Starting phenix.real_space_refine on Sat Apr 6 02:30:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pda_17608/04_2024/8pda_17608_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pda_17608/04_2024/8pda_17608.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pda_17608/04_2024/8pda_17608_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pda_17608/04_2024/8pda_17608_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pda_17608/04_2024/8pda_17608_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pda_17608/04_2024/8pda_17608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pda_17608/04_2024/8pda_17608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pda_17608/04_2024/8pda_17608_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pda_17608/04_2024/8pda_17608_updated.pdb" } resolution = 3.58 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= 0.008 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 29 5.16 5 C 4413 2.51 5 N 1110 2.21 5 O 1180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 714": "OD1" <-> "OD2" Residue "A ASP 722": "OD1" <-> "OD2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A GLU 798": "OE1" <-> "OE2" Residue "A TYR 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 938": "OE1" <-> "OE2" Residue "A TYR 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 960": "OD1" <-> "OD2" Residue "A TYR 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6736 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 6563 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 378} Link IDs: {'PTRANS': 38, 'TRANS': 934} Chain breaks: 11 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1456 Unresolved non-hydrogen angles: 1867 Unresolved non-hydrogen dihedrals: 1257 Unresolved non-hydrogen chiralities: 124 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 20, 'TYR:plan': 20, 'ASN:plan1': 18, 'TRP:plan': 9, 'HIS:plan': 10, 'PHE:plan': 30, 'GLU:plan': 28, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 803 Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 173 Unusual residues: {'PCW': 3, 'PX6': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 4.27, per 1000 atoms: 0.63 Number of scatterers: 6736 At special positions: 0 Unit cell: (111.507, 97.888, 137.894, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 4 15.00 O 1180 8.00 N 1110 7.00 C 4413 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: 2.87 Conformation dependent library (CDL) restraints added in 1.3 seconds 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1850 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 1 sheets defined 68.0% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 67 through 76 Processing helix chain 'A' and resid 108 through 111 Processing helix chain 'A' and resid 114 through 161 Proline residue: A 146 - end of helix Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.970A pdb=" N ILE A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 225 removed outlier: 3.933A pdb=" N GLN A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLN A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 469 through 524 removed outlier: 3.574A pdb=" N PHE A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 477 " --> pdb=" O ILE A 473 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA A 479 " --> pdb=" O TYR A 475 " (cutoff:3.500A) Proline residue: A 494 - end of helix removed outlier: 3.918A pdb=" N GLY A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 534 removed outlier: 4.046A pdb=" N LYS A 534 " --> pdb=" O ASN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 562 removed outlier: 3.566A pdb=" N ILE A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 553 " --> pdb=" O HIS A 549 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 Proline residue: A 576 - end of helix Processing helix chain 'A' and resid 608 through 654 removed outlier: 3.706A pdb=" N LEU A 612 " --> pdb=" O PRO A 608 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 634 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE A 637 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Proline residue: A 638 - end of helix removed outlier: 5.094A pdb=" N CYS A 651 " --> pdb=" O PHE A 647 " (cutoff:3.500A) Proline residue: A 652 - end of helix Processing helix chain 'A' and resid 663 through 666 No H-bonds generated for 'chain 'A' and resid 663 through 666' Processing helix chain 'A' and resid 671 through 697 removed outlier: 3.820A pdb=" N VAL A 677 " --> pdb=" O SER A 674 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR A 678 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 725 removed outlier: 3.949A pdb=" N ILE A 725 " --> pdb=" O HIS A 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 721 through 725' Processing helix chain 'A' and resid 728 through 755 Processing helix chain 'A' and resid 771 through 773 No H-bonds generated for 'chain 'A' and resid 771 through 773' Processing helix chain 'A' and resid 781 through 798 removed outlier: 3.763A pdb=" N ILE A 786 " --> pdb=" O LYS A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 821 removed outlier: 3.628A pdb=" N LYS A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 828 No H-bonds generated for 'chain 'A' and resid 825 through 828' Processing helix chain 'A' and resid 834 through 836 No H-bonds generated for 'chain 'A' and resid 834 through 836' Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 852 through 857 Processing helix chain 'A' and resid 869 through 878 Processing helix chain 'A' and resid 906 through 908 No H-bonds generated for 'chain 'A' and resid 906 through 908' Processing helix chain 'A' and resid 926 through 936 Processing helix chain 'A' and resid 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' Processing helix chain 'A' and resid 964 through 1006 removed outlier: 3.666A pdb=" N LEU A 968 " --> pdb=" O ARG A 964 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU A 969 " --> pdb=" O TYR A 965 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) Proline residue: A1001 - end of helix Processing helix chain 'A' and resid 1014 through 1020 Processing helix chain 'A' and resid 1030 through 1050 Processing helix chain 'A' and resid 1095 through 1105 removed outlier: 3.610A pdb=" N SER A1103 " --> pdb=" O ALA A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1146 removed outlier: 3.659A pdb=" N ALA A1119 " --> pdb=" O MET A1115 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A1140 " --> pdb=" O ASP A1136 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS A1141 " --> pdb=" O GLY A1137 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR A1142 " --> pdb=" O ILE A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1163 removed outlier: 3.684A pdb=" N TRP A1162 " --> pdb=" O GLY A1158 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE A1163 " --> pdb=" O ASN A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1194 removed outlier: 4.079A pdb=" N LEU A1169 " --> pdb=" O TYR A1165 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU A1170 " --> pdb=" O ASP A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1233 Proline residue: A1225 - end of helix Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1267 through 1308 removed outlier: 3.708A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A1305 " --> pdb=" O VAL A1301 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 891 through 896 removed outlier: 3.823A pdb=" N VAL A 891 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 895 " --> pdb=" O TYR A 953 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1320 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: 1.96 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1097 1.32 - 1.44: 1760 1.44 - 1.57: 3946 1.57 - 1.69: 7 1.69 - 1.81: 48 Bond restraints: 6858 Sorted by residual: bond pdb=" C GLU A1304 " pdb=" O GLU A1304 " ideal model delta sigma weight residual 1.237 1.316 -0.079 1.17e-02 7.31e+03 4.57e+01 bond pdb=" CA SER A 799 " pdb=" CB SER A 799 " ideal model delta sigma weight residual 1.526 1.456 0.070 1.51e-02 4.39e+03 2.13e+01 bond pdb=" CA SER A 800 " pdb=" CB SER A 800 " ideal model delta sigma weight residual 1.537 1.457 0.081 1.76e-02 3.23e+03 2.09e+01 bond pdb=" N ILE A 111 " pdb=" CA ILE A 111 " ideal model delta sigma weight residual 1.461 1.510 -0.049 1.23e-02 6.61e+03 1.57e+01 bond pdb=" N VAL A 957 " pdb=" CA VAL A 957 " ideal model delta sigma weight residual 1.457 1.492 -0.035 9.00e-03 1.23e+04 1.49e+01 ... (remaining 6853 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.90: 140 105.90 - 112.92: 3631 112.92 - 119.94: 2356 119.94 - 126.95: 3168 126.95 - 133.97: 53 Bond angle restraints: 9348 Sorted by residual: angle pdb=" CA GLU A 798 " pdb=" C GLU A 798 " pdb=" N SER A 799 " ideal model delta sigma weight residual 117.30 123.36 -6.06 1.16e+00 7.43e-01 2.73e+01 angle pdb=" N VAL A 803 " pdb=" CA VAL A 803 " pdb=" C VAL A 803 " ideal model delta sigma weight residual 112.12 108.35 3.77 8.40e-01 1.42e+00 2.02e+01 angle pdb=" O GLU A 798 " pdb=" C GLU A 798 " pdb=" N SER A 799 " ideal model delta sigma weight residual 122.12 117.52 4.60 1.06e+00 8.90e-01 1.88e+01 angle pdb=" N TYR A 802 " pdb=" CA TYR A 802 " pdb=" C TYR A 802 " ideal model delta sigma weight residual 111.56 105.70 5.86 1.38e+00 5.25e-01 1.80e+01 angle pdb=" C GLU A 798 " pdb=" N SER A 799 " pdb=" CA SER A 799 " ideal model delta sigma weight residual 122.06 116.43 5.63 1.39e+00 5.18e-01 1.64e+01 ... (remaining 9343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3603 17.86 - 35.72: 314 35.72 - 53.58: 79 53.58 - 71.44: 30 71.44 - 89.30: 4 Dihedral angle restraints: 4030 sinusoidal: 1183 harmonic: 2847 Sorted by residual: dihedral pdb=" C HIS A 94 " pdb=" N HIS A 94 " pdb=" CA HIS A 94 " pdb=" CB HIS A 94 " ideal model delta harmonic sigma weight residual -122.60 -133.00 10.40 0 2.50e+00 1.60e-01 1.73e+01 dihedral pdb=" CA MET A 65 " pdb=" C MET A 65 " pdb=" N HIS A 66 " pdb=" CA HIS A 66 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA TYR A 965 " pdb=" C TYR A 965 " pdb=" N MET A 966 " pdb=" CA MET A 966 " ideal model delta harmonic sigma weight residual 180.00 163.24 16.76 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 4027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 997 0.072 - 0.143: 108 0.143 - 0.215: 24 0.215 - 0.287: 3 0.287 - 0.358: 2 Chirality restraints: 1134 Sorted by residual: chirality pdb=" CA HIS A 94 " pdb=" N HIS A 94 " pdb=" C HIS A 94 " pdb=" CB HIS A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ARG A 43 " pdb=" N ARG A 43 " pdb=" C ARG A 43 " pdb=" CB ARG A 43 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ARG A 894 " pdb=" N ARG A 894 " pdb=" C ARG A 894 " pdb=" CB ARG A 894 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1131 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 PCW A1703 " -0.072 2.00e-02 2.50e+03 7.11e-02 5.06e+01 pdb=" C19 PCW A1703 " 0.076 2.00e-02 2.50e+03 pdb=" C20 PCW A1703 " 0.066 2.00e-02 2.50e+03 pdb=" C21 PCW A1703 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 PCW A1703 " 0.058 2.00e-02 2.50e+03 5.85e-02 3.42e+01 pdb=" C39 PCW A1703 " -0.055 2.00e-02 2.50e+03 pdb=" C40 PCW A1703 " -0.062 2.00e-02 2.50e+03 pdb=" C41 PCW A1703 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 111 " 0.025 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C ILE A 111 " -0.082 2.00e-02 2.50e+03 pdb=" O ILE A 111 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO A 112 " 0.029 2.00e-02 2.50e+03 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 849 2.75 - 3.29: 6459 3.29 - 3.83: 10714 3.83 - 4.36: 10226 4.36 - 4.90: 19521 Nonbonded interactions: 47769 Sorted by model distance: nonbonded pdb=" O GLN A 98 " pdb=" CB GLU A1313 " model vdw 2.217 3.440 nonbonded pdb=" NZ LYS A 154 " pdb=" O2P PCW A1702 " model vdw 2.325 2.520 nonbonded pdb=" O LYS A 567 " pdb=" ND1 HIS A 568 " model vdw 2.340 2.520 nonbonded pdb=" OG SER A1024 " pdb=" OD1 ASN A1029 " model vdw 2.390 2.440 nonbonded pdb=" N ASP A 169 " pdb=" OD1 ASP A 169 " model vdw 2.419 2.520 ... (remaining 47764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.080 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 22.640 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 : 0.006 0.081 6858 Z= 0.443 Angle : 0.825 8.957 9348 Z= 0.523 Chirality : 0.052 0.358 1134 Planarity : 0.006 0.071 1174 Dihedral : 16.041 89.305 2180 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.40 % Allowed : 28.77 % Favored : 70.82 % 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: 1.89 (0.28), residues: 949 helix: 2.79 (0.21), residues: 635 sheet: -1.30 (1.31), residues: 16 loop : -2.25 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 149 HIS 0.004 0.001 HIS A 753 PHE 0.010 0.001 PHE A 496 TYR 0.013 0.001 TYR A 965 ARG 0.001 0.000 ARG A 702 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.712 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 75 average time/residue: 0.1464 time to fit residues: 15.9079 Evaluate side-chains 69 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6858 Z= 0.259 Angle : 0.518 5.434 9348 Z= 0.276 Chirality : 0.039 0.132 1134 Planarity : 0.005 0.045 1174 Dihedral : 9.202 81.666 1158 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 3.82 % Allowed : 27.77 % Favored : 68.41 % 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: 1.87 (0.28), residues: 949 helix: 2.56 (0.20), residues: 640 sheet: -1.06 (1.38), residues: 16 loop : -1.81 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 149 HIS 0.005 0.001 HIS A 753 PHE 0.014 0.001 PHE A 993 TYR 0.016 0.001 TYR A 965 ARG 0.002 0.000 ARG A 697 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 698 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8425 (pttp) REVERT: A 893 MET cc_start: 0.8132 (mtp) cc_final: 0.7803 (mtp) outliers start: 19 outliers final: 11 residues processed: 81 average time/residue: 0.1451 time to fit residues: 17.3978 Evaluate side-chains 75 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 698 LYS Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 802 TYR Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1024 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.5980 chunk 27 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 95 optimal weight: 30.0000 chunk 78 optimal weight: 4.9990 chunk 87 optimal weight: 50.0000 chunk 30 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6858 Z= 0.297 Angle : 0.530 5.328 9348 Z= 0.283 Chirality : 0.040 0.142 1134 Planarity : 0.004 0.048 1174 Dihedral : 9.628 84.527 1156 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 5.84 % Allowed : 27.77 % Favored : 66.40 % 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: 1.84 (0.28), residues: 949 helix: 2.51 (0.21), residues: 638 sheet: -1.18 (1.31), residues: 16 loop : -1.68 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 149 HIS 0.005 0.001 HIS A 753 PHE 0.014 0.001 PHE A 647 TYR 0.017 0.001 TYR A 965 ARG 0.002 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 66 time to evaluate : 0.807 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 86 average time/residue: 0.1327 time to fit residues: 17.0848 Evaluate side-chains 82 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 802 TYR Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1024 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 50.0000 chunk 66 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 46 optimal weight: 0.0170 chunk 83 optimal weight: 50.0000 chunk 25 optimal weight: 3.9990 overall best weight: 3.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 6858 Z= 0.453 Angle : 0.628 5.975 9348 Z= 0.333 Chirality : 0.043 0.154 1134 Planarity : 0.005 0.054 1174 Dihedral : 9.875 72.754 1156 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 7.24 % Allowed : 26.96 % Favored : 65.79 % 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: 1.57 (0.29), residues: 949 helix: 2.26 (0.21), residues: 639 sheet: -1.49 (1.27), residues: 16 loop : -1.70 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 662 HIS 0.007 0.001 HIS A 753 PHE 0.019 0.002 PHE A 647 TYR 0.016 0.002 TYR A 965 ARG 0.002 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 63 time to evaluate : 0.814 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 93 average time/residue: 0.1411 time to fit residues: 19.5911 Evaluate side-chains 88 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 802 TYR Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1040 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 50.0000 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6858 Z= 0.157 Angle : 0.462 6.235 9348 Z= 0.245 Chirality : 0.038 0.179 1134 Planarity : 0.004 0.046 1174 Dihedral : 9.184 84.901 1156 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.82 % Allowed : 31.19 % Favored : 66.00 % 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: 2.04 (0.29), residues: 949 helix: 2.61 (0.21), residues: 634 sheet: -0.85 (1.34), residues: 16 loop : -1.44 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 688 HIS 0.005 0.001 HIS A 753 PHE 0.010 0.001 PHE A 614 TYR 0.015 0.001 TYR A 965 ARG 0.001 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.680 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 78 average time/residue: 0.1433 time to fit residues: 16.6448 Evaluate side-chains 73 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 802 TYR Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1040 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 40.0000 chunk 49 optimal weight: 0.5980 chunk 90 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6858 Z= 0.196 Angle : 0.474 5.578 9348 Z= 0.251 Chirality : 0.038 0.144 1134 Planarity : 0.004 0.044 1174 Dihedral : 9.033 81.490 1156 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.82 % Allowed : 30.38 % Favored : 65.79 % 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: 2.06 (0.29), residues: 949 helix: 2.59 (0.21), residues: 641 sheet: -0.87 (1.36), residues: 16 loop : -1.45 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 149 HIS 0.005 0.001 HIS A 753 PHE 0.011 0.001 PHE A 647 TYR 0.015 0.001 TYR A 965 ARG 0.001 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 0.744 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 77 average time/residue: 0.1357 time to fit residues: 15.6050 Evaluate side-chains 78 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 802 TYR Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 949 TYR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1040 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 58 optimal weight: 40.0000 chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 57 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6858 Z= 0.148 Angle : 0.457 7.689 9348 Z= 0.239 Chirality : 0.038 0.159 1134 Planarity : 0.004 0.043 1174 Dihedral : 8.752 85.891 1156 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.42 % Allowed : 30.38 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.29), residues: 949 helix: 2.70 (0.21), residues: 639 sheet: -0.68 (1.41), residues: 16 loop : -1.39 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 688 HIS 0.004 0.001 HIS A 753 PHE 0.009 0.001 PHE A 647 TYR 0.014 0.001 TYR A 965 ARG 0.001 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.702 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 17 residues processed: 77 average time/residue: 0.1436 time to fit residues: 16.5850 Evaluate side-chains 81 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 802 TYR Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1040 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.3980 chunk 28 optimal weight: 30.0000 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 40.0000 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 8 optimal weight: 40.0000 chunk 73 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 89 optimal weight: 30.0000 chunk 81 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6858 Z= 0.336 Angle : 0.556 6.553 9348 Z= 0.293 Chirality : 0.041 0.140 1134 Planarity : 0.004 0.044 1174 Dihedral : 9.217 76.657 1156 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.02 % Allowed : 29.98 % Favored : 66.00 % 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: 1.97 (0.29), residues: 949 helix: 2.48 (0.21), residues: 646 sheet: -0.69 (1.43), residues: 16 loop : -1.46 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 149 HIS 0.007 0.001 HIS A 753 PHE 0.014 0.001 PHE A 647 TYR 0.015 0.002 TYR A 965 ARG 0.003 0.000 ARG A 702 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 0.688 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 77 average time/residue: 0.1376 time to fit residues: 15.8626 Evaluate side-chains 80 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 802 TYR Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1040 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 50.0000 chunk 89 optimal weight: 30.0000 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 26 optimal weight: 40.0000 chunk 78 optimal weight: 5.9990 chunk 82 optimal weight: 30.0000 chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 92 optimal weight: 50.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 6858 Z= 0.422 Angle : 0.622 6.289 9348 Z= 0.328 Chirality : 0.043 0.149 1134 Planarity : 0.005 0.046 1174 Dihedral : 9.585 73.605 1156 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.43 % Allowed : 29.98 % Favored : 65.59 % 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: 1.66 (0.29), residues: 949 helix: 2.25 (0.21), residues: 648 sheet: -0.95 (1.36), residues: 16 loop : -1.60 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 662 HIS 0.007 0.001 HIS A 753 PHE 0.016 0.002 PHE A 647 TYR 0.016 0.002 TYR A 965 ARG 0.003 0.000 ARG A 702 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.743 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 18 residues processed: 80 average time/residue: 0.1404 time to fit residues: 16.4329 Evaluate side-chains 79 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 802 TYR Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1040 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 96 optimal weight: 50.0000 chunk 88 optimal weight: 20.0000 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 50.0000 chunk 81 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6858 Z= 0.172 Angle : 0.480 6.999 9348 Z= 0.252 Chirality : 0.038 0.158 1134 Planarity : 0.004 0.045 1174 Dihedral : 8.740 84.854 1156 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.02 % Allowed : 31.39 % Favored : 65.59 % 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: 2.05 (0.29), residues: 949 helix: 2.57 (0.21), residues: 642 sheet: -0.61 (1.44), residues: 16 loop : -1.45 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 688 HIS 0.005 0.001 HIS A 753 PHE 0.023 0.001 PHE A 993 TYR 0.015 0.001 TYR A 965 ARG 0.001 0.000 ARG A 755 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.730 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 15 residues processed: 73 average time/residue: 0.1415 time to fit residues: 15.6179 Evaluate side-chains 75 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 802 TYR Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1040 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 11 optimal weight: 0.0770 chunk 21 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 14 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 50.0000 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.214026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.182898 restraints weight = 9634.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.175189 restraints weight = 14562.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.164898 restraints weight = 10586.928| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6858 Z= 0.204 Angle : 0.511 11.484 9348 Z= 0.263 Chirality : 0.039 0.142 1134 Planarity : 0.004 0.044 1174 Dihedral : 8.656 82.089 1156 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.82 % Allowed : 32.19 % Favored : 64.99 % 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: 2.15 (0.29), residues: 949 helix: 2.61 (0.21), residues: 646 sheet: -0.55 (1.45), residues: 16 loop : -1.36 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 149 HIS 0.005 0.001 HIS A 753 PHE 0.024 0.001 PHE A 993 TYR 0.015 0.001 TYR A 965 ARG 0.002 0.000 ARG A 702 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1352.48 seconds wall clock time: 26 minutes 30.98 seconds (1590.98 seconds total)