Starting phenix.real_space_refine on Mon Aug 5 03:54:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6t_41080/08_2024/8t6t_41080.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6t_41080/08_2024/8t6t_41080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6t_41080/08_2024/8t6t_41080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6t_41080/08_2024/8t6t_41080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6t_41080/08_2024/8t6t_41080.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t6t_41080/08_2024/8t6t_41080.cif" } resolution = 3.04 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= 0.011 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 126 5.49 5 S 18 5.16 5 C 7378 2.51 5 N 2160 2.21 5 O 2624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 273": "OD1" <-> "OD2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "A ASP 1117": "OD1" <-> "OD2" Residue "A PHE 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A PHE 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12306 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 9585 Classifications: {'peptide': 1168} Link IDs: {'PTRANS': 33, 'TRANS': 1134} Chain breaks: 5 Chain: "B" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 2035 Classifications: {'RNA': 95} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 51, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 84} Chain: "C" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Time building chain proxies: 8.17, per 1000 atoms: 0.66 Number of scatterers: 12306 At special positions: 0 Unit cell: (87.486, 129.979, 122.48, 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 18 16.00 P 126 15.00 O 2624 8.00 N 2160 7.00 C 7378 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=0, symmetry=0 Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 1.7 seconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2230 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 9 sheets defined 52.9% alpha, 8.3% beta 45 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 4.859A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.910A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.810A pdb=" N ASP A 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.603A pdb=" N LEU A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 removed outlier: 5.207A pdb=" N GLU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.659A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 4.139A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 342 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix removed outlier: 3.652A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.042A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.057A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.855A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.686A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 3.950A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.801A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 637 through 640 Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.513A pdb=" N MET A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 731 through 751 removed outlier: 4.302A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.839A pdb=" N HIS A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL A 931 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.182A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.450A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A1000 " --> pdb=" O ALA A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1009 removed outlier: 3.843A pdb=" N PHE A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1042 Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1169 through 1177 removed outlier: 4.747A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 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 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1280 Processing helix chain 'A' and resid 1283 through 1297 removed outlier: 3.501A pdb=" N HIS A1297 " --> pdb=" O ALA A1293 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.568A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.680A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1340 through 1344' Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 958 removed outlier: 6.199A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU A 958 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A 761 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 762 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE A 11 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.466A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU A1214 " --> pdb=" O GLN A1221 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN A1221 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 253 Processing sheet with id=AA4, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.893A pdb=" N ALA A 538 " --> pdb=" O TYR A 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1049 through 1051 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1065 removed outlier: 3.515A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA8, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 4.186A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1324 through 1325 419 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 216 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 6.17 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2643 1.33 - 1.45: 3315 1.45 - 1.57: 6559 1.57 - 1.69: 255 1.69 - 1.81: 35 Bond restraints: 12807 Sorted by residual: bond pdb=" O3' DA D 38 " pdb=" P DC D 39 " ideal model delta sigma weight residual 1.607 1.639 -0.032 1.50e-02 4.44e+03 4.52e+00 bond pdb=" O3' DA C 14 " pdb=" P DC C 15 " ideal model delta sigma weight residual 1.607 1.639 -0.032 1.50e-02 4.44e+03 4.51e+00 bond pdb=" CB LYS A 942 " pdb=" CG LYS A 942 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 4.06e+00 bond pdb=" C2' DG D 41 " pdb=" C1' DG D 41 " ideal model delta sigma weight residual 1.525 1.487 0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C1' DA D 40 " pdb=" N9 DA D 40 " ideal model delta sigma weight residual 1.460 1.497 -0.037 2.00e-02 2.50e+03 3.50e+00 ... (remaining 12802 not shown) Histogram of bond angle deviations from ideal: 88.79 - 99.20: 4 99.20 - 109.61: 2655 109.61 - 120.02: 9814 120.02 - 130.43: 5255 130.43 - 140.84: 116 Bond angle restraints: 17844 Sorted by residual: angle pdb=" C2' DC C 15 " pdb=" C1' DC C 15 " pdb=" N1 DC C 15 " ideal model delta sigma weight residual 113.50 130.61 -17.11 1.50e+00 4.44e-01 1.30e+02 angle pdb=" P DC D 44 " pdb=" O5' DC D 44 " pdb=" C5' DC D 44 " ideal model delta sigma weight residual 120.00 135.60 -15.60 1.50e+00 4.44e-01 1.08e+02 angle pdb=" C1' DA D 43 " pdb=" N9 DA D 43 " pdb=" C4 DA D 43 " ideal model delta sigma weight residual 127.05 111.76 15.29 1.50e+00 4.44e-01 1.04e+02 angle pdb=" O4' DA D 40 " pdb=" C1' DA D 40 " pdb=" N9 DA D 40 " ideal model delta sigma weight residual 108.40 123.40 -15.00 1.50e+00 4.44e-01 9.99e+01 angle pdb=" P DA C 14 " pdb=" O5' DA C 14 " pdb=" C5' DA C 14 " ideal model delta sigma weight residual 120.00 134.53 -14.53 1.50e+00 4.44e-01 9.38e+01 ... (remaining 17839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.38: 7336 33.38 - 66.76: 423 66.76 - 100.14: 36 100.14 - 133.52: 2 133.52 - 166.90: 4 Dihedral angle restraints: 7801 sinusoidal: 4363 harmonic: 3438 Sorted by residual: dihedral pdb=" CA ASN A 726 " pdb=" C ASN A 726 " pdb=" N LEU A 727 " pdb=" CA LEU A 727 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA GLU A1056 " pdb=" C GLU A1056 " pdb=" N ILE A1057 " pdb=" CA ILE A1057 " ideal model delta harmonic sigma weight residual -180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE A1057 " pdb=" C ILE A1057 " pdb=" N ARG A1058 " pdb=" CA ARG A1058 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 7798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 2015 0.260 - 0.520: 24 0.520 - 0.781: 5 0.781 - 1.041: 6 1.041 - 1.301: 5 Chirality restraints: 2055 Sorted by residual: chirality pdb=" C1' DC D 39 " pdb=" O4' DC D 39 " pdb=" C2' DC D 39 " pdb=" N1 DC D 39 " both_signs ideal model delta sigma weight residual False 2.47 1.17 1.30 2.00e-01 2.50e+01 4.23e+01 chirality pdb=" C1' DC C 21 " pdb=" O4' DC C 21 " pdb=" C2' DC C 21 " pdb=" N1 DC C 21 " both_signs ideal model delta sigma weight residual False 2.47 1.21 1.26 2.00e-01 2.50e+01 3.95e+01 chirality pdb=" C1' DC C 15 " pdb=" O4' DC C 15 " pdb=" C2' DC C 15 " pdb=" N1 DC C 15 " both_signs ideal model delta sigma weight residual False 2.47 1.35 1.12 2.00e-01 2.50e+01 3.14e+01 ... (remaining 2052 not shown) Planarity restraints: 1798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG C 12 " -0.056 2.00e-02 2.50e+03 2.48e-02 1.85e+01 pdb=" N9 DG C 12 " 0.051 2.00e-02 2.50e+03 pdb=" C8 DG C 12 " 0.014 2.00e-02 2.50e+03 pdb=" N7 DG C 12 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG C 12 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG C 12 " 0.015 2.00e-02 2.50e+03 pdb=" O6 DG C 12 " -0.034 2.00e-02 2.50e+03 pdb=" N1 DG C 12 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG C 12 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DG C 12 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DG C 12 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG C 12 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC C 15 " -0.055 2.00e-02 2.50e+03 2.62e-02 1.55e+01 pdb=" N1 DC C 15 " 0.038 2.00e-02 2.50e+03 pdb=" C2 DC C 15 " 0.008 2.00e-02 2.50e+03 pdb=" O2 DC C 15 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC C 15 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC C 15 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC C 15 " -0.021 2.00e-02 2.50e+03 pdb=" C5 DC C 15 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC C 15 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 17 " -0.048 2.00e-02 2.50e+03 2.06e-02 1.27e+01 pdb=" N9 DG C 17 " 0.047 2.00e-02 2.50e+03 pdb=" C8 DG C 17 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG C 17 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG C 17 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG C 17 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG C 17 " -0.020 2.00e-02 2.50e+03 pdb=" N1 DG C 17 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG C 17 " 0.009 2.00e-02 2.50e+03 pdb=" N2 DG C 17 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG C 17 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG C 17 " 0.006 2.00e-02 2.50e+03 ... (remaining 1795 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1687 2.76 - 3.29: 11492 3.29 - 3.83: 21918 3.83 - 4.36: 26310 4.36 - 4.90: 40799 Nonbonded interactions: 102206 Sorted by model distance: nonbonded pdb=" O GLN A 83 " pdb=" OG SER A 87 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR A1167 " pdb=" OE1 GLU A1170 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR A 404 " pdb=" OD1 ASP A 406 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR A 474 " pdb=" OD1 ASN A 477 " model vdw 2.261 3.040 nonbonded pdb=" OD1 ASN A 14 " pdb=" OG SER A 55 " model vdw 2.286 3.040 ... (remaining 102201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 5.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 41.390 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 : 0.005 0.060 12807 Z= 0.333 Angle : 1.337 25.807 17844 Z= 0.710 Chirality : 0.105 1.301 2055 Planarity : 0.005 0.055 1798 Dihedral : 18.875 166.901 5571 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.48 % Allowed : 9.43 % Favored : 90.10 % 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: -1.61 (0.23), residues: 1156 helix: -0.72 (0.21), residues: 516 sheet: -1.81 (0.45), residues: 110 loop : -1.10 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A1136 HIS 0.007 0.001 HIS A 329 PHE 0.025 0.003 PHE A 553 TYR 0.025 0.002 TYR A 973 ARG 0.012 0.001 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 629 ARG cc_start: 0.8636 (tpp80) cc_final: 0.8189 (tpp80) REVERT: A 631 MET cc_start: 0.7538 (mtm) cc_final: 0.7157 (mtm) REVERT: A 1148 LYS cc_start: 0.8914 (mptt) cc_final: 0.8696 (mmtp) REVERT: A 1269 ILE cc_start: 0.9593 (mt) cc_final: 0.9384 (mt) outliers start: 5 outliers final: 1 residues processed: 74 average time/residue: 0.2916 time to fit residues: 31.0863 Evaluate side-chains 57 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1241 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS A1256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12807 Z= 0.391 Angle : 0.668 7.278 17844 Z= 0.356 Chirality : 0.043 0.237 2055 Planarity : 0.004 0.052 1798 Dihedral : 20.072 178.179 3076 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.57 % Allowed : 8.67 % Favored : 88.76 % 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: -1.01 (0.23), residues: 1156 helix: -0.02 (0.22), residues: 522 sheet: -1.52 (0.47), residues: 102 loop : -1.05 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1136 HIS 0.004 0.001 HIS A 930 PHE 0.011 0.001 PHE A1181 TYR 0.019 0.002 TYR A 362 ARG 0.020 0.001 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 65 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7154 (ptp) REVERT: A 652 LYS cc_start: 0.8822 (ptmt) cc_final: 0.8354 (pttp) REVERT: A 654 ARG cc_start: 0.8394 (tpp-160) cc_final: 0.8164 (tpp-160) REVERT: A 1148 LYS cc_start: 0.8985 (mptt) cc_final: 0.8774 (mmtm) outliers start: 27 outliers final: 14 residues processed: 86 average time/residue: 0.2854 time to fit residues: 35.1205 Evaluate side-chains 71 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 8.9990 chunk 36 optimal weight: 0.0870 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 GLN A 341 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12807 Z= 0.222 Angle : 0.570 8.111 17844 Z= 0.305 Chirality : 0.039 0.217 2055 Planarity : 0.003 0.051 1798 Dihedral : 19.918 177.528 3074 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.81 % Allowed : 11.14 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1156 helix: 0.36 (0.22), residues: 534 sheet: -1.45 (0.47), residues: 104 loop : -0.89 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 476 HIS 0.003 0.001 HIS A 329 PHE 0.008 0.001 PHE A 432 TYR 0.013 0.001 TYR A 362 ARG 0.004 0.000 ARG A1317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8223 (pp30) REVERT: A 390 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8759 (mm) REVERT: A 627 GLU cc_start: 0.8157 (pm20) cc_final: 0.7950 (pm20) REVERT: A 631 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7206 (ptp) REVERT: A 648 MET cc_start: 0.8678 (mpp) cc_final: 0.8432 (mpp) REVERT: A 649 LYS cc_start: 0.9182 (mmtm) cc_final: 0.8871 (mmmm) REVERT: A 652 LYS cc_start: 0.8805 (ptmt) cc_final: 0.8229 (pttp) REVERT: A 1148 LYS cc_start: 0.8955 (mptt) cc_final: 0.8725 (mmtm) outliers start: 19 outliers final: 11 residues processed: 78 average time/residue: 0.2807 time to fit residues: 31.7351 Evaluate side-chains 72 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 33 optimal weight: 0.0870 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 983 HIS A1066 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12807 Z= 0.272 Angle : 0.563 7.595 17844 Z= 0.300 Chirality : 0.039 0.190 2055 Planarity : 0.003 0.049 1798 Dihedral : 19.884 177.991 3074 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.81 % Allowed : 11.71 % Favored : 86.48 % 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: -0.44 (0.24), residues: 1156 helix: 0.51 (0.22), residues: 538 sheet: -1.42 (0.47), residues: 104 loop : -0.83 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 476 HIS 0.004 0.001 HIS A 930 PHE 0.008 0.001 PHE A 432 TYR 0.018 0.001 TYR A1242 ARG 0.003 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8787 (mm) REVERT: A 627 GLU cc_start: 0.8187 (pm20) cc_final: 0.7903 (pm20) REVERT: A 649 LYS cc_start: 0.9202 (mmtm) cc_final: 0.8876 (mmmm) REVERT: A 652 LYS cc_start: 0.8805 (ptmt) cc_final: 0.8218 (pttp) REVERT: A 654 ARG cc_start: 0.8058 (tpp-160) cc_final: 0.7611 (tpp-160) REVERT: A 1148 LYS cc_start: 0.8955 (mptt) cc_final: 0.8744 (mmtm) REVERT: A 1303 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8061 (ttm170) outliers start: 19 outliers final: 12 residues processed: 74 average time/residue: 0.2990 time to fit residues: 31.6989 Evaluate side-chains 71 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1146 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 0 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1264 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12807 Z= 0.191 Angle : 0.530 8.468 17844 Z= 0.281 Chirality : 0.038 0.177 2055 Planarity : 0.003 0.049 1798 Dihedral : 19.800 178.823 3074 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.81 % Allowed : 12.38 % Favored : 85.81 % 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: -0.28 (0.24), residues: 1156 helix: 0.64 (0.22), residues: 544 sheet: -1.29 (0.48), residues: 104 loop : -0.76 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS A 329 PHE 0.007 0.001 PHE A 518 TYR 0.017 0.001 TYR A1242 ARG 0.002 0.000 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.5934 (pt0) REVERT: A 390 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8803 (mm) REVERT: A 511 HIS cc_start: 0.8508 (m90) cc_final: 0.8118 (m-70) REVERT: A 654 ARG cc_start: 0.8068 (tpp-160) cc_final: 0.7606 (tpp-160) REVERT: A 662 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8158 (pp) REVERT: A 1148 LYS cc_start: 0.8974 (mptt) cc_final: 0.8244 (mmmt) REVERT: A 1303 ARG cc_start: 0.8611 (ttm-80) cc_final: 0.8146 (ttm170) outliers start: 19 outliers final: 13 residues processed: 75 average time/residue: 0.2843 time to fit residues: 30.5979 Evaluate side-chains 71 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 0.4980 chunk 30 optimal weight: 0.0870 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1066 ASN A1262 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12807 Z= 0.164 Angle : 0.526 9.265 17844 Z= 0.277 Chirality : 0.037 0.176 2055 Planarity : 0.003 0.048 1798 Dihedral : 19.728 179.237 3074 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.81 % Allowed : 12.57 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.08 (0.24), residues: 1156 helix: 0.79 (0.22), residues: 546 sheet: -1.16 (0.49), residues: 104 loop : -0.65 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS A 930 PHE 0.030 0.001 PHE A 518 TYR 0.016 0.001 TYR A1242 ARG 0.003 0.000 ARG A1122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.5940 (pt0) REVERT: A 390 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8806 (mm) REVERT: A 511 HIS cc_start: 0.8521 (m90) cc_final: 0.8107 (m-70) REVERT: A 627 GLU cc_start: 0.8255 (pm20) cc_final: 0.7841 (pm20) REVERT: A 652 LYS cc_start: 0.8704 (ptmt) cc_final: 0.8155 (pttp) REVERT: A 654 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.7635 (tpp-160) REVERT: A 662 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7936 (pp) REVERT: A 933 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6280 (mp10) REVERT: A 1071 GLU cc_start: 0.8325 (tp30) cc_final: 0.7878 (tp30) REVERT: A 1303 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8333 (ttm-80) outliers start: 19 outliers final: 11 residues processed: 74 average time/residue: 0.2855 time to fit residues: 30.4162 Evaluate side-chains 70 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 0.0270 chunk 90 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 overall best weight: 2.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 12807 Z= 0.411 Angle : 0.603 8.350 17844 Z= 0.317 Chirality : 0.042 0.194 2055 Planarity : 0.004 0.046 1798 Dihedral : 19.778 177.278 3074 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.71 % Allowed : 13.24 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.24), residues: 1156 helix: 0.64 (0.22), residues: 547 sheet: -1.31 (0.48), residues: 104 loop : -0.74 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 476 HIS 0.007 0.001 HIS A 930 PHE 0.012 0.001 PHE A 518 TYR 0.018 0.001 TYR A 362 ARG 0.004 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 55 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8860 (mm) REVERT: A 511 HIS cc_start: 0.8502 (m90) cc_final: 0.8084 (m-70) REVERT: A 654 ARG cc_start: 0.8162 (tpp-160) cc_final: 0.7674 (tpp-160) REVERT: A 662 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7883 (pp) REVERT: A 1071 GLU cc_start: 0.8456 (tp30) cc_final: 0.7938 (tp30) REVERT: A 1303 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.8045 (ttm170) outliers start: 18 outliers final: 13 residues processed: 68 average time/residue: 0.2890 time to fit residues: 28.4676 Evaluate side-chains 69 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.0770 chunk 73 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12807 Z= 0.183 Angle : 0.536 8.468 17844 Z= 0.280 Chirality : 0.038 0.177 2055 Planarity : 0.003 0.047 1798 Dihedral : 19.781 178.272 3074 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.52 % Allowed : 13.52 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1156 helix: 0.82 (0.22), residues: 547 sheet: -1.17 (0.49), residues: 104 loop : -0.61 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS A 329 PHE 0.038 0.001 PHE A 518 TYR 0.013 0.001 TYR A1242 ARG 0.002 0.000 ARG A1122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8805 (mm) REVERT: A 511 HIS cc_start: 0.8492 (m90) cc_final: 0.8082 (m-70) REVERT: A 637 LYS cc_start: 0.9523 (mmmm) cc_final: 0.9262 (mmmm) REVERT: A 654 ARG cc_start: 0.8082 (tpp-160) cc_final: 0.7606 (tpp-160) REVERT: A 662 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7759 (pp) REVERT: A 933 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6215 (mp10) REVERT: A 1071 GLU cc_start: 0.8371 (tp30) cc_final: 0.7896 (tp30) REVERT: A 1303 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8107 (ttm170) outliers start: 16 outliers final: 12 residues processed: 71 average time/residue: 0.2692 time to fit residues: 28.0687 Evaluate side-chains 69 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12807 Z= 0.220 Angle : 0.557 10.756 17844 Z= 0.288 Chirality : 0.038 0.177 2055 Planarity : 0.003 0.046 1798 Dihedral : 19.735 177.771 3074 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.43 % Allowed : 13.81 % Favored : 84.76 % 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: -0.07 (0.24), residues: 1156 helix: 0.80 (0.22), residues: 554 sheet: -1.13 (0.50), residues: 104 loop : -0.67 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.003 0.001 HIS A 930 PHE 0.008 0.001 PHE A 518 TYR 0.013 0.001 TYR A1242 ARG 0.002 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 307 ARG cc_start: 0.7889 (mmp-170) cc_final: 0.7408 (mmp-170) REVERT: A 390 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8838 (mm) REVERT: A 511 HIS cc_start: 0.8518 (m90) cc_final: 0.8093 (m-70) REVERT: A 637 LYS cc_start: 0.9520 (mmmm) cc_final: 0.9255 (mmmm) REVERT: A 654 ARG cc_start: 0.8089 (tpp-160) cc_final: 0.7663 (tpp80) REVERT: A 662 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7742 (pp) REVERT: A 1071 GLU cc_start: 0.8387 (tp30) cc_final: 0.7903 (tp30) REVERT: A 1303 ARG cc_start: 0.8586 (ttm-80) cc_final: 0.8090 (ttm170) outliers start: 15 outliers final: 13 residues processed: 65 average time/residue: 0.2675 time to fit residues: 25.8417 Evaluate side-chains 69 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 221 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 933 GLN Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9808 > 50: distance: 33 - 41: 23.863 distance: 41 - 42: 15.274 distance: 42 - 43: 22.709 distance: 42 - 45: 34.883 distance: 43 - 44: 48.942 distance: 43 - 49: 43.598 distance: 45 - 46: 25.850 distance: 46 - 47: 46.751 distance: 46 - 48: 52.163 distance: 49 - 50: 7.336 distance: 50 - 51: 48.135 distance: 50 - 53: 32.878 distance: 51 - 52: 30.032 distance: 51 - 60: 57.848 distance: 53 - 54: 14.065 distance: 54 - 55: 8.240 distance: 54 - 56: 13.731 distance: 55 - 57: 15.598 distance: 56 - 58: 28.087 distance: 57 - 59: 21.532 distance: 58 - 59: 25.302 distance: 60 - 61: 40.506 distance: 61 - 62: 25.071 distance: 61 - 64: 11.854 distance: 62 - 63: 41.187 distance: 62 - 68: 15.155 distance: 64 - 65: 41.996 distance: 65 - 66: 32.755 distance: 65 - 67: 17.571 distance: 68 - 69: 18.871 distance: 69 - 70: 26.702 distance: 69 - 72: 22.872 distance: 70 - 71: 64.571 distance: 70 - 76: 28.455 distance: 71 - 100: 37.804 distance: 72 - 73: 23.811 distance: 73 - 74: 28.540 distance: 73 - 75: 39.701 distance: 76 - 77: 15.088 distance: 77 - 78: 25.093 distance: 77 - 80: 41.968 distance: 78 - 79: 41.558 distance: 78 - 85: 9.950 distance: 79 - 109: 42.708 distance: 80 - 81: 54.179 distance: 81 - 82: 38.003 distance: 82 - 83: 31.948 distance: 83 - 84: 17.349 distance: 85 - 86: 16.996 distance: 86 - 87: 4.475 distance: 86 - 89: 56.105 distance: 87 - 88: 27.644 distance: 87 - 92: 17.173 distance: 88 - 118: 23.498 distance: 89 - 90: 56.744 distance: 89 - 91: 35.240 distance: 92 - 93: 42.338 distance: 93 - 94: 52.496 distance: 93 - 96: 39.492 distance: 94 - 95: 39.414 distance: 94 - 100: 57.623 distance: 95 - 126: 30.827 distance: 96 - 97: 45.198 distance: 97 - 98: 57.861 distance: 98 - 99: 50.465 distance: 100 - 101: 23.334 distance: 101 - 102: 19.438 distance: 101 - 104: 37.475 distance: 102 - 103: 39.858 distance: 102 - 109: 21.648 distance: 104 - 105: 25.096 distance: 105 - 106: 14.059 distance: 106 - 107: 23.176 distance: 107 - 108: 25.959 distance: 109 - 110: 28.311 distance: 110 - 111: 33.099 distance: 110 - 113: 36.974 distance: 111 - 112: 38.887 distance: 111 - 118: 30.524 distance: 113 - 114: 40.884 distance: 114 - 115: 39.755 distance: 115 - 116: 23.218 distance: 115 - 117: 38.739 distance: 118 - 119: 34.451 distance: 119 - 120: 29.855 distance: 119 - 122: 20.958 distance: 120 - 121: 40.392 distance: 120 - 126: 28.750 distance: 122 - 123: 39.407 distance: 123 - 124: 46.532 distance: 123 - 125: 16.792