Starting phenix.real_space_refine on Fri Feb 16 03:01:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcb_9066/02_2024/6mcb_9066_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcb_9066/02_2024/6mcb_9066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcb_9066/02_2024/6mcb_9066.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcb_9066/02_2024/6mcb_9066.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcb_9066/02_2024/6mcb_9066_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mcb_9066/02_2024/6mcb_9066_updated.pdb" } resolution = 3.4 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= 0.000 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 118 5.49 5 S 28 5.16 5 C 8544 2.51 5 N 2459 2.21 5 O 3038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A ARG 783": "NH1" <-> "NH2" Residue "A PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 919": "NH1" <-> "NH2" Residue "A TYR 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1114": "NH1" <-> "NH2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1333": "NH1" <-> "NH2" Residue "A ARG 1335": "NH1" <-> "NH2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14187 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2494 Unusual residues: {'GTP': 1} Classifications: {'RNA': 115, 'undetermined': 1} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 41} Link IDs: {'rna2p': 18, 'rna3p': 96, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain: "A" Number of atoms: 10747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1364, 10747 Classifications: {'peptide': 1364} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 35, 'TRANS': 1328} Unresolved non-hydrogen bonds: 407 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 360 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 193 Chain: "C" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 121} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Time building chain proxies: 8.35, per 1000 atoms: 0.59 Number of scatterers: 14187 At special positions: 0 Unit cell: (136.12, 117.86, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 118 15.00 O 3038 8.00 N 2459 7.00 C 8544 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: 6.35 Conformation dependent library (CDL) restraints added in 2.5 seconds 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2834 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 8 sheets defined 41.1% alpha, 6.0% beta 28 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 7.69 Creating SS restraints... Processing helix chain 'A' and resid 60 through 93 removed outlier: 5.435A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 122 through 131 removed outlier: 3.595A pdb=" N VAL A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 151 through 163 Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.934A pdb=" N LEU A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 246 Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.786A pdb=" N ASP A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 Processing helix chain 'A' and resid 318 through 342 Processing helix chain 'A' and resid 348 through 351 No H-bonds generated for 'chain 'A' and resid 348 through 351' Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 369 through 381 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 391 through 394 No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.765A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 409' Processing helix chain 'A' and resid 412 through 425 Processing helix chain 'A' and resid 431 through 434 No H-bonds generated for 'chain 'A' and resid 431 through 434' Processing helix chain 'A' and resid 437 through 444 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 513 through 526 removed outlier: 4.972A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 604 through 607 No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 611 through 625 removed outlier: 4.274A pdb=" N ASP A 614 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 616 " --> pdb=" O GLU A 613 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 617 " --> pdb=" O ASP A 614 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 625 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 636 removed outlier: 3.638A pdb=" N ARG A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 641 removed outlier: 4.206A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 638 through 641' Processing helix chain 'A' and resid 648 through 651 No H-bonds generated for 'chain 'A' and resid 648 through 651' Processing helix chain 'A' and resid 664 through 667 No H-bonds generated for 'chain 'A' and resid 664 through 667' Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 693 through 697 Processing helix chain 'A' and resid 704 through 712 removed outlier: 3.554A pdb=" N ALA A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 731 through 750 Processing helix chain 'A' and resid 770 through 772 No H-bonds generated for 'chain 'A' and resid 770 through 772' Processing helix chain 'A' and resid 777 through 791 Processing helix chain 'A' and resid 809 through 816 Processing helix chain 'A' and resid 873 through 887 removed outlier: 3.582A pdb=" N LYS A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ASN A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TYR A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 900 Processing helix chain 'A' and resid 910 through 921 removed outlier: 4.300A pdb=" N GLN A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 939 Processing helix chain 'A' and resid 960 through 969 Processing helix chain 'A' and resid 980 through 1000 removed outlier: 3.759A pdb=" N HIS A 983 " --> pdb=" O ASN A 980 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS A 985 " --> pdb=" O HIS A 982 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 993 " --> pdb=" O ASN A 990 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 994 " --> pdb=" O ALA A 991 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 995 " --> pdb=" O VAL A 992 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 996 " --> pdb=" O VAL A 993 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A1000 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1008 removed outlier: 4.960A pdb=" N SER A1006 " --> pdb=" O LYS A1003 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A1008 " --> pdb=" O GLU A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1046 removed outlier: 3.702A pdb=" N PHE A1046 " --> pdb=" O MET A1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1043 through 1046' Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 3.594A pdb=" N SER A1088 " --> pdb=" O ARG A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1131 No H-bonds generated for 'chain 'A' and resid 1128 through 1131' Processing helix chain 'A' and resid 1171 through 1176 Processing helix chain 'A' and resid 1178 through 1185 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1230 through 1240 Processing helix chain 'A' and resid 1249 through 1261 Processing helix chain 'A' and resid 1263 through 1277 removed outlier: 3.514A pdb=" N ILE A1270 " --> pdb=" O ASP A1267 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A1273 " --> pdb=" O ILE A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1296 Processing helix chain 'A' and resid 1302 through 1315 removed outlier: 4.835A pdb=" N THR A1314 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 18 removed outlier: 3.540A pdb=" N ALA C 11 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 37 removed outlier: 3.614A pdb=" N HIS C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 33 through 37' Processing helix chain 'C' and resid 105 through 113 removed outlier: 4.097A pdb=" N MET C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 954 through 957 removed outlier: 3.558A pdb=" N ILE A 759 " --> pdb=" O LYS A 954 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN A1093 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 52 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL A1095 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 29 through 33 removed outlier: 3.760A pdb=" N LYS A 45 " --> pdb=" O LYS A 30 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 34 through 36 removed outlier: 7.028A pdb=" N GLU A1357 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 838 through 840 Processing sheet with id= E, first strand: chain 'A' and resid 1145 through 1151 Processing sheet with id= F, first strand: chain 'A' and resid 1203 through 1205 Processing sheet with id= G, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.777A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 41 through 46 removed outlier: 3.631A pdb=" N ASP C 76 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU C 93 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU C 74 " --> pdb=" O GLU C 93 " (cutoff:3.500A) 379 hydrogen bonds defined for protein. 1029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 5.89 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2207 1.31 - 1.44: 4470 1.44 - 1.56: 7731 1.56 - 1.69: 232 1.69 - 1.82: 52 Bond restraints: 14692 Sorted by residual: bond pdb=" C6 GTP B 1 " pdb=" O6 GTP B 1 " ideal model delta sigma weight residual 1.230 1.387 -0.157 2.00e-02 2.50e+03 6.17e+01 bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.422 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" CB ARG A 139 " pdb=" CG ARG A 139 " ideal model delta sigma weight residual 1.520 1.420 0.100 3.00e-02 1.11e+03 1.11e+01 bond pdb=" C5 GTP B 1 " pdb=" C6 GTP B 1 " ideal model delta sigma weight residual 1.390 1.457 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C LYS A 377 " pdb=" N PRO A 378 " ideal model delta sigma weight residual 1.335 1.378 -0.042 1.30e-02 5.92e+03 1.06e+01 ... (remaining 14687 not shown) Histogram of bond angle deviations from ideal: 96.36 - 104.29: 576 104.29 - 112.22: 7457 112.22 - 120.15: 6581 120.15 - 128.07: 5562 128.07 - 136.00: 266 Bond angle restraints: 20442 Sorted by residual: angle pdb=" C PRO C 29 " pdb=" N ASP C 30 " pdb=" CA ASP C 30 " ideal model delta sigma weight residual 121.54 134.10 -12.56 1.91e+00 2.74e-01 4.32e+01 angle pdb=" N TYR A1326 " pdb=" CA TYR A1326 " pdb=" C TYR A1326 " ideal model delta sigma weight residual 110.52 103.33 7.19 1.48e+00 4.57e-01 2.36e+01 angle pdb=" CB ARG A 139 " pdb=" CG ARG A 139 " pdb=" CD ARG A 139 " ideal model delta sigma weight residual 111.30 100.31 10.99 2.30e+00 1.89e-01 2.28e+01 angle pdb=" C ASP C 30 " pdb=" N PHE C 31 " pdb=" CA PHE C 31 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.17e+01 angle pdb=" O3' A B 86 " pdb=" C3' A B 86 " pdb=" C2' A B 86 " ideal model delta sigma weight residual 113.70 120.45 -6.75 1.50e+00 4.44e-01 2.02e+01 ... (remaining 20437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 8587 35.45 - 70.89: 343 70.89 - 106.34: 42 106.34 - 141.79: 2 141.79 - 177.24: 4 Dihedral angle restraints: 8978 sinusoidal: 4598 harmonic: 4380 Sorted by residual: dihedral pdb=" CA ASP C 30 " pdb=" C ASP C 30 " pdb=" N PHE C 31 " pdb=" CA PHE C 31 " ideal model delta harmonic sigma weight residual 180.00 128.96 51.04 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA THR C 28 " pdb=" C THR C 28 " pdb=" N PRO C 29 " pdb=" CA PRO C 29 " ideal model delta harmonic sigma weight residual 180.00 132.07 47.93 0 5.00e+00 4.00e-02 9.19e+01 dihedral pdb=" O4' C B 88 " pdb=" C1' C B 88 " pdb=" N1 C B 88 " pdb=" C2 C B 88 " ideal model delta sinusoidal sigma weight residual 200.00 42.87 157.13 1 1.50e+01 4.44e-03 8.20e+01 ... (remaining 8975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1943 0.074 - 0.149: 405 0.149 - 0.223: 48 0.223 - 0.297: 8 0.297 - 0.372: 3 Chirality restraints: 2407 Sorted by residual: chirality pdb=" C3' C B 35 " pdb=" C4' C B 35 " pdb=" O3' C B 35 " pdb=" C2' C B 35 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C1' A B 45 " pdb=" O4' A B 45 " pdb=" C2' A B 45 " pdb=" N9 A B 45 " both_signs ideal model delta sigma weight residual False 2.46 2.11 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB ILE A 956 " pdb=" CA ILE A 956 " pdb=" CG1 ILE A 956 " pdb=" CG2 ILE A 956 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 2404 not shown) Planarity restraints: 2197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 39 " -0.044 2.00e-02 2.50e+03 2.55e-02 1.46e+01 pdb=" N1 U B 39 " 0.047 2.00e-02 2.50e+03 pdb=" C2 U B 39 " -0.018 2.00e-02 2.50e+03 pdb=" O2 U B 39 " 0.010 2.00e-02 2.50e+03 pdb=" N3 U B 39 " 0.022 2.00e-02 2.50e+03 pdb=" C4 U B 39 " -0.020 2.00e-02 2.50e+03 pdb=" O4 U B 39 " -0.011 2.00e-02 2.50e+03 pdb=" C5 U B 39 " -0.004 2.00e-02 2.50e+03 pdb=" C6 U B 39 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 45 " 0.040 2.00e-02 2.50e+03 1.88e-02 9.68e+00 pdb=" N9 A B 45 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A B 45 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A B 45 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A B 45 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B 45 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 45 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A B 45 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A B 45 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A B 45 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A B 45 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 82 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C VAL C 82 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL C 82 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN C 83 " 0.018 2.00e-02 2.50e+03 ... (remaining 2194 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3432 2.78 - 3.31: 12859 3.31 - 3.84: 25395 3.84 - 4.37: 29235 4.37 - 4.90: 46324 Nonbonded interactions: 117245 Sorted by model distance: nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.253 2.440 nonbonded pdb=" OG1 THR A 404 " pdb=" OD1 ASP A 406 " model vdw 2.265 2.440 nonbonded pdb=" OG1 THR A 560 " pdb=" O ASP A 585 " model vdw 2.274 2.440 nonbonded pdb=" OG1 THR A 525 " pdb=" O ARG A 691 " model vdw 2.289 2.440 nonbonded pdb=" O ILE A 305 " pdb=" OG SER A 320 " model vdw 2.290 2.440 ... (remaining 117240 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.020 Extract box with map and model: 7.700 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 46.480 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 : 0.010 0.157 14692 Z= 0.630 Angle : 1.143 14.042 20442 Z= 0.608 Chirality : 0.061 0.372 2407 Planarity : 0.007 0.072 2197 Dihedral : 17.613 177.237 6144 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.22 % Favored : 92.65 % Rotamer: Outliers : 0.65 % Allowed : 6.27 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.35 % 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: -4.48 (0.16), residues: 1483 helix: -3.17 (0.13), residues: 665 sheet: -2.38 (0.42), residues: 125 loop : -2.79 (0.19), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A1074 HIS 0.023 0.003 HIS A 328 PHE 0.040 0.004 PHE A1008 TYR 0.040 0.003 TYR A 450 ARG 0.022 0.002 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 223 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.5279 (ptt) cc_final: 0.4965 (mmt) REVERT: A 551 LEU cc_start: 0.7891 (tp) cc_final: 0.7616 (tt) REVERT: A 825 ASP cc_start: 0.7591 (m-30) cc_final: 0.6068 (p0) REVERT: A 913 LYS cc_start: 0.7377 (mttp) cc_final: 0.7132 (mttt) REVERT: A 933 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8512 (tm-30) REVERT: A 1257 LEU cc_start: 0.8947 (tm) cc_final: 0.8742 (tm) REVERT: A 1357 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7075 (mt-10) REVERT: C 110 LYS cc_start: 0.8645 (mttt) cc_final: 0.8429 (mtmm) outliers start: 8 outliers final: 3 residues processed: 226 average time/residue: 0.2987 time to fit residues: 95.7939 Evaluate side-chains 135 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 369 GLN A 412 HIS A 504 ASN A 522 ASN A 612 ASN A 723 HIS A 767 ASN A 803 ASN A 899 ASN A 971 GLN A1241 HIS C 7 GLN C 114 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14692 Z= 0.193 Angle : 0.636 10.963 20442 Z= 0.327 Chirality : 0.041 0.356 2407 Planarity : 0.005 0.061 2197 Dihedral : 19.910 175.622 3372 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.81 % Rotamer: Outliers : 3.01 % Allowed : 10.42 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -3.09 (0.19), residues: 1483 helix: -1.77 (0.17), residues: 671 sheet: -2.06 (0.43), residues: 127 loop : -2.27 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1074 HIS 0.008 0.001 HIS A 328 PHE 0.029 0.002 PHE C 31 TYR 0.028 0.001 TYR C 10 ARG 0.006 0.001 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 187 time to evaluate : 1.458 Fit side-chains REVERT: A 74 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.6822 (mpt90) REVERT: A 152 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7229 (ptt90) REVERT: A 534 MET cc_start: 0.5325 (ptt) cc_final: 0.4983 (mmt) REVERT: A 631 MET cc_start: 0.7478 (mmm) cc_final: 0.6989 (mmt) REVERT: A 634 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: A 825 ASP cc_start: 0.7573 (m-30) cc_final: 0.6148 (p0) REVERT: A 879 MET cc_start: 0.4639 (mmt) cc_final: 0.3963 (mmt) REVERT: A 913 LYS cc_start: 0.7295 (mttp) cc_final: 0.7029 (mttt) REVERT: A 933 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 1089 MET cc_start: 0.8245 (mmm) cc_final: 0.7678 (mmm) REVERT: A 1179 ILE cc_start: 0.8616 (pt) cc_final: 0.7523 (pt) REVERT: C 20 MET cc_start: 0.8032 (pp-130) cc_final: 0.7517 (ppp) REVERT: C 106 GLU cc_start: 0.8110 (tt0) cc_final: 0.7804 (tt0) outliers start: 37 outliers final: 19 residues processed: 208 average time/residue: 0.2771 time to fit residues: 84.5140 Evaluate side-chains 167 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 152 ARG Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.0060 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 0.2980 chunk 128 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 49 optimal weight: 0.2980 chunk 116 optimal weight: 5.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 240 ASN A 758 ASN A 971 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14692 Z= 0.154 Angle : 0.587 9.854 20442 Z= 0.298 Chirality : 0.039 0.318 2407 Planarity : 0.004 0.043 2197 Dihedral : 19.614 176.726 3372 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.86 % Favored : 95.01 % Rotamer: Outliers : 2.61 % Allowed : 13.84 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -2.43 (0.20), residues: 1483 helix: -1.05 (0.19), residues: 670 sheet: -1.91 (0.42), residues: 137 loop : -2.07 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 PHE 0.027 0.001 PHE C 31 TYR 0.020 0.001 TYR C 50 ARG 0.004 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 1.504 Fit side-chains REVERT: A 74 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7629 (mtt90) REVERT: A 215 ARG cc_start: 0.5767 (tpt170) cc_final: 0.5370 (mmm-85) REVERT: A 534 MET cc_start: 0.5353 (ptt) cc_final: 0.5022 (mmt) REVERT: A 631 MET cc_start: 0.7379 (mmm) cc_final: 0.6853 (mmt) REVERT: A 645 ASP cc_start: 0.7767 (t0) cc_final: 0.7492 (m-30) REVERT: A 738 LEU cc_start: 0.8749 (tp) cc_final: 0.8515 (tt) REVERT: A 933 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8598 (tm-30) REVERT: A 1089 MET cc_start: 0.8229 (mmm) cc_final: 0.7789 (mmm) REVERT: C 12 GLU cc_start: 0.8795 (pm20) cc_final: 0.8338 (pm20) REVERT: C 20 MET cc_start: 0.7768 (pp-130) cc_final: 0.7188 (ppp) REVERT: C 122 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.6023 (pp) outliers start: 32 outliers final: 14 residues processed: 190 average time/residue: 0.2557 time to fit residues: 73.3011 Evaluate side-chains 155 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 122 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 153 optimal weight: 0.0060 chunk 137 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 251 ASN A 899 ASN C 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14692 Z= 0.215 Angle : 0.596 9.573 20442 Z= 0.303 Chirality : 0.041 0.310 2407 Planarity : 0.004 0.040 2197 Dihedral : 19.435 176.282 3370 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.92 % Favored : 94.94 % Rotamer: Outliers : 4.07 % Allowed : 14.33 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -2.09 (0.20), residues: 1483 helix: -0.70 (0.19), residues: 671 sheet: -1.84 (0.43), residues: 136 loop : -1.96 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 PHE 0.023 0.002 PHE C 17 TYR 0.023 0.001 TYR C 10 ARG 0.005 0.001 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 151 time to evaluate : 1.477 Fit side-chains REVERT: A 74 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.6701 (mpt90) REVERT: A 215 ARG cc_start: 0.5982 (tpt170) cc_final: 0.5521 (mmm-85) REVERT: A 523 GLU cc_start: 0.7441 (tt0) cc_final: 0.7223 (tt0) REVERT: A 534 MET cc_start: 0.5373 (ptt) cc_final: 0.5031 (mmt) REVERT: A 631 MET cc_start: 0.7500 (mmm) cc_final: 0.7088 (mmt) REVERT: A 634 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: A 933 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8635 (tm-30) REVERT: A 1089 MET cc_start: 0.8283 (mmm) cc_final: 0.7930 (mmm) outliers start: 50 outliers final: 31 residues processed: 180 average time/residue: 0.2453 time to fit residues: 68.3406 Evaluate side-chains 168 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 111 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 78 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 698 HIS A 971 GLN C 37 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14692 Z= 0.303 Angle : 0.641 9.525 20442 Z= 0.327 Chirality : 0.043 0.315 2407 Planarity : 0.004 0.040 2197 Dihedral : 19.440 176.996 3370 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.41 % Favored : 93.53 % Rotamer: Outliers : 4.07 % Allowed : 15.47 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -2.11 (0.21), residues: 1483 helix: -0.70 (0.19), residues: 676 sheet: -1.75 (0.42), residues: 142 loop : -2.00 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 PHE 0.021 0.002 PHE C 31 TYR 0.027 0.002 TYR C 50 ARG 0.005 0.001 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 143 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6751 (mpt90) REVERT: A 215 ARG cc_start: 0.6365 (tpt170) cc_final: 0.5678 (mmm-85) REVERT: A 523 GLU cc_start: 0.7461 (tt0) cc_final: 0.7225 (tt0) REVERT: A 534 MET cc_start: 0.5428 (ptt) cc_final: 0.5105 (mmt) REVERT: A 631 MET cc_start: 0.7589 (mmm) cc_final: 0.7197 (mmt) REVERT: A 634 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: A 933 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8668 (tm-30) REVERT: A 1089 MET cc_start: 0.8306 (mmm) cc_final: 0.8013 (mmm) REVERT: A 1106 SER cc_start: 0.8934 (p) cc_final: 0.8713 (m) outliers start: 50 outliers final: 37 residues processed: 174 average time/residue: 0.2553 time to fit residues: 69.1941 Evaluate side-chains 180 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 141 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1049 GLU Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 148 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 971 GLN C 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14692 Z= 0.183 Angle : 0.576 9.433 20442 Z= 0.292 Chirality : 0.040 0.312 2407 Planarity : 0.003 0.039 2197 Dihedral : 19.380 177.307 3370 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.88 % Rotamer: Outliers : 3.34 % Allowed : 16.29 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -1.74 (0.21), residues: 1483 helix: -0.37 (0.20), residues: 672 sheet: -1.59 (0.44), residues: 142 loop : -1.84 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 PHE 0.018 0.001 PHE C 31 TYR 0.023 0.001 TYR A 988 ARG 0.004 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 1.561 Fit side-chains REVERT: A 74 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7624 (mpt90) REVERT: A 215 ARG cc_start: 0.6268 (tpt170) cc_final: 0.5649 (mmm-85) REVERT: A 465 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.6422 (ttt) REVERT: A 523 GLU cc_start: 0.7390 (tt0) cc_final: 0.7145 (tt0) REVERT: A 534 MET cc_start: 0.5405 (ptt) cc_final: 0.5171 (mmt) REVERT: A 933 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8631 (tm-30) REVERT: A 971 GLN cc_start: 0.6768 (mt0) cc_final: 0.6305 (mp10) REVERT: A 973 TYR cc_start: 0.8667 (m-80) cc_final: 0.8047 (m-80) REVERT: A 1189 GLU cc_start: 0.7221 (tm-30) cc_final: 0.7010 (tm-30) REVERT: C 115 GLU cc_start: 0.8547 (pm20) cc_final: 0.8096 (pm20) outliers start: 41 outliers final: 29 residues processed: 178 average time/residue: 0.2433 time to fit residues: 66.5138 Evaluate side-chains 176 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 69 TYR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 111 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 129 optimal weight: 0.3980 chunk 85 optimal weight: 0.2980 chunk 153 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 70 optimal weight: 0.3980 chunk 94 optimal weight: 9.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 190 GLN A 235 ASN A 281 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14692 Z= 0.146 Angle : 0.568 9.571 20442 Z= 0.284 Chirality : 0.039 0.310 2407 Planarity : 0.003 0.038 2197 Dihedral : 19.311 178.055 3370 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 3.34 % Allowed : 17.43 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -1.44 (0.21), residues: 1483 helix: -0.08 (0.20), residues: 665 sheet: -1.19 (0.45), residues: 132 loop : -1.77 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1074 HIS 0.006 0.001 HIS A 328 PHE 0.021 0.001 PHE A1327 TYR 0.021 0.001 TYR C 10 ARG 0.004 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 154 time to evaluate : 1.423 Fit side-chains REVERT: A 74 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7563 (mtt90) REVERT: A 215 ARG cc_start: 0.6236 (tpt170) cc_final: 0.5604 (mmm-85) REVERT: A 409 SER cc_start: 0.7877 (p) cc_final: 0.7650 (t) REVERT: A 523 GLU cc_start: 0.7417 (tt0) cc_final: 0.7096 (tt0) REVERT: A 933 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8638 (tm-30) REVERT: A 964 SER cc_start: 0.8755 (t) cc_final: 0.8293 (p) REVERT: A 1189 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6944 (tm-30) REVERT: C 12 GLU cc_start: 0.8754 (pm20) cc_final: 0.8098 (pm20) outliers start: 41 outliers final: 24 residues processed: 178 average time/residue: 0.2418 time to fit residues: 65.6713 Evaluate side-chains 167 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain A residue 1356 TYR Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 91 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 14 optimal weight: 0.0060 chunk 120 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN C 113 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 14692 Z= 0.152 Angle : 0.577 15.535 20442 Z= 0.286 Chirality : 0.039 0.317 2407 Planarity : 0.003 0.037 2197 Dihedral : 19.260 177.857 3370 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.86 % Favored : 95.08 % Rotamer: Outliers : 2.61 % Allowed : 18.16 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -1.34 (0.22), residues: 1483 helix: -0.05 (0.20), residues: 675 sheet: -1.41 (0.43), residues: 142 loop : -1.60 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1074 HIS 0.006 0.001 HIS A 328 PHE 0.046 0.002 PHE A1008 TYR 0.029 0.001 TYR C 50 ARG 0.004 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 1.455 Fit side-chains REVERT: A 74 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7603 (mtt90) REVERT: A 215 ARG cc_start: 0.6226 (tpt170) cc_final: 0.5545 (mmm-85) REVERT: A 341 GLN cc_start: 0.7225 (tm-30) cc_final: 0.6976 (pp30) REVERT: A 409 SER cc_start: 0.7876 (p) cc_final: 0.7664 (t) REVERT: A 523 GLU cc_start: 0.7421 (tt0) cc_final: 0.7085 (tt0) REVERT: A 933 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8592 (tm-30) REVERT: A 1043 MET cc_start: 0.7686 (mmm) cc_final: 0.7430 (mmm) REVERT: A 1189 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6912 (tm-30) REVERT: C 12 GLU cc_start: 0.8741 (pm20) cc_final: 0.8115 (pm20) REVERT: C 31 PHE cc_start: 0.6717 (m-80) cc_final: 0.6506 (m-80) outliers start: 32 outliers final: 25 residues processed: 171 average time/residue: 0.2425 time to fit residues: 64.0344 Evaluate side-chains 162 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 111 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 135 optimal weight: 0.0980 chunk 93 optimal weight: 8.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A1286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14692 Z= 0.192 Angle : 0.591 9.761 20442 Z= 0.295 Chirality : 0.041 0.339 2407 Planarity : 0.003 0.037 2197 Dihedral : 19.220 177.659 3370 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.79 % Favored : 95.14 % Rotamer: Outliers : 2.69 % Allowed : 18.97 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -1.28 (0.22), residues: 1483 helix: 0.03 (0.20), residues: 677 sheet: -1.53 (0.43), residues: 125 loop : -1.59 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1074 HIS 0.006 0.001 HIS A 328 PHE 0.060 0.002 PHE A1008 TYR 0.025 0.001 TYR C 50 ARG 0.003 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 1.524 Fit side-chains REVERT: A 74 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7645 (mpt90) REVERT: A 215 ARG cc_start: 0.6341 (tpt170) cc_final: 0.5600 (mmm-85) REVERT: A 341 GLN cc_start: 0.7267 (tm-30) cc_final: 0.7047 (pp30) REVERT: A 409 SER cc_start: 0.8079 (p) cc_final: 0.7828 (t) REVERT: A 523 GLU cc_start: 0.7418 (tt0) cc_final: 0.7098 (tt0) REVERT: A 780 ARG cc_start: 0.7652 (ttt180) cc_final: 0.7405 (mmm-85) REVERT: A 933 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8651 (tm-30) REVERT: A 973 TYR cc_start: 0.8615 (m-80) cc_final: 0.8139 (m-80) REVERT: A 1043 MET cc_start: 0.7733 (mmm) cc_final: 0.7470 (mmm) REVERT: A 1189 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6950 (tm-30) REVERT: C 12 GLU cc_start: 0.8749 (pm20) cc_final: 0.8183 (pm20) REVERT: C 109 MET cc_start: 0.8140 (tpp) cc_final: 0.7724 (mmt) outliers start: 33 outliers final: 29 residues processed: 157 average time/residue: 0.2454 time to fit residues: 59.3427 Evaluate side-chains 162 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 111 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 0.0470 chunk 134 optimal weight: 3.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14692 Z= 0.162 Angle : 0.575 10.915 20442 Z= 0.286 Chirality : 0.040 0.362 2407 Planarity : 0.003 0.037 2197 Dihedral : 19.204 178.370 3370 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.94 % Rotamer: Outliers : 2.77 % Allowed : 19.06 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -1.04 (0.22), residues: 1483 helix: 0.20 (0.20), residues: 669 sheet: -1.10 (0.45), residues: 120 loop : -1.48 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1074 HIS 0.006 0.001 HIS A 328 PHE 0.057 0.002 PHE A1008 TYR 0.025 0.001 TYR C 50 ARG 0.007 0.000 ARG A 467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7658 (mpt90) REVERT: A 215 ARG cc_start: 0.6316 (tpt170) cc_final: 0.5568 (mmm-85) REVERT: A 261 ASP cc_start: 0.7570 (t70) cc_final: 0.6981 (m-30) REVERT: A 341 GLN cc_start: 0.7264 (tm-30) cc_final: 0.7062 (pp30) REVERT: A 409 SER cc_start: 0.8018 (p) cc_final: 0.7780 (t) REVERT: A 523 GLU cc_start: 0.7358 (tt0) cc_final: 0.7055 (tt0) REVERT: A 933 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8662 (tm-30) REVERT: A 973 TYR cc_start: 0.8583 (m-80) cc_final: 0.8136 (m-80) REVERT: A 1043 MET cc_start: 0.7763 (mmm) cc_final: 0.7525 (mmm) REVERT: A 1189 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6966 (tm-30) REVERT: A 1274 SER cc_start: 0.8433 (m) cc_final: 0.8109 (p) REVERT: C 12 GLU cc_start: 0.8689 (pm20) cc_final: 0.8217 (pm20) REVERT: C 109 MET cc_start: 0.8140 (tpp) cc_final: 0.7721 (mmt) outliers start: 34 outliers final: 28 residues processed: 158 average time/residue: 0.2566 time to fit residues: 63.1498 Evaluate side-chains 163 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 111 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.170779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.132768 restraints weight = 22265.641| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.32 r_work: 0.3764 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14692 Z= 0.215 Angle : 0.597 9.677 20442 Z= 0.298 Chirality : 0.041 0.377 2407 Planarity : 0.004 0.042 2197 Dihedral : 19.201 177.905 3370 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.79 % Favored : 95.14 % Rotamer: Outliers : 3.01 % Allowed : 18.65 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.07 % 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: -1.13 (0.22), residues: 1483 helix: 0.15 (0.20), residues: 673 sheet: -1.50 (0.44), residues: 129 loop : -1.48 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1074 HIS 0.006 0.001 HIS A 328 PHE 0.053 0.002 PHE A1008 TYR 0.025 0.001 TYR C 50 ARG 0.004 0.000 ARG A 467 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.79 seconds wall clock time: 55 minutes 31.73 seconds (3331.73 seconds total)