1407 " both_signs ideal model delta sigma weight residual False -2.33 -1.68 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CBI Y01 A1407 " pdb=" CAU Y01 A1407 " pdb=" CBE Y01 A1407 " pdb=" CBG Y01 A1407 " both_signs ideal model delta sigma weight residual False 2.94 2.52 0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 1463 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 822 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C LYS A 822 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS A 822 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY A 823 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 997 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C ALA A 997 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA A 997 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 998 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1240 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C VAL A1240 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL A1240 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A1241 " 0.014 2.00e-02 2.50e+03 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1582 2.77 - 3.30: 9748 3.30 - 3.83: 15092 3.83 - 4.37: 17092 4.37 - 4.90: 28586 Nonbonded interactions: 72100 Sorted by model distance: nonbonded pdb=" O ASN A 153 " pdb=" OD1 ASN A 153 " model vdw 2.233 3.040 nonbonded pdb=" O ARG A1164 " pdb=" OG1 THR A1170 " model vdw 2.249 3.040 nonbonded pdb=" O PRO A 381 " pdb=" OH TYR A 461 " model vdw 2.276 3.040 nonbonded pdb=" O TYR A 706 " pdb=" OG1 THR A 772 " model vdw 2.291 3.040 nonbonded pdb=" OG SER A1089 " pdb=" OE1 GLU A1096 " model vdw 2.300 3.040 ... (remaining 72095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.550 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.016 0.497 9404 Z= 0.830 Angle : 1.007 18.045 12745 Z= 0.546 Chirality : 0.071 1.590 1466 Planarity : 0.004 0.040 1596 Dihedral : 16.305 144.797 3724 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.32 % Allowed : 1.48 % Favored : 98.20 % 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 aren not related in a simple way. whole: 0.32 (0.26), residues: 1153 helix: 1.10 (0.20), residues: 759 sheet: -0.60 (0.79), residues: 39 loop : -1.60 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 485 TYR 0.016 0.001 TYR A 461 PHE 0.025 0.002 PHE A 766 TRP 0.027 0.001 TRP A 694 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.01576 ( 9403) covalent geometry : angle 1.00734 (12745) hydrogen bonds : bond 0.08503 ( 564) hydrogen bonds : angle 4.54337 ( 1662) Misc. bond : bond 0.17062 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.359 Fit side-chains REVERT: A 461 TYR cc_start: 0.7903 (t80) cc_final: 0.7606 (t80) REVERT: A 1026 MET cc_start: 0.7424 (pmm) cc_final: 0.7222 (pmm) outliers start: 3 outliers final: 1 residues processed: 162 average time/residue: 0.0951 time to fit residues: 22.0237 Evaluate side-chains 115 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 162 HIS A 276 ASN A1020 GLN A1099 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.215128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.172931 restraints weight = 14002.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.172568 restraints weight = 11869.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.175217 restraints weight = 9045.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.175365 restraints weight = 6007.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.175536 restraints weight = 5603.377| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9404 Z= 0.140 Angle : 0.654 8.939 12745 Z= 0.319 Chirality : 0.042 0.248 1466 Planarity : 0.004 0.060 1596 Dihedral : 12.086 125.777 1645 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.37 % Allowed : 10.56 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.25), residues: 1153 helix: 1.32 (0.20), residues: 751 sheet: -0.29 (0.82), residues: 39 loop : -1.62 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.017 0.001 TYR A 243 PHE 0.020 0.001 PHE A 516 TRP 0.020 0.002 TRP A1104 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9403) covalent geometry : angle 0.65372 (12745) hydrogen bonds : bond 0.04562 ( 564) hydrogen bonds : angle 4.12082 ( 1662) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.328 Fit side-chains REVERT: A 41 TYR cc_start: 0.6898 (m-80) cc_final: 0.6674 (m-80) REVERT: A 1062 LEU cc_start: 0.8416 (tp) cc_final: 0.8075 (mt) outliers start: 13 outliers final: 10 residues processed: 132 average time/residue: 0.0848 time to fit residues: 16.4716 Evaluate side-chains 119 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 704 TRP Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1257 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 114 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 749 ASN A1020 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.191203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.148682 restraints weight = 12889.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.147195 restraints weight = 19565.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.149336 restraints weight = 15178.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.151261 restraints weight = 9423.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.151660 restraints weight = 8581.803| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9404 Z= 0.269 Angle : 0.751 9.952 12745 Z= 0.369 Chirality : 0.045 0.198 1466 Planarity : 0.004 0.067 1596 Dihedral : 10.696 114.800 1644 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.43 % Allowed : 13.94 % Favored : 83.63 % 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 aren not related in a simple way. whole: 0.25 (0.25), residues: 1153 helix: 1.01 (0.19), residues: 750 sheet: -0.29 (0.85), residues: 39 loop : -1.52 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 485 TYR 0.021 0.002 TYR A 41 PHE 0.027 0.002 PHE A 339 TRP 0.019 0.002 TRP A1104 HIS 0.008 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00640 ( 9403) covalent geometry : angle 0.75125 (12745) hydrogen bonds : bond 0.05453 ( 564) hydrogen bonds : angle 4.45089 ( 1662) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.333 Fit side-chains outliers start: 23 outliers final: 17 residues processed: 140 average time/residue: 0.0812 time to fit residues: 16.8101 Evaluate side-chains 130 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 704 TRP Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1257 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 41 optimal weight: 0.0980 chunk 75 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 99 optimal weight: 0.0770 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.198003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.156258 restraints weight = 12789.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.152620 restraints weight = 17667.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.155222 restraints weight = 14536.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.156433 restraints weight = 8908.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.157010 restraints weight = 8608.332| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9404 Z= 0.128 Angle : 0.628 11.046 12745 Z= 0.301 Chirality : 0.041 0.330 1466 Planarity : 0.004 0.062 1596 Dihedral : 9.738 101.328 1644 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.53 % Allowed : 16.26 % Favored : 81.20 % 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 aren not related in a simple way. whole: 0.62 (0.25), residues: 1153 helix: 1.32 (0.19), residues: 748 sheet: -0.03 (0.87), residues: 39 loop : -1.45 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1229 TYR 0.019 0.001 TYR A 243 PHE 0.013 0.001 PHE A 200 TRP 0.017 0.001 TRP A1104 HIS 0.005 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9403) covalent geometry : angle 0.62803 (12745) hydrogen bonds : bond 0.04569 ( 564) hydrogen bonds : angle 4.10026 ( 1662) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.344 Fit side-chains REVERT: A 64 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8159 (tt) outliers start: 24 outliers final: 16 residues processed: 134 average time/residue: 0.0814 time to fit residues: 16.1204 Evaluate side-chains 130 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 704 TRP Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1165 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 68 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 89 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN A1126 ASN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.191255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.149070 restraints weight = 12972.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147449 restraints weight = 18430.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.149464 restraints weight = 14776.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.150958 restraints weight = 9501.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.151339 restraints weight = 9097.566| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9404 Z= 0.230 Angle : 0.698 11.828 12745 Z= 0.343 Chirality : 0.044 0.384 1466 Planarity : 0.004 0.063 1596 Dihedral : 9.748 96.522 1644 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.38 % Allowed : 17.00 % Favored : 79.62 % 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 aren not related in a simple way. whole: 0.40 (0.25), residues: 1153 helix: 1.09 (0.19), residues: 750 sheet: -0.15 (0.87), residues: 39 loop : -1.41 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1229 TYR 0.024 0.002 TYR A 41 PHE 0.021 0.002 PHE A 953 TRP 0.010 0.001 TRP A1104 HIS 0.007 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 9403) covalent geometry : angle 0.69775 (12745) hydrogen bonds : bond 0.05203 ( 564) hydrogen bonds : angle 4.34749 ( 1662) Misc. bond : bond 0.00084 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7958 (tt) REVERT: A 312 TYR cc_start: 0.8263 (t80) cc_final: 0.7875 (t80) REVERT: A 693 PHE cc_start: 0.6247 (OUTLIER) cc_final: 0.5165 (m-80) outliers start: 32 outliers final: 26 residues processed: 145 average time/residue: 0.0813 time to fit residues: 17.7258 Evaluate side-chains 147 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 704 TRP Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1165 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 59 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.196693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.156642 restraints weight = 12759.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.154201 restraints weight = 17924.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.156284 restraints weight = 15923.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.156582 restraints weight = 10461.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.157147 restraints weight = 10312.102| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9404 Z= 0.132 Angle : 0.628 12.886 12745 Z= 0.304 Chirality : 0.041 0.345 1466 Planarity : 0.004 0.060 1596 Dihedral : 9.288 92.266 1644 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.06 % Allowed : 18.69 % Favored : 78.25 % 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 aren not related in a simple way. whole: 0.70 (0.26), residues: 1153 helix: 1.37 (0.20), residues: 748 sheet: 0.10 (0.86), residues: 40 loop : -1.39 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1229 TYR 0.018 0.001 TYR A 243 PHE 0.023 0.001 PHE A 395 TRP 0.013 0.001 TRP A 158 HIS 0.007 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9403) covalent geometry : angle 0.62834 (12745) hydrogen bonds : bond 0.04531 ( 564) hydrogen bonds : angle 4.09815 ( 1662) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 693 PHE cc_start: 0.6086 (OUTLIER) cc_final: 0.5011 (m-80) REVERT: A 766 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7842 (t80) REVERT: A 1086 MET cc_start: 0.5459 (pmm) cc_final: 0.5029 (pmm) outliers start: 29 outliers final: 22 residues processed: 143 average time/residue: 0.0826 time to fit residues: 17.6260 Evaluate side-chains 144 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 704 TRP Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 787 MET Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1165 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 94 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.192041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.151431 restraints weight = 12863.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.149388 restraints weight = 20531.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.150687 restraints weight = 19173.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.152666 restraints weight = 12600.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.152769 restraints weight = 10611.285| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9404 Z= 0.207 Angle : 0.690 13.127 12745 Z= 0.336 Chirality : 0.043 0.371 1466 Planarity : 0.004 0.058 1596 Dihedral : 9.689 92.924 1644 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.70 % Allowed : 18.48 % Favored : 77.82 % 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 aren not related in a simple way. whole: 0.53 (0.25), residues: 1153 helix: 1.20 (0.19), residues: 751 sheet: -0.01 (0.87), residues: 40 loop : -1.37 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1229 TYR 0.017 0.001 TYR A 243 PHE 0.038 0.002 PHE A 395 TRP 0.009 0.001 TRP A 158 HIS 0.005 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 9403) covalent geometry : angle 0.68999 (12745) hydrogen bonds : bond 0.04993 ( 564) hydrogen bonds : angle 4.30240 ( 1662) Misc. bond : bond 0.00078 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 312 TYR cc_start: 0.8153 (t80) cc_final: 0.7915 (t80) REVERT: A 693 PHE cc_start: 0.6178 (OUTLIER) cc_final: 0.5101 (m-80) REVERT: A 1086 MET cc_start: 0.5621 (pmm) cc_final: 0.5245 (pmm) outliers start: 35 outliers final: 26 residues processed: 150 average time/residue: 0.0803 time to fit residues: 18.1966 Evaluate side-chains 146 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 704 TRP Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1165 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 95 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 749 ASN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.195684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.155177 restraints weight = 12667.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.153125 restraints weight = 19210.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.154830 restraints weight = 16449.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.155790 restraints weight = 11126.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.156301 restraints weight = 10585.768| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9404 Z= 0.137 Angle : 0.646 15.413 12745 Z= 0.310 Chirality : 0.042 0.440 1466 Planarity : 0.004 0.057 1596 Dihedral : 9.363 89.624 1644 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.59 % Allowed : 19.11 % Favored : 77.30 % 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 aren not related in a simple way. whole: 0.74 (0.26), residues: 1153 helix: 1.40 (0.20), residues: 750 sheet: 0.01 (0.86), residues: 40 loop : -1.38 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1229 TYR 0.017 0.001 TYR A 243 PHE 0.042 0.002 PHE A 339 TRP 0.012 0.001 TRP A 158 HIS 0.008 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9403) covalent geometry : angle 0.64612 (12745) hydrogen bonds : bond 0.04557 ( 564) hydrogen bonds : angle 4.13137 ( 1662) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 312 TYR cc_start: 0.7986 (t80) cc_final: 0.7727 (t80) REVERT: A 693 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.5033 (m-80) REVERT: A 766 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7835 (t80) REVERT: A 895 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8532 (tm-30) REVERT: A 1086 MET cc_start: 0.5496 (pmm) cc_final: 0.5131 (pmm) outliers start: 34 outliers final: 23 residues processed: 144 average time/residue: 0.0802 time to fit residues: 17.3786 Evaluate side-chains 140 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 704 TRP Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 787 MET Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1165 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 78 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 19 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.195228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.154942 restraints weight = 12640.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.152426 restraints weight = 19329.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.154180 restraints weight = 16741.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.155620 restraints weight = 11058.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.155963 restraints weight = 10255.789| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9404 Z= 0.146 Angle : 0.649 14.456 12745 Z= 0.314 Chirality : 0.043 0.423 1466 Planarity : 0.004 0.055 1596 Dihedral : 9.448 88.804 1644 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.96 % Allowed : 19.75 % Favored : 77.30 % 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 aren not related in a simple way. whole: 0.73 (0.26), residues: 1153 helix: 1.38 (0.20), residues: 751 sheet: 0.00 (0.86), residues: 40 loop : -1.38 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 485 TYR 0.017 0.001 TYR A 243 PHE 0.045 0.002 PHE A 339 TRP 0.012 0.001 TRP A 158 HIS 0.007 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9403) covalent geometry : angle 0.64879 (12745) hydrogen bonds : bond 0.04589 ( 564) hydrogen bonds : angle 4.14101 ( 1662) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.370 Fit side-chains REVERT: A 312 TYR cc_start: 0.8027 (t80) cc_final: 0.7780 (t80) REVERT: A 693 PHE cc_start: 0.6107 (OUTLIER) cc_final: 0.5047 (m-80) REVERT: A 766 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7752 (t80) REVERT: A 1086 MET cc_start: 0.5460 (pmm) cc_final: 0.5100 (pmm) outliers start: 28 outliers final: 25 residues processed: 141 average time/residue: 0.0841 time to fit residues: 17.8154 Evaluate side-chains 144 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 704 TRP Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 787 MET Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 5 optimal weight: 0.0970 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.190578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.147838 restraints weight = 12893.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.146020 restraints weight = 18813.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.147274 restraints weight = 17614.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.150553 restraints weight = 10987.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.150467 restraints weight = 7808.579| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9404 Z= 0.226 Angle : 0.731 13.861 12745 Z= 0.356 Chirality : 0.045 0.425 1466 Planarity : 0.004 0.058 1596 Dihedral : 9.645 88.918 1644 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.17 % Allowed : 19.75 % Favored : 77.09 % 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 aren not related in a simple way. whole: 0.50 (0.25), residues: 1153 helix: 1.16 (0.19), residues: 752 sheet: -0.05 (0.86), residues: 40 loop : -1.37 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 543 TYR 0.020 0.002 TYR A 41 PHE 0.042 0.002 PHE A 339 TRP 0.007 0.001 TRP A 158 HIS 0.006 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 9403) covalent geometry : angle 0.73130 (12745) hydrogen bonds : bond 0.05114 ( 564) hydrogen bonds : angle 4.36871 ( 1662) Misc. bond : bond 0.00085 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 312 TYR cc_start: 0.8133 (t80) cc_final: 0.7914 (t80) REVERT: A 693 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5092 (m-80) REVERT: A 1086 MET cc_start: 0.5587 (pmm) cc_final: 0.5255 (pmm) outliers start: 30 outliers final: 27 residues processed: 143 average time/residue: 0.0833 time to fit residues: 17.7394 Evaluate side-chains 148 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 488 ARG Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 704 TRP Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 1008 ILE Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 52 optimal weight: 0.0370 chunk 103 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.196848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.156286 restraints weight = 12490.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.154423 restraints weight = 17170.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.156121 restraints weight = 16971.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.157896 restraints weight = 10820.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.158237 restraints weight = 9394.127| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9404 Z= 0.130 Angle : 0.675 15.096 12745 Z= 0.321 Chirality : 0.042 0.426 1466 Planarity : 0.004 0.055 1596 Dihedral : 9.246 85.005 1644 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.64 % Allowed : 20.91 % Favored : 76.45 % 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 aren not related in a simple way. whole: 0.74 (0.26), residues: 1153 helix: 1.40 (0.20), residues: 750 sheet: 0.15 (0.87), residues: 40 loop : -1.42 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 485 TYR 0.017 0.001 TYR A 243 PHE 0.039 0.002 PHE A 339 TRP 0.013 0.001 TRP A 158 HIS 0.006 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9403) covalent geometry : angle 0.67520 (12745) hydrogen bonds : bond 0.04475 ( 564) hydrogen bonds : angle 4.14727 ( 1662) Misc. bond : bond 0.00015 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1463.52 seconds wall clock time: 26 minutes 4.81 seconds (1564.81 seconds total)