Starting phenix.real_space_refine on Wed May 8 14:53:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4t_16428/05_2024/8c4t_16428.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4t_16428/05_2024/8c4t_16428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4t_16428/05_2024/8c4t_16428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4t_16428/05_2024/8c4t_16428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4t_16428/05_2024/8c4t_16428.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c4t_16428/05_2024/8c4t_16428.pdb" } resolution = 3.23 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= 0.005 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 1 5.21 5 S 56 5.16 5 C 6683 2.51 5 N 1757 2.21 5 O 1950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 249": "OD1" <-> "OD2" Residue "A ASP 327": "OD1" <-> "OD2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 551": "OD1" <-> "OD2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "A TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 913": "OD1" <-> "OD2" Residue "A TYR 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1028": "OD1" <-> "OD2" Residue "A PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1195": "OD1" <-> "OD2" Residue "A PHE 1202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1369": "OD1" <-> "OD2" Residue "A TYR 1382": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 10459 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 10199 Classifications: {'peptide': 1268} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1227} Chain breaks: 12 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 259 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.83, per 1000 atoms: 0.56 Number of scatterers: 10459 At special positions: 0 Unit cell: (96.18, 100.76, 120.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 12 15.00 Mg 1 11.99 O 1950 8.00 N 1757 7.00 C 6683 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: 4.07 Conformation dependent library (CDL) restraints added in 1.7 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 59.7% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.550A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 282 removed outlier: 3.960A pdb=" N GLN A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 3.768A pdb=" N ASN A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 379 through 390 Processing helix chain 'A' and resid 409 through 429 Processing helix chain 'A' and resid 450 through 463 removed outlier: 4.404A pdb=" N GLN A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 490 removed outlier: 3.634A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 572 Processing helix chain 'A' and resid 572 through 593 Processing helix chain 'A' and resid 597 through 614 Processing helix chain 'A' and resid 616 through 634 removed outlier: 3.837A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 654 through 674 removed outlier: 3.699A pdb=" N VAL A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 659 " --> pdb=" O SER A 655 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 removed outlier: 3.831A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 760 removed outlier: 3.555A pdb=" N HIS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU A 744 " --> pdb=" O LYS A 740 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.808A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.613A pdb=" N LYS A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 829 Processing helix chain 'A' and resid 847 through 859 Processing helix chain 'A' and resid 864 through 872 Processing helix chain 'A' and resid 898 through 918 removed outlier: 4.282A pdb=" N ASN A 918 " --> pdb=" O ALA A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 947 removed outlier: 4.567A pdb=" N LEU A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 992 removed outlier: 4.077A pdb=" N ARG A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1020 through 1029 Processing helix chain 'A' and resid 1034 through 1042 Processing helix chain 'A' and resid 1062 through 1084 Processing helix chain 'A' and resid 1116 through 1126 Processing helix chain 'A' and resid 1128 through 1134 removed outlier: 3.914A pdb=" N PHE A1132 " --> pdb=" O LEU A1129 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A1133 " --> pdb=" O HIS A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1152 removed outlier: 3.911A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1195 removed outlier: 4.502A pdb=" N LEU A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A1194 " --> pdb=" O LEU A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1219 Processing helix chain 'A' and resid 1221 through 1241 Processing helix chain 'A' and resid 1250 through 1255 removed outlier: 3.879A pdb=" N GLN A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1272 through 1279 Processing helix chain 'A' and resid 1282 through 1298 removed outlier: 3.760A pdb=" N LEU A1288 " --> pdb=" O SER A1284 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A1295 " --> pdb=" O ARG A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1321 Processing helix chain 'A' and resid 1354 through 1365 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1375 through 1388 Processing helix chain 'A' and resid 1389 through 1396 Processing helix chain 'A' and resid 1403 through 1412 removed outlier: 4.383A pdb=" N GLN A1409 " --> pdb=" O ARG A1405 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA A1410 " --> pdb=" O PHE A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 Processing helix chain 'A' and resid 1443 through 1457 Processing helix chain 'A' and resid 1464 through 1471 Processing helix chain 'A' and resid 1503 through 1511 removed outlier: 3.575A pdb=" N ILE A1507 " --> pdb=" O ILE A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1530 through 1545 Processing helix chain 'A' and resid 1552 through 1560 Processing helix chain 'A' and resid 1583 through 1593 Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 removed outlier: 3.535A pdb=" N TYR A 637 " --> pdb=" O VAL A1164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA4, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA6, first strand: chain 'A' and resid 833 through 837 removed outlier: 4.532A pdb=" N SER A 844 " --> pdb=" O GLY A 835 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 893 through 897 removed outlier: 7.214A pdb=" N ALA A 877 " --> pdb=" O ASP A1016 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE A1018 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA A 879 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 949 through 952 Processing sheet with id=AA9, first strand: chain 'A' and resid 1169 through 1171 Processing sheet with id=AB1, first strand: chain 'A' and resid 1417 through 1419 Processing sheet with id=AB2, first strand: chain 'A' and resid 1474 through 1479 removed outlier: 3.572A pdb=" N ASP A1474 " --> pdb=" O ARG A1600 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1486 through 1489 593 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1654 1.29 - 1.42: 2895 1.42 - 1.55: 6043 1.55 - 1.68: 23 1.68 - 1.82: 93 Bond restraints: 10708 Sorted by residual: bond pdb=" C ILE A 572 " pdb=" O ILE A 572 " ideal model delta sigma weight residual 1.236 1.153 0.083 1.19e-02 7.06e+03 4.91e+01 bond pdb=" C GLU A 575 " pdb=" O GLU A 575 " ideal model delta sigma weight residual 1.236 1.168 0.069 1.22e-02 6.72e+03 3.16e+01 bond pdb=" CA ALA A 573 " pdb=" CB ALA A 573 " ideal model delta sigma weight residual 1.534 1.455 0.079 1.71e-02 3.42e+03 2.11e+01 bond pdb=" N ILE A1183 " pdb=" CA ILE A1183 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.50e-03 1.78e+04 1.95e+01 bond pdb=" C ALA A 573 " pdb=" O ALA A 573 " ideal model delta sigma weight residual 1.236 1.181 0.054 1.34e-02 5.57e+03 1.63e+01 ... (remaining 10703 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.13: 277 106.13 - 113.11: 5804 113.11 - 120.09: 3738 120.09 - 127.07: 4557 127.07 - 134.05: 143 Bond angle restraints: 14519 Sorted by residual: angle pdb=" N GLU A 575 " pdb=" CA GLU A 575 " pdb=" CB GLU A 575 " ideal model delta sigma weight residual 110.20 101.89 8.31 1.49e+00 4.50e-01 3.11e+01 angle pdb=" CA ILE A 572 " pdb=" C ILE A 572 " pdb=" O ILE A 572 " ideal model delta sigma weight residual 120.78 114.30 6.48 1.25e+00 6.40e-01 2.69e+01 angle pdb=" C ILE A 572 " pdb=" CA ILE A 572 " pdb=" CB ILE A 572 " ideal model delta sigma weight residual 111.29 103.93 7.36 1.64e+00 3.72e-01 2.01e+01 angle pdb=" C3' A C 5 " pdb=" C2' A C 5 " pdb=" O2' A C 5 " ideal model delta sigma weight residual 110.70 117.36 -6.66 1.50e+00 4.44e-01 1.97e+01 angle pdb=" CA GLN A1575 " pdb=" C GLN A1575 " pdb=" O GLN A1575 " ideal model delta sigma weight residual 121.82 116.57 5.25 1.21e+00 6.83e-01 1.88e+01 ... (remaining 14514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.13: 6045 29.13 - 58.25: 351 58.25 - 87.37: 27 87.37 - 116.50: 1 116.50 - 145.62: 1 Dihedral angle restraints: 6425 sinusoidal: 2696 harmonic: 3729 Sorted by residual: dihedral pdb=" O4' U C 7 " pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sinusoidal sigma weight residual 200.00 54.38 145.62 1 1.50e+01 4.44e-03 7.79e+01 dihedral pdb=" O4' U C 1 " pdb=" C1' U C 1 " pdb=" N1 U C 1 " pdb=" C2 U C 1 " ideal model delta sinusoidal sigma weight residual -160.00 -65.74 -94.26 1 1.50e+01 4.44e-03 4.58e+01 dihedral pdb=" C VAL A1578 " pdb=" N VAL A1578 " pdb=" CA VAL A1578 " pdb=" CB VAL A1578 " ideal model delta harmonic sigma weight residual -122.00 -135.04 13.04 0 2.50e+00 1.60e-01 2.72e+01 ... (remaining 6422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1595 0.111 - 0.222: 29 0.222 - 0.334: 7 0.334 - 0.445: 1 0.445 - 0.556: 1 Chirality restraints: 1633 Sorted by residual: chirality pdb=" P A C 2 " pdb=" OP1 A C 2 " pdb=" OP2 A C 2 " pdb=" O5' A C 2 " both_signs ideal model delta sigma weight residual True 2.41 -1.85 0.56 2.00e-01 2.50e+01 7.73e+00 chirality pdb=" CA VAL A1578 " pdb=" N VAL A1578 " pdb=" C VAL A1578 " pdb=" CB VAL A1578 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CB VAL A1578 " pdb=" CA VAL A1578 " pdb=" CG1 VAL A1578 " pdb=" CG2 VAL A1578 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 1630 not shown) Planarity restraints: 1779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 573 " 0.013 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C ALA A 573 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA A 573 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE A 574 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 571 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.39e+00 pdb=" C ASN A 571 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN A 571 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 572 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1574 " 0.009 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C VAL A1574 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL A1574 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A1575 " 0.012 2.00e-02 2.50e+03 ... (remaining 1776 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 242 2.70 - 3.25: 10204 3.25 - 3.80: 17062 3.80 - 4.35: 22353 4.35 - 4.90: 37668 Nonbonded interactions: 87529 Sorted by model distance: nonbonded pdb=" OH TYR A 341 " pdb=" OH TYR A 353 " model vdw 2.148 2.440 nonbonded pdb=" OH TYR A 230 " pdb=" OE2 GLU A 870 " model vdw 2.222 2.440 nonbonded pdb=" OE2 GLU A 275 " pdb=" OH TYR A 661 " model vdw 2.262 2.440 nonbonded pdb=" O ARG A 714 " pdb=" OG SER A 718 " model vdw 2.265 2.440 nonbonded pdb=" OD1 ASP A 242 " pdb=" NH2 ARG A 774 " model vdw 2.267 2.520 ... (remaining 87524 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=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: 1.680 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: 4.070 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 31.500 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.003 0.083 10708 Z= 0.229 Angle : 0.580 9.729 14519 Z= 0.333 Chirality : 0.047 0.556 1633 Planarity : 0.004 0.046 1779 Dihedral : 16.975 145.624 4005 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.36 % Allowed : 22.05 % Favored : 77.59 % Cbeta Deviations : 0.17 % 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: 0.76 (0.23), residues: 1242 helix: 1.48 (0.19), residues: 695 sheet: -0.43 (0.52), residues: 87 loop : -0.78 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 PHE 0.014 0.001 PHE A 585 TYR 0.010 0.001 TYR A1306 ARG 0.005 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 1.149 Fit side-chains REVERT: A 575 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: A 1577 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7408 (p0) outliers start: 4 outliers final: 1 residues processed: 134 average time/residue: 0.2468 time to fit residues: 46.3343 Evaluate side-chains 123 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1577 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 chunk 51 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 HIS ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.0651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10708 Z= 0.218 Angle : 0.489 8.691 14519 Z= 0.253 Chirality : 0.038 0.193 1633 Planarity : 0.004 0.038 1779 Dihedral : 9.840 143.524 1548 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.59 % Allowed : 20.98 % Favored : 76.43 % 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: 1.03 (0.24), residues: 1242 helix: 1.74 (0.19), residues: 711 sheet: -0.52 (0.51), residues: 96 loop : -0.78 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 PHE 0.017 0.001 PHE A 585 TYR 0.009 0.001 TYR A 352 ARG 0.004 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: A 429 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8660 (tt) REVERT: A 1057 LEU cc_start: 0.8696 (mt) cc_final: 0.8398 (mp) outliers start: 29 outliers final: 17 residues processed: 153 average time/residue: 0.2351 time to fit residues: 50.7801 Evaluate side-chains 140 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 653 LYS Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 124 optimal weight: 0.0270 chunk 102 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10708 Z= 0.189 Angle : 0.464 8.218 14519 Z= 0.239 Chirality : 0.037 0.200 1633 Planarity : 0.003 0.041 1779 Dihedral : 9.469 143.305 1543 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.04 % Allowed : 21.25 % Favored : 75.71 % 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: 1.23 (0.24), residues: 1242 helix: 1.93 (0.19), residues: 703 sheet: -0.44 (0.51), residues: 101 loop : -0.70 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 PHE 0.016 0.001 PHE A 585 TYR 0.013 0.001 TYR A1509 ARG 0.003 0.000 ARG A1427 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: A 858 ASN cc_start: 0.7366 (m-40) cc_final: 0.7137 (m-40) REVERT: A 1305 LEU cc_start: 0.8782 (tp) cc_final: 0.8497 (tt) outliers start: 34 outliers final: 19 residues processed: 153 average time/residue: 0.2443 time to fit residues: 53.3195 Evaluate side-chains 143 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1464 TRP Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.0070 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 60 optimal weight: 0.0370 chunk 109 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10708 Z= 0.203 Angle : 0.465 8.527 14519 Z= 0.238 Chirality : 0.037 0.148 1633 Planarity : 0.003 0.045 1779 Dihedral : 9.354 143.043 1543 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.57 % Allowed : 20.89 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.23), residues: 1242 helix: 1.92 (0.19), residues: 703 sheet: -0.40 (0.52), residues: 99 loop : -0.68 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 PHE 0.016 0.001 PHE A 585 TYR 0.014 0.001 TYR A1509 ARG 0.002 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 855 TYR cc_start: 0.8301 (t80) cc_final: 0.7678 (t80) REVERT: A 858 ASN cc_start: 0.7265 (m-40) cc_final: 0.7024 (m110) REVERT: A 1305 LEU cc_start: 0.8805 (tp) cc_final: 0.8524 (tt) outliers start: 40 outliers final: 29 residues processed: 157 average time/residue: 0.2368 time to fit residues: 54.7794 Evaluate side-chains 152 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1283 MET Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1464 TRP Chi-restraints excluded: chain A residue 1471 ILE Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10708 Z= 0.340 Angle : 0.539 9.929 14519 Z= 0.275 Chirality : 0.040 0.151 1633 Planarity : 0.004 0.050 1779 Dihedral : 9.414 140.912 1543 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.93 % Allowed : 20.62 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1242 helix: 1.63 (0.19), residues: 709 sheet: -0.44 (0.50), residues: 101 loop : -0.78 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 742 PHE 0.023 0.002 PHE A 585 TYR 0.015 0.002 TYR A 352 ARG 0.003 0.000 ARG A1238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 124 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 855 TYR cc_start: 0.8347 (t80) cc_final: 0.7831 (t80) REVERT: A 858 ASN cc_start: 0.7319 (m-40) cc_final: 0.7046 (m110) REVERT: A 1305 LEU cc_start: 0.8858 (tp) cc_final: 0.8590 (tt) REVERT: A 1488 ARG cc_start: 0.7248 (mmt180) cc_final: 0.6946 (mmt180) REVERT: A 1511 PHE cc_start: 0.8592 (m-80) cc_final: 0.8362 (m-80) outliers start: 44 outliers final: 35 residues processed: 158 average time/residue: 0.2297 time to fit residues: 51.3387 Evaluate side-chains 154 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 918 ASN Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1030 MET Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1464 TRP Chi-restraints excluded: chain A residue 1471 ILE Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 122 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 56 optimal weight: 0.0470 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10708 Z= 0.157 Angle : 0.458 9.138 14519 Z= 0.233 Chirality : 0.036 0.138 1633 Planarity : 0.003 0.052 1779 Dihedral : 9.245 143.288 1543 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.95 % Allowed : 21.70 % Favored : 75.36 % 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: 1.22 (0.23), residues: 1242 helix: 1.94 (0.19), residues: 702 sheet: -0.47 (0.51), residues: 99 loop : -0.72 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 473 HIS 0.004 0.001 HIS A 732 PHE 0.014 0.001 PHE A 585 TYR 0.016 0.001 TYR A1509 ARG 0.003 0.000 ARG A 566 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 855 TYR cc_start: 0.8228 (t80) cc_final: 0.7782 (t80) REVERT: A 858 ASN cc_start: 0.7288 (m-40) cc_final: 0.7057 (m110) REVERT: A 1305 LEU cc_start: 0.8873 (tp) cc_final: 0.8616 (tt) REVERT: A 1451 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7377 (mm-40) outliers start: 33 outliers final: 22 residues processed: 149 average time/residue: 0.2467 time to fit residues: 52.7262 Evaluate side-chains 144 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1464 TRP Chi-restraints excluded: chain A residue 1471 ILE Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10708 Z= 0.343 Angle : 0.537 10.061 14519 Z= 0.274 Chirality : 0.040 0.158 1633 Planarity : 0.004 0.053 1779 Dihedral : 9.344 141.135 1543 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.75 % Allowed : 20.98 % Favored : 75.27 % 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: 1.00 (0.23), residues: 1242 helix: 1.74 (0.19), residues: 703 sheet: -0.54 (0.50), residues: 101 loop : -0.79 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 742 PHE 0.023 0.002 PHE A 585 TYR 0.017 0.002 TYR A1509 ARG 0.004 0.000 ARG A1238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 122 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: A 855 TYR cc_start: 0.8309 (t80) cc_final: 0.7883 (t80) REVERT: A 858 ASN cc_start: 0.7312 (m-40) cc_final: 0.7057 (m110) REVERT: A 1305 LEU cc_start: 0.8889 (tp) cc_final: 0.8635 (tt) REVERT: A 1488 ARG cc_start: 0.7215 (mmt180) cc_final: 0.6929 (mmt180) outliers start: 42 outliers final: 32 residues processed: 155 average time/residue: 0.2448 time to fit residues: 53.7946 Evaluate side-chains 153 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 840 ASP Chi-restraints excluded: chain A residue 847 VAL Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1012 VAL Chi-restraints excluded: chain A residue 1030 MET Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1464 TRP Chi-restraints excluded: chain A residue 1471 ILE Chi-restraints excluded: chain A residue 1506 VAL Chi-restraints excluded: chain A residue 1527 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/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-5322/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-5322/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-5322/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-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/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-5322/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-5322/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: 71.596 > 50: distance: 1 - 25: 33.675 distance: 6 - 34: 36.142 distance: 16 - 43: 33.026 distance: 21 - 25: 33.973 distance: 22 - 52: 32.534 distance: 26 - 29: 39.667 distance: 27 - 28: 39.912 distance: 27 - 34: 39.313 distance: 28 - 61: 49.931 distance: 30 - 31: 45.845 distance: 31 - 32: 43.980 distance: 32 - 33: 55.891 distance: 34 - 35: 38.957 distance: 35 - 38: 34.561 distance: 36 - 37: 56.630 distance: 36 - 43: 56.020 distance: 37 - 73: 55.873 distance: 38 - 39: 7.855 distance: 39 - 40: 40.748 distance: 40 - 42: 66.451 distance: 43 - 44: 55.954 distance: 45 - 46: 40.917 distance: 45 - 52: 39.443 distance: 47 - 48: 56.540 distance: 48 - 49: 15.595 distance: 49 - 50: 45.523 distance: 49 - 51: 13.264 distance: 53 - 54: 39.267 distance: 53 - 56: 23.032 distance: 54 - 61: 25.626 distance: 56 - 57: 40.937 distance: 57 - 58: 50.851 distance: 58 - 59: 10.562 distance: 59 - 60: 40.491 distance: 61 - 62: 24.612 distance: 62 - 63: 68.346 distance: 62 - 65: 39.610 distance: 63 - 73: 40.459 distance: 65 - 66: 43.441 distance: 66 - 67: 44.735 distance: 66 - 68: 45.875 distance: 67 - 69: 39.916 distance: 68 - 70: 39.904 distance: 69 - 71: 31.285 distance: 70 - 71: 8.987 distance: 71 - 72: 56.699 distance: 75 - 76: 40.387 distance: 75 - 77: 40.845 distance: 76 - 100: 69.932 distance: 78 - 79: 41.191 distance: 78 - 81: 55.578 distance: 79 - 80: 40.312 distance: 79 - 86: 28.093 distance: 80 - 107: 31.971 distance: 81 - 82: 39.037 distance: 83 - 84: 40.189 distance: 86 - 87: 48.855 distance: 87 - 88: 39.148 distance: 87 - 90: 41.867 distance: 88 - 89: 38.953 distance: 88 - 92: 51.008 distance: 89 - 114: 35.464 distance: 90 - 91: 40.009 distance: 92 - 93: 30.915 distance: 93 - 96: 41.406 distance: 94 - 95: 38.743 distance: 94 - 100: 39.708 distance: 95 - 122: 34.462 distance: 96 - 97: 39.205 distance: 97 - 98: 40.198 distance: 97 - 99: 43.549 distance: 100 - 101: 55.781 distance: 101 - 104: 40.624 distance: 102 - 103: 39.874 distance: 102 - 107: 33.471 distance: 104 - 106: 39.523