Starting phenix.real_space_refine on Mon May 12 19:11:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pee_17630/05_2025/8pee_17630.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pee_17630/05_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_17630/05_2025/8pee_17630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pee_17630/05_2025/8pee_17630.map" model { file = "/net/cci-nas-00/data/ceres_data/8pee_17630/05_2025/8pee_17630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pee_17630/05_2025/8pee_17630.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.93, per 1000 atoms: 0.64 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: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.99 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: 2.93 Time building geometry restraints manager: 2.86 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: 1.270 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.990 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (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 TRP 0.027 0.001 TRP A 694 HIS 0.004 0.001 HIS A 60 PHE 0.025 0.002 PHE A 766 TYR 0.016 0.001 TYR A 461 ARG 0.005 0.001 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.08503 ( 564) hydrogen bonds : angle 4.54337 ( 1662) covalent geometry : bond 0.01576 ( 9403) covalent geometry : angle 1.00734 (12745) 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 : 0.938 Fit side-chains REVERT: A 461 TYR cc_start: 0.7903 (t80) cc_final: 0.7612 (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: 0.2012 time to fit residues: 46.1659 Evaluate side-chains 117 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 30.0000 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 A1020 GLN A1099 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 = 0.4331 r_free = 0.4331 target = 0.195794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.155147 restraints weight = 12701.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.152158 restraints weight = 19337.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.154330 restraints weight = 17386.219| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9404 Z= 0.198 Angle : 0.697 8.601 12745 Z= 0.343 Chirality : 0.043 0.244 1466 Planarity : 0.004 0.065 1596 Dihedral : 12.070 125.529 1645 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.69 % Allowed : 10.77 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1153 helix: 1.18 (0.19), residues: 751 sheet: -0.32 (0.83), residues: 39 loop : -1.63 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1104 HIS 0.004 0.001 HIS A 60 PHE 0.020 0.002 PHE A 516 TYR 0.018 0.002 TYR A 243 ARG 0.004 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.04986 ( 564) hydrogen bonds : angle 4.27605 ( 1662) covalent geometry : bond 0.00461 ( 9403) covalent geometry : angle 0.69720 (12745) Misc. bond : bond 0.00027 ( 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 138 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.046 Fit side-chains REVERT: A 41 TYR cc_start: 0.7128 (m-80) cc_final: 0.6892 (m-80) REVERT: A 1062 LEU cc_start: 0.8428 (tp) cc_final: 0.8056 (mt) outliers start: 16 outliers final: 10 residues processed: 132 average time/residue: 0.1951 time to fit residues: 37.7620 Evaluate side-chains 120 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 188 MET Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 462 LEU 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 83 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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** A 276 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 = 0.4339 r_free = 0.4339 target = 0.196655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.156870 restraints weight = 12908.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.153949 restraints weight = 19490.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.156182 restraints weight = 18007.302| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1570 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= 0.154 Angle : 0.651 11.131 12745 Z= 0.312 Chirality : 0.041 0.221 1466 Planarity : 0.004 0.064 1596 Dihedral : 10.511 114.350 1645 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.11 % Allowed : 13.94 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1153 helix: 1.32 (0.19), residues: 748 sheet: -0.20 (0.84), residues: 39 loop : -1.53 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1104 HIS 0.004 0.001 HIS A 60 PHE 0.020 0.001 PHE A 339 TYR 0.017 0.001 TYR A 243 ARG 0.011 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.04689 ( 564) hydrogen bonds : angle 4.13305 ( 1662) covalent geometry : bond 0.00349 ( 9403) covalent geometry : angle 0.65092 (12745) Misc. bond : bond 0.00003 ( 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 136 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.013 Fit side-chains REVERT: A 41 TYR cc_start: 0.7038 (m-80) cc_final: 0.6784 (m-80) outliers start: 20 outliers final: 14 residues processed: 125 average time/residue: 0.1861 time to fit residues: 34.9790 Evaluate side-chains 120 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 301 LEU 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 871 GLU 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 1111 ILE Chi-restraints excluded: chain A residue 1165 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 overall best weight: 2.7584 ------------------------------------------------------------------------------- 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** 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 = 0.4272 r_free = 0.4272 target = 0.189882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.148623 restraints weight = 12758.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147735 restraints weight = 22182.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.149222 restraints weight = 19982.584| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 9404 Z= 0.272 Angle : 0.745 10.577 12745 Z= 0.366 Chirality : 0.045 0.322 1466 Planarity : 0.004 0.068 1596 Dihedral : 10.116 103.388 1644 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.48 % Allowed : 15.10 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1153 helix: 0.98 (0.19), residues: 749 sheet: -0.14 (0.88), residues: 39 loop : -1.45 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 132 HIS 0.008 0.001 HIS A 60 PHE 0.028 0.002 PHE A 339 TYR 0.019 0.002 TYR A 41 ARG 0.006 0.001 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.05505 ( 564) hydrogen bonds : angle 4.48932 ( 1662) covalent geometry : bond 0.00650 ( 9403) covalent geometry : angle 0.74461 (12745) Misc. bond : bond 0.00109 ( 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 155 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 1.005 Fit side-chains REVERT: A 41 TYR cc_start: 0.7335 (m-80) cc_final: 0.7117 (m-80) outliers start: 33 outliers final: 25 residues processed: 144 average time/residue: 0.1876 time to fit residues: 39.5187 Evaluate side-chains 138 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 117 ILE Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 276 ASN 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 734 VAL Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 844 ILE 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 1111 ILE Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1257 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 67 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 37 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 749 ASN ** 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 = 0.4327 r_free = 0.4327 target = 0.195464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.155076 restraints weight = 12751.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.151563 restraints weight = 20225.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.153349 restraints weight = 17280.065| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2165 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= 0.133 Angle : 0.624 11.003 12745 Z= 0.302 Chirality : 0.041 0.325 1466 Planarity : 0.004 0.063 1596 Dihedral : 9.639 95.956 1644 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.17 % Allowed : 18.37 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1153 helix: 1.31 (0.19), residues: 748 sheet: -0.05 (0.87), residues: 39 loop : -1.47 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 158 HIS 0.005 0.001 HIS A 162 PHE 0.021 0.001 PHE A 395 TYR 0.019 0.001 TYR A 243 ARG 0.005 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 564) hydrogen bonds : angle 4.13427 ( 1662) covalent geometry : bond 0.00289 ( 9403) covalent geometry : angle 0.62399 (12745) Misc. bond : bond 0.00020 ( 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 155 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7052 (m-80) cc_final: 0.6809 (m-80) REVERT: A 182 ILE cc_start: 0.8370 (pt) cc_final: 0.7937 (pt) REVERT: A 766 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7807 (t80) REVERT: A 1086 MET cc_start: 0.5182 (pmm) cc_final: 0.4707 (pmm) outliers start: 30 outliers final: 18 residues processed: 144 average time/residue: 0.1854 time to fit residues: 39.3401 Evaluate side-chains 131 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 130 SER 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 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 704 TRP 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 936 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 19 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4308 r_free = 0.4308 target = 0.193473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.152677 restraints weight = 12646.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.149716 restraints weight = 20209.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.151827 restraints weight = 17888.701| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9404 Z= 0.175 Angle : 0.657 13.132 12745 Z= 0.320 Chirality : 0.042 0.352 1466 Planarity : 0.004 0.061 1596 Dihedral : 9.561 95.157 1644 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.01 % Allowed : 18.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1153 helix: 1.31 (0.19), residues: 748 sheet: -0.12 (0.88), residues: 39 loop : -1.43 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 158 HIS 0.004 0.001 HIS A 60 PHE 0.033 0.002 PHE A 395 TYR 0.017 0.001 TYR A 243 ARG 0.004 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.04823 ( 564) hydrogen bonds : angle 4.20937 ( 1662) covalent geometry : bond 0.00407 ( 9403) covalent geometry : angle 0.65742 (12745) Misc. bond : bond 0.00041 ( 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 159 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7150 (m-80) cc_final: 0.6882 (m-80) REVERT: A 766 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7728 (t80) REVERT: A 1086 MET cc_start: 0.5346 (pmm) cc_final: 0.4940 (pmm) REVERT: A 1118 LEU cc_start: 0.6111 (OUTLIER) cc_final: 0.5819 (mt) REVERT: A 1141 ILE cc_start: 0.8996 (mp) cc_final: 0.8783 (mt) outliers start: 38 outliers final: 25 residues processed: 149 average time/residue: 0.1784 time to fit residues: 39.2411 Evaluate side-chains 140 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 130 SER 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 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 704 TRP Chi-restraints excluded: chain A residue 734 VAL 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 1118 LEU 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 83 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 105 optimal weight: 0.0980 chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS ** 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 = 0.4347 r_free = 0.4347 target = 0.197775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.157316 restraints weight = 12774.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.155541 restraints weight = 17542.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.157152 restraints weight = 15683.549| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2443 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= 0.125 Angle : 0.628 14.427 12745 Z= 0.303 Chirality : 0.041 0.333 1466 Planarity : 0.004 0.058 1596 Dihedral : 9.249 91.236 1644 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.80 % Allowed : 19.01 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1153 helix: 1.46 (0.20), residues: 748 sheet: 0.11 (0.87), residues: 40 loop : -1.41 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1104 HIS 0.009 0.001 HIS A 162 PHE 0.023 0.001 PHE A 395 TYR 0.020 0.001 TYR A 461 ARG 0.005 0.000 ARG A1229 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 564) hydrogen bonds : angle 4.08606 ( 1662) covalent geometry : bond 0.00269 ( 9403) covalent geometry : angle 0.62775 (12745) Misc. bond : bond 0.00013 ( 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 161 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6884 (m-80) cc_final: 0.6616 (m-80) REVERT: A 182 ILE cc_start: 0.8372 (pt) cc_final: 0.7928 (pt) REVERT: A 693 PHE cc_start: 0.6113 (OUTLIER) cc_final: 0.5063 (m-80) REVERT: A 766 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7867 (t80) REVERT: A 1086 MET cc_start: 0.5317 (pmm) cc_final: 0.4900 (pmm) REVERT: A 1118 LEU cc_start: 0.6086 (tp) cc_final: 0.5796 (mt) REVERT: A 1141 ILE cc_start: 0.8930 (mp) cc_final: 0.8701 (mt) outliers start: 36 outliers final: 24 residues processed: 151 average time/residue: 0.1772 time to fit residues: 39.6538 Evaluate side-chains 147 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 117 ILE Chi-restraints excluded: chain A residue 130 SER 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 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 734 VAL 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 825 THR Chi-restraints excluded: chain A residue 833 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 0.0040 chunk 21 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.194899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.155024 restraints weight = 12891.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.153509 restraints weight = 20461.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.155117 restraints weight = 18452.325| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9404 Z= 0.162 Angle : 0.646 14.512 12745 Z= 0.314 Chirality : 0.042 0.344 1466 Planarity : 0.004 0.057 1596 Dihedral : 9.433 90.754 1644 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.48 % Allowed : 19.85 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1153 helix: 1.40 (0.20), residues: 749 sheet: 0.07 (0.87), residues: 40 loop : -1.38 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1104 HIS 0.007 0.001 HIS A 162 PHE 0.038 0.002 PHE A 339 TYR 0.016 0.001 TYR A 243 ARG 0.005 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 564) hydrogen bonds : angle 4.16327 ( 1662) covalent geometry : bond 0.00377 ( 9403) covalent geometry : angle 0.64579 (12745) Misc. bond : bond 0.00032 ( 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 154 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.6948 (mtt) cc_final: 0.6196 (mtt) REVERT: A 41 TYR cc_start: 0.6983 (m-80) cc_final: 0.6719 (m-80) REVERT: A 693 PHE cc_start: 0.6153 (OUTLIER) cc_final: 0.5127 (m-80) REVERT: A 766 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7735 (t80) REVERT: A 1086 MET cc_start: 0.5330 (pmm) cc_final: 0.4937 (pmm) REVERT: A 1118 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5795 (mt) REVERT: A 1141 ILE cc_start: 0.8900 (mp) cc_final: 0.8684 (mt) outliers start: 33 outliers final: 25 residues processed: 145 average time/residue: 0.1788 time to fit residues: 38.5355 Evaluate side-chains 142 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 117 ILE Chi-restraints excluded: chain A residue 130 SER 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 734 VAL 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 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 1118 LEU 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 9 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 2 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 30.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS ** 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 = 0.4335 r_free = 0.4335 target = 0.196242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.153969 restraints weight = 12763.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.150639 restraints weight = 17706.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.153524 restraints weight = 14628.382| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9404 Z= 0.137 Angle : 0.645 15.385 12745 Z= 0.310 Chirality : 0.042 0.368 1466 Planarity : 0.004 0.056 1596 Dihedral : 9.296 88.444 1644 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.70 % Allowed : 19.96 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1153 helix: 1.45 (0.20), residues: 751 sheet: 0.08 (0.87), residues: 40 loop : -1.40 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1104 HIS 0.007 0.001 HIS A 162 PHE 0.043 0.002 PHE A 339 TYR 0.016 0.001 TYR A 243 ARG 0.005 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 564) hydrogen bonds : angle 4.09971 ( 1662) covalent geometry : bond 0.00310 ( 9403) covalent geometry : angle 0.64483 (12745) Misc. bond : bond 0.00012 ( 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 157 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6889 (m-80) cc_final: 0.6613 (m-80) REVERT: A 182 ILE cc_start: 0.8431 (pt) cc_final: 0.8007 (pt) REVERT: A 693 PHE cc_start: 0.6169 (OUTLIER) cc_final: 0.5153 (m-80) REVERT: A 766 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7885 (t80) REVERT: A 1086 MET cc_start: 0.5407 (pmm) cc_final: 0.5015 (pmm) REVERT: A 1141 ILE cc_start: 0.8900 (mp) cc_final: 0.8690 (mt) outliers start: 35 outliers final: 26 residues processed: 144 average time/residue: 0.1774 time to fit residues: 37.7631 Evaluate side-chains 145 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 117 ILE Chi-restraints excluded: chain A residue 130 SER 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 734 VAL 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 904 VAL Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 940 PHE 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 11 optimal weight: 0.8980 chunk 46 optimal weight: 20.0000 chunk 81 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 97 optimal weight: 0.0060 chunk 96 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS ** 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 = 0.4313 r_free = 0.4313 target = 0.194132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.154069 restraints weight = 12787.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.151063 restraints weight = 21083.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.152863 restraints weight = 17644.166| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9404 Z= 0.173 Angle : 0.672 15.500 12745 Z= 0.325 Chirality : 0.043 0.369 1466 Planarity : 0.004 0.056 1596 Dihedral : 9.355 88.246 1644 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.38 % Allowed : 19.96 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.26), residues: 1153 helix: 1.34 (0.19), residues: 750 sheet: 0.02 (0.87), residues: 40 loop : -1.35 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1104 HIS 0.005 0.001 HIS A 60 PHE 0.042 0.002 PHE A 339 TYR 0.016 0.001 TYR A 243 ARG 0.005 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 564) hydrogen bonds : angle 4.20394 ( 1662) covalent geometry : bond 0.00405 ( 9403) covalent geometry : angle 0.67247 (12745) Misc. bond : bond 0.00043 ( 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 153 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.022 Fit side-chains REVERT: A 41 TYR cc_start: 0.6985 (m-80) cc_final: 0.6716 (m-80) REVERT: A 693 PHE cc_start: 0.6176 (OUTLIER) cc_final: 0.5155 (m-80) REVERT: A 766 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7763 (t80) REVERT: A 1086 MET cc_start: 0.5508 (pmm) cc_final: 0.5128 (pmm) REVERT: A 1141 ILE cc_start: 0.8914 (mp) cc_final: 0.8705 (mt) outliers start: 32 outliers final: 25 residues processed: 144 average time/residue: 0.1769 time to fit residues: 37.5985 Evaluate side-chains 142 residues out of total 947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 117 ILE Chi-restraints excluded: chain A residue 130 SER 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 734 VAL 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 936 ILE Chi-restraints excluded: chain A residue 940 PHE 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 1 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 30.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS ** 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 = 0.4327 r_free = 0.4327 target = 0.195642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.155191 restraints weight = 12575.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151809 restraints weight = 20031.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.153673 restraints weight = 17589.689| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9404 Z= 0.156 Angle : 0.674 15.711 12745 Z= 0.324 Chirality : 0.042 0.384 1466 Planarity : 0.004 0.056 1596 Dihedral : 9.285 86.642 1644 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.17 % Allowed : 20.59 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1153 helix: 1.36 (0.20), residues: 750 sheet: 0.06 (0.86), residues: 40 loop : -1.37 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1104 HIS 0.003 0.001 HIS A 60 PHE 0.047 0.002 PHE A 339 TYR 0.020 0.001 TYR A 461 ARG 0.008 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 564) hydrogen bonds : angle 4.16286 ( 1662) covalent geometry : bond 0.00362 ( 9403) covalent geometry : angle 0.67405 (12745) Misc. bond : bond 0.00033 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2607.25 seconds wall clock time: 46 minutes 42.31 seconds (2802.31 seconds total)