Starting phenix.real_space_refine on Mon Mar 11 00:25:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd0_17597/03_2024/8pd0_17597_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd0_17597/03_2024/8pd0_17597.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd0_17597/03_2024/8pd0_17597_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/8pd0_17597/03_2024/8pd0_17597_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd0_17597/03_2024/8pd0_17597_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd0_17597/03_2024/8pd0_17597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd0_17597/03_2024/8pd0_17597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd0_17597/03_2024/8pd0_17597_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd0_17597/03_2024/8pd0_17597_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 4137 2.51 5 N 1017 2.21 5 O 1087 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 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-5265/modules/chem_data/mon_lib" Total number of atoms: 6274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 6101 Classifications: {'peptide': 880} Incomplete info: {'truncation_to_alanine': 298} Link IDs: {'PTRANS': 31, 'TRANS': 848} Chain breaks: 11 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1171 Unresolved non-hydrogen angles: 1506 Unresolved non-hydrogen dihedrals: 1012 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 7, 'TYR:plan': 16, 'ASN:plan1': 14, 'TRP:plan': 8, 'ASP:plan': 14, 'PHE:plan': 27, 'GLU:plan': 21, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 651 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: 4.10, per 1000 atoms: 0.65 Number of scatterers: 6274 At special positions: 0 Unit cell: (82.5664, 97.888, 137.043, 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 1087 8.00 N 1017 7.00 C 4137 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: 2.78 Conformation dependent library (CDL) restraints added in 1.2 seconds 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1674 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 1 sheets defined 72.8% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 113 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 1303 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) 455 hydrogen bonds defined for protein. 1296 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: 1.90 Time building geometry restraints manager: 3.02 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: 1001 1.32 - 1.44: 1670 1.44 - 1.57: 3669 1.57 - 1.69: 7 1.69 - 1.81: 48 Bond restraints: 6395 Sorted by residual: 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 bond pdb=" C4 PX6 A1704 " pdb=" O5 PX6 A1704 " ideal model delta sigma weight residual 1.399 1.329 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C ARG A 894 " pdb=" N VAL A 895 " ideal model delta sigma weight residual 1.329 1.299 0.030 1.00e-02 1.00e+04 8.90e+00 bond pdb=" C2 PX6 A1704 " pdb=" O7 PX6 A1704 " ideal model delta sigma weight residual 1.399 1.457 -0.058 2.00e-02 2.50e+03 8.44e+00 bond pdb=" N VAL A 955 " pdb=" CA VAL A 955 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.37e+00 ... (remaining 6390 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.90: 132 105.90 - 112.92: 3400 112.92 - 119.94: 2130 119.94 - 126.95: 2988 126.95 - 133.97: 52 Bond angle restraints: 8702 Sorted by residual: angle pdb=" C TYR A 956 " pdb=" N VAL A 957 " pdb=" CA VAL A 957 " ideal model delta sigma weight residual 123.33 120.23 3.10 8.70e-01 1.32e+00 1.27e+01 angle pdb=" CA ARG A 894 " pdb=" C ARG A 894 " pdb=" O ARG A 894 " ideal model delta sigma weight residual 120.38 116.99 3.39 1.09e+00 8.42e-01 9.65e+00 angle pdb=" CA PRO A 958 " pdb=" C PRO A 958 " pdb=" N PRO A 959 " ideal model delta sigma weight residual 117.93 121.58 -3.65 1.20e+00 6.94e-01 9.26e+00 angle pdb=" C5 PX6 A1704 " pdb=" C4 PX6 A1704 " pdb=" O5 PX6 A1704 " ideal model delta sigma weight residual 120.00 111.04 8.96 3.00e+00 1.11e-01 8.91e+00 angle pdb=" C ARG A 894 " pdb=" N VAL A 895 " pdb=" CA VAL A 895 " ideal model delta sigma weight residual 121.88 126.27 -4.39 1.63e+00 3.76e-01 7.26e+00 ... (remaining 8697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3330 17.86 - 35.72: 315 35.72 - 53.58: 79 53.58 - 71.44: 30 71.44 - 89.30: 4 Dihedral angle restraints: 3758 sinusoidal: 1180 harmonic: 2578 Sorted by residual: 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 dihedral pdb=" N ASN A 150 " pdb=" CA ASN A 150 " pdb=" CB ASN A 150 " pdb=" CG ASN A 150 " ideal model delta sinusoidal sigma weight residual -180.00 -120.21 -59.79 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG A 225 " pdb=" CB ARG A 225 " pdb=" CG ARG A 225 " pdb=" CD ARG A 225 " ideal model delta sinusoidal sigma weight residual 180.00 120.44 59.56 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 834 0.049 - 0.097: 185 0.097 - 0.146: 25 0.146 - 0.194: 1 0.194 - 0.243: 1 Chirality restraints: 1046 Sorted by residual: 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 chirality pdb=" CB VAL A 955 " pdb=" CA VAL A 955 " pdb=" CG1 VAL A 955 " pdb=" CG2 VAL A 955 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA VAL A 955 " pdb=" N VAL A 955 " pdb=" C VAL A 955 " pdb=" CB VAL A 955 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1043 not shown) Planarity restraints: 1080 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=" C18 PCW A1702 " 0.048 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C19 PCW A1702 " -0.050 2.00e-02 2.50e+03 pdb=" C20 PCW A1702 " -0.044 2.00e-02 2.50e+03 pdb=" C21 PCW A1702 " 0.046 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2128 2.84 - 3.35: 6023 3.35 - 3.87: 9681 3.87 - 4.38: 9324 4.38 - 4.90: 17843 Nonbonded interactions: 44999 Sorted by model distance: 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 nonbonded pdb=" O TRP A 781 " pdb=" OG1 THR A 785 " model vdw 2.441 2.440 ... (remaining 44994 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: 3.340 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: 6.190 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 22.300 Find NCS groups from input model: 0.190 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 : 0.004 0.070 6395 Z= 0.290 Angle : 0.629 8.957 8702 Z= 0.299 Chirality : 0.039 0.243 1046 Planarity : 0.005 0.071 1080 Dihedral : 16.375 89.305 2084 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.40 % Allowed : 28.63 % Favored : 70.97 % 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: 2.27 (0.30), residues: 856 helix: 2.85 (0.21), residues: 616 sheet: -1.30 (1.31), residues: 16 loop : -2.43 (0.37), residues: 224 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) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.715 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 69 average time/residue: 0.1528 time to fit residues: 15.0687 Evaluate side-chains 64 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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: 88 random chunks: chunk 74 optimal weight: 50.0000 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.0050 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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: 0.7751 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6395 Z= 0.204 Angle : 0.479 5.801 8702 Z= 0.256 Chirality : 0.038 0.130 1046 Planarity : 0.004 0.043 1080 Dihedral : 9.203 87.844 1065 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.62 % Allowed : 27.82 % Favored : 69.56 % 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: 2.26 (0.30), residues: 856 helix: 2.73 (0.21), residues: 622 sheet: -1.05 (1.35), residues: 16 loop : -2.23 (0.40), residues: 218 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 0.013 0.001 PHE A 993 TYR 0.015 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) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 893 MET cc_start: 0.8069 (mtp) cc_final: 0.7731 (mtp) outliers start: 13 outliers final: 6 residues processed: 73 average time/residue: 0.1462 time to fit residues: 15.5251 Evaluate side-chains 67 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 765 ASN Chi-restraints excluded: chain A residue 947 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 80 optimal weight: 20.0000 chunk 86 optimal weight: 100.0000 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: 0.7744 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6395 Z= 0.185 Angle : 0.461 5.281 8702 Z= 0.245 Chirality : 0.037 0.132 1046 Planarity : 0.004 0.042 1080 Dihedral : 8.885 86.324 1063 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.23 % Allowed : 27.22 % Favored : 69.56 % 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: 2.34 (0.30), residues: 856 helix: 2.78 (0.21), residues: 620 sheet: -0.49 (1.40), residues: 16 loop : -2.17 (0.40), residues: 220 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 0.009 0.001 PHE A 647 TYR 0.015 0.001 TYR A 965 ARG 0.001 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.768 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 72 average time/residue: 0.1440 time to fit residues: 15.7019 Evaluate side-chains 69 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 765 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 80 optimal weight: 50.0000 chunk 85 optimal weight: 50.0000 chunk 76 optimal weight: 50.0000 chunk 22 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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: 0.7884 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 6395 Z= 0.473 Angle : 0.627 5.683 8702 Z= 0.333 Chirality : 0.043 0.151 1046 Planarity : 0.005 0.048 1080 Dihedral : 10.233 83.914 1063 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.65 % Allowed : 27.02 % Favored : 67.34 % 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: 1.88 (0.30), residues: 856 helix: 2.47 (0.21), residues: 623 sheet: -1.20 (1.25), residues: 16 loop : -2.46 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 662 HIS 0.006 0.001 HIS A 753 PHE 0.018 0.002 PHE A 647 TYR 0.018 0.002 TYR A1027 ARG 0.002 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 58 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 807 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7713 (mp) outliers start: 28 outliers final: 16 residues processed: 79 average time/residue: 0.1343 time to fit residues: 15.6668 Evaluate side-chains 76 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 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 807 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 0.0270 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.9042 ------------------------------------------------------------------------------- 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: 0.7769 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6395 Z= 0.181 Angle : 0.477 5.858 8702 Z= 0.252 Chirality : 0.038 0.155 1046 Planarity : 0.004 0.044 1080 Dihedral : 9.739 86.459 1063 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.02 % Allowed : 29.64 % Favored : 67.34 % 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 (0.30), residues: 856 helix: 2.68 (0.21), residues: 616 sheet: -0.69 (1.33), residues: 16 loop : -2.12 (0.41), residues: 224 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 0.011 0.001 PHE A 614 TYR 0.016 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) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.623 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 74 average time/residue: 0.1348 time to fit residues: 14.6646 Evaluate side-chains 73 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 684 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 788 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 50.0000 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.0010 chunk 20 optimal weight: 7.9990 chunk 85 optimal weight: 50.0000 chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- 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: 0.7799 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6395 Z= 0.234 Angle : 0.496 5.365 8702 Z= 0.262 Chirality : 0.039 0.129 1046 Planarity : 0.004 0.045 1080 Dihedral : 9.632 80.476 1063 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.44 % Allowed : 28.83 % Favored : 66.73 % 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: 2.27 (0.30), residues: 856 helix: 2.75 (0.21), residues: 617 sheet: -0.75 (1.34), residues: 16 loop : -2.17 (0.42), residues: 223 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 614 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) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.752 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 18 residues processed: 78 average time/residue: 0.1332 time to fit residues: 15.2924 Evaluate side-chains 80 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 490 SER 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 684 LEU Chi-restraints excluded: chain A residue 695 MET 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 788 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7748 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6395 Z= 0.170 Angle : 0.467 5.606 8702 Z= 0.245 Chirality : 0.037 0.136 1046 Planarity : 0.004 0.043 1080 Dihedral : 9.288 84.592 1063 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.43 % Allowed : 29.84 % Favored : 66.73 % 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: 2.39 (0.31), residues: 856 helix: 2.83 (0.21), residues: 617 sheet: -0.59 (1.41), residues: 16 loop : -2.09 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 149 HIS 0.005 0.001 HIS A 753 PHE 0.010 0.001 PHE A 647 TYR 0.015 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) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 0.678 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 74 average time/residue: 0.1421 time to fit residues: 15.2018 Evaluate side-chains 77 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 665 SER Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 788 LEU 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: 88 random chunks: chunk 50 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 40.0000 chunk 57 optimal weight: 0.0010 chunk 41 optimal weight: 0.0370 chunk 7 optimal weight: 0.0770 chunk 66 optimal weight: 3.9990 chunk 77 optimal weight: 80.0000 chunk 81 optimal weight: 10.0000 chunk 74 optimal weight: 50.0000 overall best weight: 1.2226 ------------------------------------------------------------------------------- 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: 0.7782 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6395 Z= 0.218 Angle : 0.485 5.634 8702 Z= 0.256 Chirality : 0.038 0.129 1046 Planarity : 0.004 0.044 1080 Dihedral : 9.162 81.713 1063 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.23 % Allowed : 29.03 % Favored : 66.73 % 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: 2.36 (0.31), residues: 856 helix: 2.80 (0.21), residues: 618 sheet: -0.45 (1.46), residues: 16 loop : -2.12 (0.42), residues: 222 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 0.010 0.001 PHE A 647 TYR 0.014 0.001 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) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 61 time to evaluate : 0.738 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 21 residues processed: 77 average time/residue: 0.1378 time to fit residues: 15.7577 Evaluate side-chains 82 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 61 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 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 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 695 MET 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 788 LEU 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: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 74 optimal weight: 50.0000 chunk 78 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 83 optimal weight: 50.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7746 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6395 Z= 0.166 Angle : 0.465 6.035 8702 Z= 0.244 Chirality : 0.037 0.132 1046 Planarity : 0.004 0.043 1080 Dihedral : 8.940 84.363 1063 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.63 % Allowed : 29.84 % Favored : 66.53 % 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: 2.38 (0.31), residues: 856 helix: 2.82 (0.21), residues: 621 sheet: -0.39 (1.48), residues: 16 loop : -2.23 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 149 HIS 0.004 0.001 HIS A 753 PHE 0.009 0.001 PHE A 614 TYR 0.015 0.001 TYR A 965 ARG 0.002 0.000 ARG A 702 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.694 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 16 residues processed: 77 average time/residue: 0.1359 time to fit residues: 15.4358 Evaluate side-chains 79 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 665 SER Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 788 LEU 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: 88 random chunks: chunk 51 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 50.0000 chunk 80 optimal weight: 30.0000 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 0.0070 chunk 53 optimal weight: 40.0000 chunk 42 optimal weight: 0.0870 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 50.0000 overall best weight: 1.5980 ------------------------------------------------------------------------------- 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: 0.7809 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6395 Z= 0.272 Angle : 0.525 6.500 8702 Z= 0.276 Chirality : 0.039 0.130 1046 Planarity : 0.004 0.043 1080 Dihedral : 9.197 79.421 1063 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.44 % Allowed : 29.03 % Favored : 66.53 % 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: 2.24 (0.30), residues: 856 helix: 2.71 (0.21), residues: 622 sheet: -0.50 (1.47), residues: 16 loop : -2.26 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 149 HIS 0.006 0.001 HIS A 753 PHE 0.012 0.001 PHE A 647 TYR 0.015 0.001 TYR A 965 ARG 0.002 0.000 ARG A 702 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1712 Ramachandran restraints generated. 856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.722 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 20 residues processed: 78 average time/residue: 0.1337 time to fit residues: 15.3683 Evaluate side-chains 82 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 62 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 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 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 695 MET 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 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: 88 random chunks: chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 8 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 0.0030 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.193073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.165098 restraints weight = 9077.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.162242 restraints weight = 15327.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.160837 restraints weight = 14305.787| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6395 Z= 0.160 Angle : 0.475 7.820 8702 Z= 0.248 Chirality : 0.037 0.134 1046 Planarity : 0.004 0.043 1080 Dihedral : 8.896 85.397 1063 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.43 % Allowed : 30.04 % Favored : 66.53 % 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: 2.38 (0.30), residues: 856 helix: 2.84 (0.21), residues: 619 sheet: -0.35 (1.49), residues: 16 loop : -2.23 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 149 HIS 0.004 0.001 HIS A 753 PHE 0.010 0.001 PHE A 614 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: 1322.81 seconds wall clock time: 24 minutes 51.37 seconds (1491.37 seconds total)