Starting phenix.real_space_refine on Fri Jul 19 23:46:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pee_17630/07_2024/8pee_17630.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pee_17630/07_2024/8pee_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pee_17630/07_2024/8pee_17630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pee_17630/07_2024/8pee_17630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pee_17630/07_2024/8pee_17630.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pee_17630/07_2024/8pee_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 Residue "A GLU 239": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A GLU 1096": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.70, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 3.90 Conformation dependent library (CDL) restraints added in 1.7 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: 0.93 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: 3.04 Time building geometry restraints manager: 4.25 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: 98.43 - 105.54: 162 105.54 - 112.65: 4970 112.65 - 119.75: 3256 119.75 - 126.86: 4265 126.86 - 133.97: 92 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 2.440 nonbonded pdb=" O PRO A 381 " pdb=" OH TYR A 461 " model vdw 2.276 2.440 nonbonded pdb=" O TYR A 706 " pdb=" OG1 THR A 772 " model vdw 2.291 2.440 nonbonded pdb=" OG SER A1089 " pdb=" OE1 GLU A1096 " model vdw 2.300 2.440 ... (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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.400 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: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.090 ------------------------------------------------------------------------------- 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 9403 Z= 1.133 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 1.020 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: 0.2026 time to fit residues: 46.2673 Evaluate side-chains 117 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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: 0.7980 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 90 optimal weight: 0.0970 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 30.0000 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9403 Z= 0.258 Angle : 0.667 8.815 12745 Z= 0.325 Chirality : 0.042 0.251 1466 Planarity : 0.004 0.063 1596 Dihedral : 12.047 120.901 1645 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.69 % Allowed : 10.35 % Favored : 87.96 % 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: 0.50 (0.25), residues: 1153 helix: 1.28 (0.19), residues: 754 sheet: -0.34 (0.82), residues: 39 loop : -1.65 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1104 HIS 0.004 0.001 HIS A 60 PHE 0.018 0.002 PHE A 516 TYR 0.017 0.001 TYR A 243 ARG 0.004 0.000 ARG A 170 *********************** 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 fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.010 Fit side-chains REVERT: A 41 TYR cc_start: 0.7076 (m-80) cc_final: 0.6837 (m-80) REVERT: A 1062 LEU cc_start: 0.8615 (tp) cc_final: 0.8158 (mt) outliers start: 16 outliers final: 9 residues processed: 130 average time/residue: 0.1802 time to fit residues: 34.7199 Evaluate side-chains 117 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL 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 301 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 113 optimal weight: 0.1980 chunk 93 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9403 Z= 0.181 Angle : 0.630 12.765 12745 Z= 0.299 Chirality : 0.040 0.225 1466 Planarity : 0.004 0.060 1596 Dihedral : 10.222 103.092 1644 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.22 % Allowed : 12.46 % Favored : 85.32 % 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: 0.68 (0.26), residues: 1153 helix: 1.43 (0.20), residues: 752 sheet: -0.16 (0.84), residues: 39 loop : -1.59 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1104 HIS 0.004 0.001 HIS A 162 PHE 0.019 0.001 PHE A 339 TYR 0.016 0.001 TYR A 243 ARG 0.003 0.000 ARG A1229 *********************** 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 142 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.008 Fit side-chains REVERT: A 41 TYR cc_start: 0.6959 (m-80) cc_final: 0.6668 (m-80) REVERT: A 1062 LEU cc_start: 0.8638 (tp) cc_final: 0.8155 (mt) REVERT: A 1086 MET cc_start: 0.5386 (ptp) cc_final: 0.5171 (ptp) outliers start: 21 outliers final: 15 residues processed: 131 average time/residue: 0.1748 time to fit residues: 34.9945 Evaluate side-chains 126 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 188 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 409 LEU 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 940 PHE 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 103 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 29 optimal weight: 0.0980 chunk 92 optimal weight: 9.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 9403 Z= 0.441 Angle : 0.756 10.655 12745 Z= 0.374 Chirality : 0.045 0.227 1466 Planarity : 0.004 0.066 1596 Dihedral : 10.046 94.359 1644 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.38 % Allowed : 14.78 % Favored : 81.84 % 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: 0.23 (0.25), residues: 1153 helix: 1.00 (0.19), residues: 750 sheet: -0.13 (0.87), residues: 39 loop : -1.57 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 132 HIS 0.009 0.002 HIS A 60 PHE 0.018 0.002 PHE A 900 TYR 0.019 0.002 TYR A 41 ARG 0.004 0.000 ARG A 355 *********************** 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 156 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 1.011 Fit side-chains REVERT: A 41 TYR cc_start: 0.7355 (m-80) cc_final: 0.7089 (m-80) REVERT: A 395 PHE cc_start: 0.7777 (t80) cc_final: 0.7507 (t80) outliers start: 32 outliers final: 23 residues processed: 143 average time/residue: 0.1783 time to fit residues: 37.6816 Evaluate side-chains 143 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 169 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 195 THR 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 409 LEU 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 1008 ILE Chi-restraints excluded: chain A residue 1016 SER 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 63 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 99 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN A 749 ASN A1020 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9403 Z= 0.189 Angle : 0.620 11.564 12745 Z= 0.299 Chirality : 0.042 0.349 1466 Planarity : 0.004 0.061 1596 Dihedral : 9.652 92.075 1644 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.27 % Allowed : 17.21 % Favored : 79.51 % 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: 0.63 (0.25), residues: 1153 helix: 1.33 (0.19), residues: 750 sheet: 0.01 (0.87), residues: 39 loop : -1.47 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 158 HIS 0.006 0.001 HIS A 162 PHE 0.013 0.001 PHE A 196 TYR 0.018 0.001 TYR A 243 ARG 0.003 0.000 ARG A1229 *********************** 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 fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7066 (m-80) cc_final: 0.6779 (m-80) REVERT: A 182 ILE cc_start: 0.8373 (pt) cc_final: 0.7937 (pt) REVERT: A 766 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7839 (t80) outliers start: 31 outliers final: 23 residues processed: 146 average time/residue: 0.1949 time to fit residues: 41.8410 Evaluate side-chains 142 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 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 409 LEU 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 766 PHE 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 940 PHE Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1167 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 111 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 0.0070 chunk 107 optimal weight: 5.9990 overall best weight: 2.1204 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9403 Z= 0.328 Angle : 0.689 12.210 12745 Z= 0.338 Chirality : 0.043 0.367 1466 Planarity : 0.004 0.060 1596 Dihedral : 9.716 92.977 1644 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.01 % Allowed : 17.85 % Favored : 78.14 % 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: 0.48 (0.25), residues: 1153 helix: 1.21 (0.19), residues: 748 sheet: -0.09 (0.87), residues: 39 loop : -1.49 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 158 HIS 0.007 0.001 HIS A 60 PHE 0.022 0.002 PHE A 395 TYR 0.016 0.001 TYR A 243 ARG 0.004 0.000 ARG A1229 *********************** 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 158 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 120 time to evaluate : 1.080 Fit side-chains REVERT: A 41 TYR cc_start: 0.7199 (m-80) cc_final: 0.6868 (m-80) REVERT: A 312 TYR cc_start: 0.7847 (t80) cc_final: 0.7630 (t80) REVERT: A 517 ASP cc_start: 0.6315 (m-30) cc_final: 0.5981 (p0) REVERT: A 693 PHE cc_start: 0.6266 (OUTLIER) cc_final: 0.5206 (m-80) REVERT: A 1141 ILE cc_start: 0.9161 (mp) cc_final: 0.8952 (mt) outliers start: 38 outliers final: 29 residues processed: 144 average time/residue: 0.1859 time to fit residues: 40.2848 Evaluate side-chains 143 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 143 ILE 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 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 409 LEU 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 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 940 PHE Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1167 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 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 A1020 GLN A1126 ASN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9403 Z= 0.179 Angle : 0.623 13.715 12745 Z= 0.301 Chirality : 0.041 0.351 1466 Planarity : 0.004 0.058 1596 Dihedral : 9.291 89.028 1644 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.01 % Allowed : 18.80 % 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: 0.73 (0.26), residues: 1153 helix: 1.42 (0.20), residues: 751 sheet: 0.12 (0.88), residues: 40 loop : -1.47 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 158 HIS 0.008 0.001 HIS A 162 PHE 0.020 0.001 PHE A 953 TYR 0.017 0.001 TYR A 243 ARG 0.003 0.000 ARG A1229 *********************** 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 167 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 129 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 182 ILE cc_start: 0.8327 (pt) cc_final: 0.7878 (pt) REVERT: A 693 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.5090 (m-80) REVERT: A 766 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7842 (t80) outliers start: 38 outliers final: 29 residues processed: 153 average time/residue: 0.1835 time to fit residues: 41.3697 Evaluate side-chains 152 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 197 PHE 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 409 LEU Chi-restraints excluded: chain A residue 459 VAL 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 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 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 Chi-restraints excluded: chain A residue 1167 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9403 Z= 0.206 Angle : 0.629 14.142 12745 Z= 0.305 Chirality : 0.042 0.383 1466 Planarity : 0.004 0.054 1596 Dihedral : 9.306 88.043 1644 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.33 % Allowed : 19.32 % 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: 0.75 (0.26), residues: 1153 helix: 1.43 (0.20), residues: 752 sheet: 0.05 (0.87), residues: 40 loop : -1.44 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 158 HIS 0.007 0.001 HIS A 162 PHE 0.038 0.002 PHE A 395 TYR 0.016 0.001 TYR A 243 ARG 0.004 0.000 ARG A1229 *********************** 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 165 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 124 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 182 ILE cc_start: 0.8403 (pt) cc_final: 0.7954 (pt) REVERT: A 693 PHE cc_start: 0.6148 (OUTLIER) cc_final: 0.5114 (m-80) REVERT: A 766 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7799 (t80) outliers start: 41 outliers final: 34 residues processed: 151 average time/residue: 0.1847 time to fit residues: 41.6329 Evaluate side-chains 157 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 121 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 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 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 409 LEU Chi-restraints excluded: chain A residue 459 VAL 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 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 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 1016 SER Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1167 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 102 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 0.044 9403 Z= 0.203 Angle : 0.633 13.737 12745 Z= 0.309 Chirality : 0.042 0.391 1466 Planarity : 0.004 0.056 1596 Dihedral : 9.189 86.644 1644 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.22 % Allowed : 19.43 % 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: 0.78 (0.26), residues: 1153 helix: 1.45 (0.20), residues: 753 sheet: 0.06 (0.87), residues: 40 loop : -1.42 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 158 HIS 0.008 0.001 HIS A 162 PHE 0.031 0.002 PHE A 395 TYR 0.016 0.001 TYR A 243 ARG 0.003 0.000 ARG A1229 *********************** 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 164 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 124 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 182 ILE cc_start: 0.8386 (pt) cc_final: 0.7936 (pt) REVERT: A 693 PHE cc_start: 0.6144 (OUTLIER) cc_final: 0.5127 (m-80) REVERT: A 766 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7815 (t80) outliers start: 40 outliers final: 35 residues processed: 150 average time/residue: 0.1828 time to fit residues: 40.7722 Evaluate side-chains 155 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 118 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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 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 409 LEU Chi-restraints excluded: chain A residue 459 VAL 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 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 885 GLU 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 1016 SER Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1167 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 70 optimal weight: 0.0870 chunk 55 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 0.0770 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9403 Z= 0.164 Angle : 0.633 15.504 12745 Z= 0.306 Chirality : 0.042 0.406 1466 Planarity : 0.004 0.052 1596 Dihedral : 9.001 83.973 1644 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.27 % Allowed : 21.12 % Favored : 75.61 % 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: 0.94 (0.26), residues: 1153 helix: 1.61 (0.20), residues: 745 sheet: -0.52 (0.81), residues: 46 loop : -1.31 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A1104 HIS 0.008 0.001 HIS A 162 PHE 0.029 0.001 PHE A 395 TYR 0.015 0.001 TYR A 243 ARG 0.004 0.000 ARG A1106 ********************** 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 151 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 182 ILE cc_start: 0.8308 (pt) cc_final: 0.7814 (pt) REVERT: A 693 PHE cc_start: 0.6094 (OUTLIER) cc_final: 0.5085 (m-80) REVERT: A 766 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7817 (t80) outliers start: 31 outliers final: 27 residues processed: 138 average time/residue: 0.1798 time to fit residues: 36.6958 Evaluate side-chains 146 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 68 MET 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 195 THR Chi-restraints excluded: chain A residue 197 PHE 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 409 LEU Chi-restraints excluded: chain A residue 459 VAL 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 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 885 GLU Chi-restraints excluded: chain A residue 940 PHE Chi-restraints excluded: chain A residue 1042 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1167 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 0.0370 overall best weight: 0.9660 ------------------------------------------------------------------------------- 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 ** 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 = 0.4340 r_free = 0.4340 target = 0.196792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.156611 restraints weight = 12695.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.152488 restraints weight = 19167.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.154682 restraints weight = 16294.632| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9403 Z= 0.204 Angle : 0.643 14.785 12745 Z= 0.312 Chirality : 0.042 0.422 1466 Planarity : 0.004 0.054 1596 Dihedral : 8.989 83.691 1644 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.80 % Allowed : 20.70 % Favored : 75.50 % 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: 0.87 (0.26), residues: 1153 helix: 1.50 (0.20), residues: 754 sheet: 0.11 (0.87), residues: 40 loop : -1.39 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1104 HIS 0.003 0.001 HIS A 60 PHE 0.029 0.001 PHE A 395 TYR 0.015 0.001 TYR A 243 ARG 0.003 0.000 ARG A 485 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1848.24 seconds wall clock time: 34 minutes 13.30 seconds (2053.30 seconds total)