Starting phenix.real_space_refine on Mon Mar 11 07:59:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4x_24180/03_2024/7n4x_24180_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4x_24180/03_2024/7n4x_24180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4x_24180/03_2024/7n4x_24180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4x_24180/03_2024/7n4x_24180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4x_24180/03_2024/7n4x_24180_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4x_24180/03_2024/7n4x_24180_updated.pdb" } resolution = 3.33 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 4992 2.51 5 N 1218 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 534": "OD1" <-> "OD2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 733": "OE1" <-> "OE2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 913": "OE1" <-> "OE2" Residue "A PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1067": "NH1" <-> "NH2" Residue "A ARG 1070": "NH1" <-> "NH2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "A ARG 1081": "NH1" <-> "NH2" Residue "A GLU 1091": "OE1" <-> "OE2" Residue "A PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1187": "NH1" <-> "NH2" Residue "A GLU 1203": "OE1" <-> "OE2" Residue "A GLU 1276": "OE1" <-> "OE2" Residue "A GLU 1282": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7647 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7423 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 50, 'TRANS': 902} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Unusual residues: {'CLR': 3, 'NAG': 4} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.46, per 1000 atoms: 0.58 Number of scatterers: 7647 At special positions: 0 Unit cell: (134.113, 93.296, 79.135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1392 8.00 N 1218 7.00 C 4992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 925 " distance=2.02 Simple disulfide: pdb=" SG CYS A 966 " - pdb=" SG CYS A1024 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 993 " distance=2.03 Simple disulfide: pdb=" SG CYS A 980 " - pdb=" SG CYS A 989 " distance=2.03 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 Atom "HETATM 7561 O5 NAG A1404 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1401 " - " ASN A 431 " " NAG A1402 " - " ASN A 464 " " NAG A1403 " - " ASN A 506 " " NAG A1404 " - " ASN A1075 " " NAG B 1 " - " ASN A 497 " " NAG C 1 " - " ASN A 909 " " NAG D 1 " - " ASN A1037 " Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.4 seconds 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1790 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 7 sheets defined 55.2% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 352 through 372 Proline residue: A 362 - end of helix removed outlier: 4.834A pdb=" N GLY A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 438 through 452 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 518 through 527 Processing helix chain 'A' and resid 552 through 555 No H-bonds generated for 'chain 'A' and resid 552 through 555' Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 586 through 606 Processing helix chain 'A' and resid 620 through 629 removed outlier: 3.618A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 650 removed outlier: 3.903A pdb=" N SER A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 663 No H-bonds generated for 'chain 'A' and resid 660 through 663' Processing helix chain 'A' and resid 666 through 689 Processing helix chain 'A' and resid 702 through 723 removed outlier: 4.671A pdb=" N ASP A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 714 " --> pdb=" O GLY A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 763 Proline residue: A 745 - end of helix removed outlier: 4.595A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 803 removed outlier: 3.563A pdb=" N SER A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 834 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 843 through 866 removed outlier: 4.618A pdb=" N GLY A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N HIS A 866 " --> pdb=" O TYR A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 892 Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 930 through 939 Processing helix chain 'A' and resid 953 through 960 Processing helix chain 'A' and resid 1005 through 1016 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1028 through 1031 No H-bonds generated for 'chain 'A' and resid 1028 through 1031' Processing helix chain 'A' and resid 1059 through 1082 removed outlier: 3.549A pdb=" N ASP A1079 " --> pdb=" O ASN A1075 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1106 No H-bonds generated for 'chain 'A' and resid 1104 through 1106' Processing helix chain 'A' and resid 1109 through 1129 Proline residue: A1122 - end of helix Processing helix chain 'A' and resid 1135 through 1159 Processing helix chain 'A' and resid 1165 through 1190 removed outlier: 4.328A pdb=" N VAL A1179 " --> pdb=" O VAL A1175 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU A1180 " --> pdb=" O GLY A1176 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A1181 " --> pdb=" O MET A1177 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1224 removed outlier: 4.195A pdb=" N MET A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Proline residue: A1222 - end of helix Processing helix chain 'A' and resid 1227 through 1229 No H-bonds generated for 'chain 'A' and resid 1227 through 1229' Processing helix chain 'A' and resid 1233 through 1238 Processing helix chain 'A' and resid 1241 through 1265 removed outlier: 6.350A pdb=" N LEU A1258 " --> pdb=" O GLY A1254 " (cutoff:3.500A) Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1271 through 1275 Processing helix chain 'A' and resid 1277 through 1281 removed outlier: 4.103A pdb=" N GLU A1281 " --> pdb=" O LYS A1278 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 406 through 408 Processing sheet with id= B, first strand: chain 'A' and resid 614 through 616 Processing sheet with id= C, first strand: chain 'A' and resid 420 through 423 Processing sheet with id= D, first strand: chain 'A' and resid 455 through 458 removed outlier: 3.779A pdb=" N ARG A 463 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 505 through 509 Processing sheet with id= F, first strand: chain 'A' and resid 1050 through 1052 Processing sheet with id= G, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 3.786A pdb=" N THR A1046 " --> pdb=" O ASN A1037 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 3.35 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: 1372 1.33 - 1.45: 1956 1.45 - 1.58: 4441 1.58 - 1.70: 0 1.70 - 1.82: 69 Bond restraints: 7838 Sorted by residual: bond pdb=" N ILE A 470 " pdb=" CA ILE A 470 " ideal model delta sigma weight residual 1.456 1.499 -0.042 9.50e-03 1.11e+04 1.98e+01 bond pdb=" N TYR A 579 " pdb=" CA TYR A 579 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.68e+01 bond pdb=" N LEU A 818 " pdb=" CA LEU A 818 " ideal model delta sigma weight residual 1.456 1.491 -0.036 8.70e-03 1.32e+04 1.67e+01 bond pdb=" N LEU A1109 " pdb=" CA LEU A1109 " ideal model delta sigma weight residual 1.463 1.491 -0.028 6.90e-03 2.10e+04 1.63e+01 bond pdb=" N LEU A1221 " pdb=" CA LEU A1221 " ideal model delta sigma weight residual 1.462 1.493 -0.032 8.50e-03 1.38e+04 1.38e+01 ... (remaining 7833 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.74: 265 106.74 - 113.95: 4384 113.95 - 121.17: 3638 121.17 - 128.38: 2365 128.38 - 135.59: 40 Bond angle restraints: 10692 Sorted by residual: angle pdb=" N VAL A 813 " pdb=" CA VAL A 813 " pdb=" C VAL A 813 " ideal model delta sigma weight residual 113.10 108.53 4.57 9.70e-01 1.06e+00 2.22e+01 angle pdb=" C ARG A 846 " pdb=" N GLY A 847 " pdb=" CA GLY A 847 " ideal model delta sigma weight residual 119.94 124.95 -5.01 1.11e+00 8.12e-01 2.03e+01 angle pdb=" C MET A 684 " pdb=" N GLY A 685 " pdb=" CA GLY A 685 " ideal model delta sigma weight residual 119.94 124.94 -5.00 1.11e+00 8.12e-01 2.03e+01 angle pdb=" C SER A1137 " pdb=" N GLY A1138 " pdb=" CA GLY A1138 " ideal model delta sigma weight residual 119.98 124.91 -4.93 1.11e+00 8.12e-01 1.97e+01 angle pdb=" N ARG A1279 " pdb=" CA ARG A1279 " pdb=" C ARG A1279 " ideal model delta sigma weight residual 113.28 107.87 5.41 1.22e+00 6.72e-01 1.97e+01 ... (remaining 10687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.73: 4641 24.73 - 49.47: 245 49.47 - 74.20: 25 74.20 - 98.93: 15 98.93 - 123.66: 4 Dihedral angle restraints: 4930 sinusoidal: 2154 harmonic: 2776 Sorted by residual: dihedral pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 158.22 -65.22 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CA PRO A 815 " pdb=" C PRO A 815 " pdb=" N GLN A 816 " pdb=" CA GLN A 816 " ideal model delta harmonic sigma weight residual -180.00 -154.33 -25.67 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CB CYS A 980 " pdb=" SG CYS A 980 " pdb=" SG CYS A 989 " pdb=" CB CYS A 989 " ideal model delta sinusoidal sigma weight residual 93.00 53.79 39.21 1 1.00e+01 1.00e-02 2.16e+01 ... (remaining 4927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.938: 1269 0.938 - 1.875: 2 1.875 - 2.813: 1 2.813 - 3.750: 0 3.750 - 4.688: 2 Chirality restraints: 1274 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 2.29 -4.69 2.00e-02 2.50e+03 5.49e+04 chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A1075 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 1.70 -4.10 2.00e-01 2.50e+01 4.21e+02 chirality pdb=" C1 NAG A1403 " pdb=" ND2 ASN A 506 " pdb=" C2 NAG A1403 " pdb=" O5 NAG A1403 " both_signs ideal model delta sigma weight residual False -2.40 -0.48 -1.92 2.00e-01 2.50e+01 9.20e+01 ... (remaining 1271 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.247 2.00e-02 2.50e+03 2.05e-01 5.28e+02 pdb=" C7 NAG B 1 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.341 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 431 " -0.115 2.00e-02 2.50e+03 1.88e-01 4.41e+02 pdb=" CG ASN A 431 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 431 " -0.068 2.00e-02 2.50e+03 pdb=" ND2 ASN A 431 " 0.336 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " -0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 909 " -0.149 2.00e-02 2.50e+03 1.66e-01 3.45e+02 pdb=" CG ASN A 909 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN A 909 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 909 " 0.265 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.202 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 125 2.69 - 3.24: 7117 3.24 - 3.79: 11743 3.79 - 4.35: 15672 4.35 - 4.90: 27233 Nonbonded interactions: 61890 Sorted by model distance: nonbonded pdb=" OG SER A 912 " pdb=" O5 NAG C 1 " model vdw 2.134 2.440 nonbonded pdb=" OG SER A 912 " pdb=" O6 NAG C 1 " model vdw 2.148 2.440 nonbonded pdb=" O VAL A 380 " pdb=" OG SER A 384 " model vdw 2.315 2.440 nonbonded pdb=" O GLY A 710 " pdb=" NE2 GLN A 787 " model vdw 2.323 2.520 nonbonded pdb=" O THR A 629 " pdb=" NE2 GLN A 700 " model vdw 2.384 2.520 ... (remaining 61885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 5.150 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.780 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 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 : 0.014 0.050 7838 Z= 0.920 Angle : 1.763 7.704 10692 Z= 1.322 Chirality : 0.211 4.688 1274 Planarity : 0.009 0.205 1321 Dihedral : 15.861 123.663 3122 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.23 % Allowed : 7.40 % Favored : 91.37 % 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: -3.15 (0.23), residues: 951 helix: -1.73 (0.18), residues: 516 sheet: -2.85 (0.54), residues: 62 loop : -2.28 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 960 HIS 0.007 0.002 HIS A1053 PHE 0.039 0.003 PHE A 791 TYR 0.025 0.002 TYR A 646 ARG 0.005 0.001 ARG A 606 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 351 TRP cc_start: 0.6880 (m100) cc_final: 0.6438 (m-10) REVERT: A 483 TYR cc_start: 0.7814 (m-80) cc_final: 0.7557 (m-80) REVERT: A 610 MET cc_start: 0.7717 (ttm) cc_final: 0.7166 (ttm) REVERT: A 657 TRP cc_start: 0.6469 (OUTLIER) cc_final: 0.5110 (t60) REVERT: A 943 GLN cc_start: 0.7452 (mm-40) cc_final: 0.7224 (mt0) REVERT: A 1091 GLU cc_start: 0.7135 (tt0) cc_final: 0.6889 (tt0) REVERT: A 1218 MET cc_start: 0.7734 (mmt) cc_final: 0.7509 (mmm) outliers start: 10 outliers final: 7 residues processed: 109 average time/residue: 0.1861 time to fit residues: 29.1592 Evaluate side-chains 77 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1255 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 397 HIS ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1253 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7838 Z= 0.215 Angle : 0.655 9.599 10692 Z= 0.302 Chirality : 0.043 0.268 1274 Planarity : 0.004 0.031 1321 Dihedral : 9.536 82.220 1442 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 2.10 % Allowed : 9.74 % Favored : 88.16 % 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: -1.07 (0.27), residues: 951 helix: 0.08 (0.22), residues: 550 sheet: -1.81 (0.56), residues: 63 loop : -1.69 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 960 HIS 0.004 0.001 HIS A 397 PHE 0.015 0.002 PHE A 791 TYR 0.015 0.001 TYR A 886 ARG 0.004 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 351 TRP cc_start: 0.6924 (m100) cc_final: 0.6492 (m-10) REVERT: A 517 ASP cc_start: 0.7627 (t0) cc_final: 0.7412 (t0) REVERT: A 560 LYS cc_start: 0.8126 (mmmt) cc_final: 0.7674 (mtpt) REVERT: A 610 MET cc_start: 0.7490 (ttm) cc_final: 0.7228 (ttm) REVERT: A 657 TRP cc_start: 0.6525 (OUTLIER) cc_final: 0.5063 (t60) REVERT: A 874 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: A 943 GLN cc_start: 0.7391 (mm-40) cc_final: 0.7182 (mt0) REVERT: A 1218 MET cc_start: 0.7740 (mmt) cc_final: 0.7487 (mmm) outliers start: 17 outliers final: 11 residues processed: 103 average time/residue: 0.1621 time to fit residues: 24.7080 Evaluate side-chains 85 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1255 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 0.0270 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 0.044 7838 Z= 0.278 Angle : 0.603 9.454 10692 Z= 0.284 Chirality : 0.042 0.280 1274 Planarity : 0.004 0.034 1321 Dihedral : 8.898 79.313 1441 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.97 % Allowed : 12.33 % Favored : 85.70 % 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: -0.70 (0.27), residues: 951 helix: 0.36 (0.23), residues: 543 sheet: -1.36 (0.58), residues: 63 loop : -1.54 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 960 HIS 0.004 0.001 HIS A 842 PHE 0.022 0.002 PHE A1124 TYR 0.015 0.001 TYR A 646 ARG 0.002 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 351 TRP cc_start: 0.6912 (m100) cc_final: 0.6472 (m-10) REVERT: A 517 ASP cc_start: 0.7652 (t0) cc_final: 0.7430 (t0) REVERT: A 560 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7657 (mtpt) REVERT: A 607 MET cc_start: 0.7997 (mmm) cc_final: 0.7765 (mtp) REVERT: A 610 MET cc_start: 0.7610 (ttm) cc_final: 0.7322 (ttm) REVERT: A 657 TRP cc_start: 0.6476 (OUTLIER) cc_final: 0.4997 (t60) REVERT: A 874 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: A 943 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7168 (mt0) REVERT: A 1218 MET cc_start: 0.7828 (mmt) cc_final: 0.7559 (mmm) outliers start: 16 outliers final: 13 residues processed: 93 average time/residue: 0.1356 time to fit residues: 19.6268 Evaluate side-chains 86 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7838 Z= 0.288 Angle : 0.588 9.570 10692 Z= 0.279 Chirality : 0.041 0.289 1274 Planarity : 0.004 0.034 1321 Dihedral : 8.301 76.090 1438 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.34 % Allowed : 13.81 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.27), residues: 951 helix: 0.39 (0.23), residues: 542 sheet: -1.18 (0.59), residues: 63 loop : -1.48 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 960 HIS 0.005 0.001 HIS A 842 PHE 0.021 0.002 PHE A1124 TYR 0.014 0.001 TYR A 646 ARG 0.002 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 351 TRP cc_start: 0.7024 (m100) cc_final: 0.6585 (m-10) REVERT: A 517 ASP cc_start: 0.7679 (t0) cc_final: 0.7404 (t0) REVERT: A 560 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7662 (mtpt) REVERT: A 610 MET cc_start: 0.7597 (ttm) cc_final: 0.6930 (ttm) REVERT: A 657 TRP cc_start: 0.6272 (OUTLIER) cc_final: 0.4870 (t60) REVERT: A 814 LYS cc_start: 0.4018 (mmtt) cc_final: 0.3232 (tptp) REVERT: A 874 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: A 943 GLN cc_start: 0.7373 (mm-40) cc_final: 0.7161 (mt0) REVERT: A 992 ASN cc_start: 0.7839 (m-40) cc_final: 0.7583 (t0) outliers start: 19 outliers final: 13 residues processed: 95 average time/residue: 0.1407 time to fit residues: 20.6223 Evaluate side-chains 91 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1047 SER Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 68 optimal weight: 0.0970 chunk 37 optimal weight: 0.0970 chunk 78 optimal weight: 0.9990 chunk 63 optimal weight: 0.0970 chunk 0 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7838 Z= 0.149 Angle : 0.528 9.573 10692 Z= 0.249 Chirality : 0.039 0.261 1274 Planarity : 0.003 0.031 1321 Dihedral : 7.720 71.303 1438 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.97 % Allowed : 14.80 % Favored : 83.23 % 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: -0.15 (0.27), residues: 951 helix: 0.72 (0.23), residues: 542 sheet: -0.68 (0.60), residues: 63 loop : -1.21 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 960 HIS 0.003 0.001 HIS A 400 PHE 0.021 0.001 PHE A1124 TYR 0.014 0.001 TYR A 646 ARG 0.001 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 351 TRP cc_start: 0.6971 (m100) cc_final: 0.6495 (m-10) REVERT: A 517 ASP cc_start: 0.7711 (t0) cc_final: 0.7394 (t0) REVERT: A 560 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7682 (mtpt) REVERT: A 610 MET cc_start: 0.7488 (ttm) cc_final: 0.6801 (ttm) REVERT: A 616 MET cc_start: 0.7218 (ttt) cc_final: 0.6847 (ttt) REVERT: A 626 ASN cc_start: 0.7168 (m110) cc_final: 0.6713 (m-40) REVERT: A 657 TRP cc_start: 0.6190 (OUTLIER) cc_final: 0.4773 (t60) REVERT: A 851 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.5837 (mm) REVERT: A 943 GLN cc_start: 0.7389 (mm-40) cc_final: 0.7185 (mt0) outliers start: 16 outliers final: 11 residues processed: 100 average time/residue: 0.1347 time to fit residues: 21.1932 Evaluate side-chains 97 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 76 optimal weight: 0.0980 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7838 Z= 0.183 Angle : 0.538 10.147 10692 Z= 0.251 Chirality : 0.039 0.262 1274 Planarity : 0.003 0.031 1321 Dihedral : 7.510 66.510 1437 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.85 % Allowed : 16.28 % Favored : 81.87 % 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: -0.06 (0.27), residues: 951 helix: 0.77 (0.23), residues: 544 sheet: -0.65 (0.60), residues: 63 loop : -1.14 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 960 HIS 0.003 0.001 HIS A 400 PHE 0.022 0.001 PHE A1124 TYR 0.014 0.001 TYR A 646 ARG 0.001 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 351 TRP cc_start: 0.6980 (m100) cc_final: 0.6511 (m-10) REVERT: A 517 ASP cc_start: 0.7693 (t0) cc_final: 0.7359 (t0) REVERT: A 560 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7621 (mtpt) REVERT: A 610 MET cc_start: 0.7552 (ttm) cc_final: 0.6841 (ttm) REVERT: A 616 MET cc_start: 0.7273 (ttt) cc_final: 0.6886 (ttt) REVERT: A 626 ASN cc_start: 0.7157 (m110) cc_final: 0.6708 (m-40) REVERT: A 657 TRP cc_start: 0.6087 (OUTLIER) cc_final: 0.4653 (t60) REVERT: A 814 LYS cc_start: 0.4167 (mmtt) cc_final: 0.3460 (tptp) REVERT: A 851 LEU cc_start: 0.6821 (tt) cc_final: 0.5827 (mm) REVERT: A 874 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: A 943 GLN cc_start: 0.7394 (mm-40) cc_final: 0.7170 (mt0) outliers start: 15 outliers final: 13 residues processed: 102 average time/residue: 0.1421 time to fit residues: 22.1335 Evaluate side-chains 101 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 77 optimal weight: 0.1980 chunk 51 optimal weight: 0.0270 chunk 91 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7838 Z= 0.156 Angle : 0.508 9.588 10692 Z= 0.240 Chirality : 0.038 0.255 1274 Planarity : 0.003 0.030 1321 Dihedral : 7.184 59.404 1437 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.22 % Allowed : 16.40 % Favored : 81.38 % 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: 0.18 (0.28), residues: 951 helix: 0.96 (0.23), residues: 544 sheet: -0.52 (0.60), residues: 63 loop : -1.04 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 960 HIS 0.003 0.001 HIS A 400 PHE 0.023 0.001 PHE A1124 TYR 0.013 0.001 TYR A 646 ARG 0.001 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 351 TRP cc_start: 0.7009 (m100) cc_final: 0.6538 (m-10) REVERT: A 517 ASP cc_start: 0.7715 (t0) cc_final: 0.7339 (t0) REVERT: A 560 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7604 (mtpt) REVERT: A 610 MET cc_start: 0.7508 (ttm) cc_final: 0.6815 (ttm) REVERT: A 616 MET cc_start: 0.7270 (ttt) cc_final: 0.6901 (ttt) REVERT: A 626 ASN cc_start: 0.7112 (m110) cc_final: 0.6678 (m-40) REVERT: A 657 TRP cc_start: 0.5935 (OUTLIER) cc_final: 0.4479 (t60) REVERT: A 814 LYS cc_start: 0.4144 (mmtt) cc_final: 0.3475 (tptp) REVERT: A 851 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.5807 (mm) REVERT: A 943 GLN cc_start: 0.7395 (mm-40) cc_final: 0.7163 (mt0) outliers start: 18 outliers final: 15 residues processed: 102 average time/residue: 0.1505 time to fit residues: 23.0507 Evaluate side-chains 104 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7838 Z= 0.200 Angle : 0.533 10.729 10692 Z= 0.249 Chirality : 0.038 0.265 1274 Planarity : 0.003 0.031 1321 Dihedral : 7.347 59.498 1437 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.59 % Allowed : 16.65 % Favored : 80.76 % 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: 0.15 (0.28), residues: 951 helix: 0.95 (0.23), residues: 539 sheet: -0.69 (0.61), residues: 64 loop : -1.04 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 960 HIS 0.003 0.001 HIS A 842 PHE 0.022 0.001 PHE A1124 TYR 0.014 0.001 TYR A 646 ARG 0.001 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 351 TRP cc_start: 0.7045 (m100) cc_final: 0.6568 (m-10) REVERT: A 517 ASP cc_start: 0.7685 (t0) cc_final: 0.7342 (t0) REVERT: A 560 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7614 (mtpt) REVERT: A 610 MET cc_start: 0.7560 (ttm) cc_final: 0.6850 (ttm) REVERT: A 616 MET cc_start: 0.7272 (ttt) cc_final: 0.6897 (ttt) REVERT: A 626 ASN cc_start: 0.7151 (m110) cc_final: 0.6710 (m-40) REVERT: A 657 TRP cc_start: 0.5871 (OUTLIER) cc_final: 0.4479 (t60) REVERT: A 814 LYS cc_start: 0.4020 (mmtt) cc_final: 0.3510 (tptp) REVERT: A 851 LEU cc_start: 0.6810 (tt) cc_final: 0.5830 (mm) REVERT: A 943 GLN cc_start: 0.7350 (mm-40) cc_final: 0.7123 (mt0) REVERT: A 1104 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7670 (pt0) outliers start: 21 outliers final: 17 residues processed: 101 average time/residue: 0.1395 time to fit residues: 21.7758 Evaluate side-chains 103 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1104 GLN Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 51 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7838 Z= 0.179 Angle : 0.520 9.579 10692 Z= 0.243 Chirality : 0.038 0.264 1274 Planarity : 0.003 0.030 1321 Dihedral : 7.248 59.517 1437 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.34 % Allowed : 16.89 % Favored : 80.76 % 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: 0.22 (0.28), residues: 951 helix: 1.01 (0.23), residues: 539 sheet: -0.61 (0.62), residues: 64 loop : -1.03 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 960 HIS 0.003 0.001 HIS A 842 PHE 0.023 0.001 PHE A1124 TYR 0.014 0.001 TYR A 646 ARG 0.001 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 351 TRP cc_start: 0.7040 (m100) cc_final: 0.6572 (m-10) REVERT: A 517 ASP cc_start: 0.7714 (t0) cc_final: 0.7337 (t0) REVERT: A 560 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7606 (mtpt) REVERT: A 610 MET cc_start: 0.7559 (ttm) cc_final: 0.6847 (ttm) REVERT: A 616 MET cc_start: 0.7272 (ttt) cc_final: 0.6897 (ttt) REVERT: A 626 ASN cc_start: 0.7176 (m110) cc_final: 0.6729 (m-40) REVERT: A 657 TRP cc_start: 0.5907 (OUTLIER) cc_final: 0.4483 (t60) REVERT: A 814 LYS cc_start: 0.4033 (mmtt) cc_final: 0.3544 (tptp) REVERT: A 851 LEU cc_start: 0.6763 (tt) cc_final: 0.5791 (mm) REVERT: A 943 GLN cc_start: 0.7364 (mm-40) cc_final: 0.7118 (mt0) REVERT: A 1104 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7667 (pt0) outliers start: 19 outliers final: 16 residues processed: 102 average time/residue: 0.1558 time to fit residues: 23.9027 Evaluate side-chains 102 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1104 GLN Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 7 optimal weight: 0.0040 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7838 Z= 0.171 Angle : 0.507 9.579 10692 Z= 0.239 Chirality : 0.038 0.263 1274 Planarity : 0.003 0.032 1321 Dihedral : 7.047 59.625 1437 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.47 % Allowed : 17.02 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.28), residues: 951 helix: 1.10 (0.23), residues: 541 sheet: -0.51 (0.63), residues: 64 loop : -1.01 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 960 HIS 0.003 0.001 HIS A 400 PHE 0.024 0.001 PHE A1124 TYR 0.013 0.001 TYR A 646 ARG 0.002 0.000 ARG A 605 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 351 TRP cc_start: 0.7041 (m100) cc_final: 0.6578 (m-10) REVERT: A 517 ASP cc_start: 0.7729 (t0) cc_final: 0.7338 (t0) REVERT: A 560 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7605 (mtpt) REVERT: A 610 MET cc_start: 0.7541 (ttm) cc_final: 0.6814 (ttm) REVERT: A 616 MET cc_start: 0.7289 (ttt) cc_final: 0.6910 (ttt) REVERT: A 626 ASN cc_start: 0.7146 (m110) cc_final: 0.6713 (m-40) REVERT: A 657 TRP cc_start: 0.5940 (OUTLIER) cc_final: 0.4635 (t60) REVERT: A 814 LYS cc_start: 0.4103 (mmtt) cc_final: 0.3696 (tptp) REVERT: A 851 LEU cc_start: 0.6765 (tt) cc_final: 0.5797 (mm) REVERT: A 943 GLN cc_start: 0.7368 (mm-40) cc_final: 0.7119 (mt0) REVERT: A 1104 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7705 (pt0) outliers start: 20 outliers final: 17 residues processed: 102 average time/residue: 0.1594 time to fit residues: 23.9697 Evaluate side-chains 102 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 657 TRP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 966 CYS Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1104 GLN Chi-restraints excluded: chain A residue 1107 THR Chi-restraints excluded: chain A residue 1120 LEU Chi-restraints excluded: chain A residue 1156 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 0.0670 chunk 31 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 54 optimal weight: 0.1980 overall best weight: 0.4320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.129082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.107153 restraints weight = 8911.602| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.34 r_work: 0.3014 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7838 Z= 0.147 Angle : 0.494 9.576 10692 Z= 0.233 Chirality : 0.037 0.256 1274 Planarity : 0.003 0.030 1321 Dihedral : 6.901 59.954 1437 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.22 % Allowed : 17.14 % Favored : 80.64 % 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 (0.28), residues: 951 helix: 1.25 (0.23), residues: 540 sheet: -0.69 (0.60), residues: 70 loop : -0.99 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 960 HIS 0.003 0.001 HIS A 400 PHE 0.024 0.001 PHE A1124 TYR 0.013 0.001 TYR A 646 ARG 0.004 0.000 ARG A 463 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1793.79 seconds wall clock time: 33 minutes 14.57 seconds (1994.57 seconds total)