Starting phenix.real_space_refine on Fri Jan 19 16:29:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/01_2024/8uw3_42637_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/01_2024/8uw3_42637.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/01_2024/8uw3_42637_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/01_2024/8uw3_42637_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/01_2024/8uw3_42637_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/01_2024/8uw3_42637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/01_2024/8uw3_42637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/01_2024/8uw3_42637_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/01_2024/8uw3_42637_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 76 5.49 5 S 45 5.16 5 C 7415 2.51 5 N 2111 2.21 5 O 2358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 12005 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1265, 10419 Classifications: {'peptide': 1265} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 50, 'TRANS': 1214} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1352 Classifications: {'RNA': 63} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 34, 'rna3p_pyr': 21} Link IDs: {'rna2p': 7, 'rna3p': 55} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Unusual residues: {'DDG': 1} Classifications: {'DNA': 9, 'undetermined': 1} Link IDs: {'rna3p': 8, None: 1} Not linked: pdbres=" DT C 12 " pdbres="DDG C 13 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'TTP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' TTP A1301 " occ=0.65 ... (27 atoms not shown) pdb=" PG TTP A1301 " occ=0.65 Time building chain proxies: 7.10, per 1000 atoms: 0.59 Number of scatterers: 12005 At special positions: 0 Unit cell: (91.53, 133.65, 110.97, 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 45 16.00 P 76 15.00 O 2358 8.00 N 2111 7.00 C 7415 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.14 Conformation dependent library (CDL) restraints added in 1.9 seconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 7 sheets defined 50.8% alpha, 7.6% beta 24 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain 'A' and resid 21 through 34 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.548A pdb=" N SER A 215 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 260 through 276 Processing helix chain 'A' and resid 284 through 310 Processing helix chain 'A' and resid 312 through 330 Processing helix chain 'A' and resid 334 through 369 Processing helix chain 'A' and resid 375 through 381 Processing helix chain 'A' and resid 404 through 419 Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.773A pdb=" N THR A 435 " --> pdb=" O LYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 Processing helix chain 'A' and resid 455 through 464 Processing helix chain 'A' and resid 479 through 502 removed outlier: 4.995A pdb=" N GLU A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU A 487 " --> pdb=" O ARG A 483 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 538 through 558 removed outlier: 4.057A pdb=" N HIS A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LYS A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 588 Processing helix chain 'A' and resid 610 through 619 Processing helix chain 'A' and resid 625 through 633 Processing helix chain 'A' and resid 664 through 681 removed outlier: 3.591A pdb=" N VAL A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 729 removed outlier: 4.288A pdb=" N GLN A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 777 through 799 removed outlier: 4.932A pdb=" N PHE A 781 " --> pdb=" O LYS A 778 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N TYR A 785 " --> pdb=" O LYS A 782 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS A 786 " --> pdb=" O GLU A 783 " (cutoff:3.500A) Proline residue: A 787 - end of helix removed outlier: 4.210A pdb=" N LYS A 798 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 827 removed outlier: 4.191A pdb=" N LEU A 818 " --> pdb=" O LYS A 814 " (cutoff:3.500A) Proline residue: A 819 - end of helix Processing helix chain 'A' and resid 834 through 848 Processing helix chain 'A' and resid 858 through 862 Processing helix chain 'A' and resid 865 through 867 No H-bonds generated for 'chain 'A' and resid 865 through 867' Processing helix chain 'A' and resid 875 through 892 removed outlier: 4.072A pdb=" N THR A 886 " --> pdb=" O THR A 882 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA A 887 " --> pdb=" O VAL A 883 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TRP A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 901 No H-bonds generated for 'chain 'A' and resid 898 through 901' Processing helix chain 'A' and resid 933 through 946 Processing helix chain 'A' and resid 963 through 966 No H-bonds generated for 'chain 'A' and resid 963 through 966' Processing helix chain 'A' and resid 971 through 980 Processing helix chain 'A' and resid 985 through 988 No H-bonds generated for 'chain 'A' and resid 985 through 988' Processing helix chain 'A' and resid 991 through 993 No H-bonds generated for 'chain 'A' and resid 991 through 993' Processing helix chain 'A' and resid 999 through 1007 Processing helix chain 'A' and resid 1010 through 1020 Processing helix chain 'A' and resid 1023 through 1030 Processing helix chain 'A' and resid 1035 through 1041 removed outlier: 3.836A pdb=" N PHE A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1060 Processing helix chain 'A' and resid 1068 through 1075 Processing helix chain 'A' and resid 1082 through 1094 Processing helix chain 'A' and resid 1099 through 1109 Processing helix chain 'A' and resid 1116 through 1123 Processing helix chain 'A' and resid 1140 through 1144 Processing helix chain 'A' and resid 1148 through 1163 Proline residue: A1152 - end of helix Processing helix chain 'A' and resid 1172 through 1177 Processing helix chain 'A' and resid 1187 through 1206 removed outlier: 4.238A pdb=" N THR A1192 " --> pdb=" O CYS A1188 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A1195 " --> pdb=" O ASP A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1237 Processing helix chain 'A' and resid 1240 through 1257 removed outlier: 5.569A pdb=" N LYS A1249 " --> pdb=" O GLY A1245 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LEU A1250 " --> pdb=" O THR A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1266 Processing sheet with id= A, first strand: chain 'A' and resid 62 through 65 removed outlier: 3.654A pdb=" N THR A 12 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 233 " --> pdb=" O THR A 12 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG A 238 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N CYS A 217 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 140 through 145 removed outlier: 8.361A pdb=" N LEU A 141 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR A 110 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N MET A 143 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 112 " --> pdb=" O MET A 143 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ASP A 145 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE A 114 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER A 103 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 177 through 179 Processing sheet with id= D, first strand: chain 'A' and resid 193 through 195 Processing sheet with id= E, first strand: chain 'A' and resid 512 through 518 Processing sheet with id= F, first strand: chain 'A' and resid 704 through 709 Processing sheet with id= G, first strand: chain 'A' and resid 765 through 768 464 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for DD residue Restraints generated for nucleic acids: 61 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 5.47 Time building geometry restraints manager: 6.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1749 1.31 - 1.43: 3688 1.43 - 1.56: 6764 1.56 - 1.69: 147 1.69 - 1.81: 71 Bond restraints: 12419 Sorted by residual: bond pdb=" C4' DDG C 13 " pdb=" C3' DDG C 13 " ideal model delta sigma weight residual 1.287 1.529 -0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C4' DDG C 13 " pdb=" O4' DDG C 13 " ideal model delta sigma weight residual 1.614 1.395 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C6 DDG C 13 " pdb=" O6 DDG C 13 " ideal model delta sigma weight residual 1.185 1.398 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" N7 DDG C 13 " pdb=" C5 DDG C 13 " ideal model delta sigma weight residual 1.329 1.470 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C5 DDG C 13 " pdb=" C6 DDG C 13 " ideal model delta sigma weight residual 1.534 1.419 0.115 2.00e-02 2.50e+03 3.32e+01 ... (remaining 12414 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.54: 721 106.54 - 113.47: 7039 113.47 - 120.40: 4716 120.40 - 127.33: 4333 127.33 - 134.26: 294 Bond angle restraints: 17103 Sorted by residual: angle pdb=" N TYR A 912 " pdb=" CA TYR A 912 " pdb=" C TYR A 912 " ideal model delta sigma weight residual 114.62 109.06 5.56 1.14e+00 7.69e-01 2.38e+01 angle pdb=" OP2 DDG C 13 " pdb=" P DDG C 13 " pdb=" O5' DDG C 13 " ideal model delta sigma weight residual 109.47 123.63 -14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" N PRO A1211 " pdb=" CA PRO A1211 " pdb=" C PRO A1211 " ideal model delta sigma weight residual 113.98 107.93 6.05 1.29e+00 6.01e-01 2.20e+01 angle pdb=" OP1 DDG C 13 " pdb=" P DDG C 13 " pdb=" O5' DDG C 13 " ideal model delta sigma weight residual 109.47 123.42 -13.95 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C THR A1115 " pdb=" CA THR A1115 " pdb=" CB THR A1115 " ideal model delta sigma weight residual 109.09 114.41 -5.32 1.51e+00 4.39e-01 1.24e+01 ... (remaining 17098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 7272 35.68 - 71.36: 245 71.36 - 107.04: 33 107.04 - 142.72: 5 142.72 - 178.41: 2 Dihedral angle restraints: 7557 sinusoidal: 3812 harmonic: 3745 Sorted by residual: dihedral pdb=" C2 TTP A1301 " pdb=" C1' TTP A1301 " pdb=" N1 TTP A1301 " pdb=" O4' TTP A1301 " ideal model delta sinusoidal sigma weight residual 301.68 162.57 139.11 1 2.00e+01 2.50e-03 4.21e+01 dihedral pdb=" O4' U B 44 " pdb=" C1' U B 44 " pdb=" N1 U B 44 " pdb=" C2 U B 44 " ideal model delta sinusoidal sigma weight residual -128.00 -50.65 -77.35 1 1.70e+01 3.46e-03 2.59e+01 dihedral pdb=" O4' A B 54 " pdb=" C1' A B 54 " pdb=" N9 A B 54 " pdb=" C4 A B 54 " ideal model delta sinusoidal sigma weight residual -106.00 -177.27 71.27 1 1.70e+01 3.46e-03 2.26e+01 ... (remaining 7554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1566 0.048 - 0.096: 295 0.096 - 0.144: 78 0.144 - 0.192: 4 0.192 - 0.240: 4 Chirality restraints: 1947 Sorted by residual: chirality pdb=" CA CYS A1213 " pdb=" N CYS A1213 " pdb=" C CYS A1213 " pdb=" CB CYS A1213 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE A 830 " pdb=" N ILE A 830 " pdb=" C ILE A 830 " pdb=" CB ILE A 830 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB THR A1115 " pdb=" CA THR A1115 " pdb=" OG1 THR A1115 " pdb=" CG2 THR A1115 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1944 not shown) Planarity restraints: 1859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 216 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C LYS A 216 " -0.040 2.00e-02 2.50e+03 pdb=" O LYS A 216 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS A 217 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1114 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C LEU A1114 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU A1114 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A1115 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 56 " 0.020 2.00e-02 2.50e+03 1.19e-02 3.92e+00 pdb=" N9 A B 56 " -0.033 2.00e-02 2.50e+03 pdb=" C8 A B 56 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 56 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A B 56 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A B 56 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A B 56 " 0.002 2.00e-02 2.50e+03 pdb=" N1 A B 56 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A B 56 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 56 " -0.001 2.00e-02 2.50e+03 pdb=" C4 A B 56 " 0.005 2.00e-02 2.50e+03 ... (remaining 1856 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 98 2.46 - 3.07: 9092 3.07 - 3.68: 20198 3.68 - 4.29: 29785 4.29 - 4.90: 46931 Nonbonded interactions: 106104 Sorted by model distance: nonbonded pdb=" O2' G B 69 " pdb=" OP1 G B 70 " model vdw 1.850 2.440 nonbonded pdb=" O2' A B 48 " pdb=" OP1 A B 49 " model vdw 1.943 2.440 nonbonded pdb=" O2' C B 43 " pdb=" O5' U B 44 " model vdw 1.956 2.440 nonbonded pdb=" O2' A B 59 " pdb=" OP2 A B 60 " model vdw 2.042 2.440 nonbonded pdb=" O ILE A 400 " pdb=" OG1 THR A 401 " model vdw 2.147 2.440 ... (remaining 106099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.65 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 3.420 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 41.480 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 0.242 12419 Z= 0.354 Angle : 0.638 14.158 17103 Z= 0.340 Chirality : 0.042 0.240 1947 Planarity : 0.004 0.033 1859 Dihedral : 16.999 178.405 5117 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.39 % Favored : 94.53 % Rotamer: Outliers : 2.51 % Allowed : 6.83 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1261 helix: 1.23 (0.20), residues: 666 sheet: -0.35 (0.48), residues: 113 loop : -0.21 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1158 HIS 0.007 0.001 HIS A1142 PHE 0.021 0.002 PHE A 651 TYR 0.016 0.001 TYR A 768 ARG 0.002 0.000 ARG A 658 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.4977 (mmm) cc_final: 0.3988 (ttm) REVERT: A 306 LYS cc_start: 0.7013 (tppt) cc_final: 0.6371 (ttpp) REVERT: A 430 ASP cc_start: 0.8187 (m-30) cc_final: 0.7977 (m-30) REVERT: A 620 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8670 (mp) REVERT: A 783 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8024 (mm-30) REVERT: A 834 MET cc_start: 0.8348 (tpp) cc_final: 0.8105 (tpt) REVERT: A 892 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7754 (mp10) REVERT: A 992 LYS cc_start: 0.8378 (mtpp) cc_final: 0.8011 (ptmm) REVERT: A 997 LYS cc_start: 0.8544 (tptt) cc_final: 0.7854 (ttpp) REVERT: A 1063 LYS cc_start: 0.7855 (mppt) cc_final: 0.7602 (mmtm) REVERT: A 1066 ASN cc_start: 0.8208 (t0) cc_final: 0.7675 (p0) REVERT: A 1119 MET cc_start: 0.8301 (mmm) cc_final: 0.8070 (mmm) REVERT: A 1130 CYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7305 (p) REVERT: A 1148 LYS cc_start: 0.8688 (pttt) cc_final: 0.8370 (ptmm) outliers start: 29 outliers final: 7 residues processed: 154 average time/residue: 0.3337 time to fit residues: 68.5664 Evaluate side-chains 94 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1130 CYS Chi-restraints excluded: chain A residue 1213 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS A 174 GLN A 254 ASN ** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN ** A1225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1266 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12419 Z= 0.211 Angle : 0.624 10.569 17103 Z= 0.318 Chirality : 0.042 0.184 1947 Planarity : 0.004 0.036 1859 Dihedral : 18.437 168.368 2405 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 3.28 % Allowed : 9.25 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.25), residues: 1261 helix: 1.19 (0.20), residues: 671 sheet: -0.16 (0.50), residues: 110 loop : -0.06 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1219 HIS 0.005 0.001 HIS A1142 PHE 0.028 0.002 PHE A 651 TYR 0.014 0.001 TYR A1112 ARG 0.010 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 101 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.5103 (mmm) cc_final: 0.4298 (ttm) REVERT: A 266 MET cc_start: 0.8402 (tpp) cc_final: 0.8113 (tpp) REVERT: A 306 LYS cc_start: 0.7076 (tppt) cc_final: 0.6427 (ttpp) REVERT: A 321 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5426 (mm) REVERT: A 369 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7337 (mtt90) REVERT: A 423 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7700 (pp) REVERT: A 834 MET cc_start: 0.8253 (tpp) cc_final: 0.8008 (tpt) REVERT: A 892 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7746 (mp-120) REVERT: A 992 LYS cc_start: 0.8301 (mtpp) cc_final: 0.7845 (pptt) REVERT: A 997 LYS cc_start: 0.8524 (tptt) cc_final: 0.7916 (ttpp) REVERT: A 1063 LYS cc_start: 0.7911 (mppt) cc_final: 0.7612 (mmtm) REVERT: A 1066 ASN cc_start: 0.8197 (t0) cc_final: 0.7529 (p0) REVERT: A 1110 MET cc_start: 0.9017 (mmp) cc_final: 0.8815 (mmm) REVERT: A 1119 MET cc_start: 0.8264 (mmm) cc_final: 0.7534 (mmm) REVERT: A 1148 LYS cc_start: 0.8562 (pttt) cc_final: 0.8284 (ptmm) REVERT: A 1189 TYR cc_start: 0.6303 (m-80) cc_final: 0.5510 (m-80) REVERT: A 1216 MET cc_start: 0.8367 (tpp) cc_final: 0.8163 (tpp) outliers start: 38 outliers final: 17 residues processed: 128 average time/residue: 0.2981 time to fit residues: 52.9872 Evaluate side-chains 101 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1213 CYS Chi-restraints excluded: chain A residue 1269 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12419 Z= 0.206 Angle : 0.578 10.535 17103 Z= 0.295 Chirality : 0.041 0.207 1947 Planarity : 0.004 0.039 1859 Dihedral : 18.161 175.852 2400 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.32 % Rotamer: Outliers : 3.98 % Allowed : 11.24 % Favored : 84.79 % 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: 0.82 (0.25), residues: 1261 helix: 1.21 (0.20), residues: 671 sheet: -0.37 (0.48), residues: 115 loop : -0.03 (0.32), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 926 HIS 0.005 0.001 HIS A1225 PHE 0.026 0.002 PHE A 651 TYR 0.020 0.001 TYR A 768 ARG 0.006 0.000 ARG A 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 85 time to evaluate : 1.493 Fit side-chains revert: symmetry clash REVERT: A 143 MET cc_start: 0.5229 (mmm) cc_final: 0.4478 (ttm) REVERT: A 266 MET cc_start: 0.8426 (tpp) cc_final: 0.8221 (tpp) REVERT: A 272 MET cc_start: 0.8370 (ppp) cc_final: 0.8092 (ppp) REVERT: A 306 LYS cc_start: 0.6943 (tppt) cc_final: 0.6429 (ttpp) REVERT: A 321 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5491 (mm) REVERT: A 369 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7253 (mtt90) REVERT: A 423 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7625 (pp) REVERT: A 428 GLU cc_start: 0.8355 (tt0) cc_final: 0.8148 (tt0) REVERT: A 834 MET cc_start: 0.8231 (tpp) cc_final: 0.7920 (tpt) REVERT: A 841 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8280 (tp30) REVERT: A 853 ARG cc_start: 0.7297 (ptm160) cc_final: 0.6838 (ptm160) REVERT: A 992 LYS cc_start: 0.8305 (mtpp) cc_final: 0.7847 (pptt) REVERT: A 997 LYS cc_start: 0.8524 (tptt) cc_final: 0.7820 (ttpp) REVERT: A 1063 LYS cc_start: 0.7879 (mppt) cc_final: 0.7547 (mmtm) REVERT: A 1119 MET cc_start: 0.8353 (mmm) cc_final: 0.8129 (mmm) REVERT: A 1148 LYS cc_start: 0.8489 (pttt) cc_final: 0.8240 (ptmm) REVERT: A 1189 TYR cc_start: 0.6219 (m-80) cc_final: 0.5507 (m-80) REVERT: A 1216 MET cc_start: 0.8266 (tpp) cc_final: 0.8018 (tpp) outliers start: 46 outliers final: 19 residues processed: 121 average time/residue: 0.2683 time to fit residues: 46.7330 Evaluate side-chains 101 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 841 GLU Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1192 THR Chi-restraints excluded: chain A residue 1269 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.0870 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 128 optimal weight: 30.0000 chunk 63 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12419 Z= 0.198 Angle : 0.574 13.464 17103 Z= 0.290 Chirality : 0.041 0.214 1947 Planarity : 0.004 0.040 1859 Dihedral : 17.997 176.280 2394 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 3.89 % Allowed : 12.10 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 1261 helix: 1.32 (0.20), residues: 667 sheet: -0.35 (0.48), residues: 110 loop : -0.12 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 926 HIS 0.006 0.001 HIS A1225 PHE 0.026 0.002 PHE A 651 TYR 0.016 0.001 TYR A 415 ARG 0.003 0.000 ARG A1195 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 89 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 143 MET cc_start: 0.5078 (mmm) cc_final: 0.4467 (ttm) REVERT: A 266 MET cc_start: 0.8376 (tpp) cc_final: 0.7734 (tpp) REVERT: A 272 MET cc_start: 0.8376 (ppp) cc_final: 0.8073 (ppp) REVERT: A 306 LYS cc_start: 0.7024 (tppt) cc_final: 0.6515 (ttpp) REVERT: A 311 ARG cc_start: 0.7206 (ppt90) cc_final: 0.6911 (mtp180) REVERT: A 321 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5791 (mm) REVERT: A 369 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7221 (mtt90) REVERT: A 423 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7665 (pp) REVERT: A 834 MET cc_start: 0.8188 (tpp) cc_final: 0.7970 (tpt) REVERT: A 841 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8282 (tp30) REVERT: A 992 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7840 (pptt) REVERT: A 997 LYS cc_start: 0.8529 (tptt) cc_final: 0.7762 (ttpp) REVERT: A 1063 LYS cc_start: 0.7860 (mppt) cc_final: 0.7500 (mmtm) REVERT: A 1119 MET cc_start: 0.8347 (mmm) cc_final: 0.8068 (mmm) REVERT: A 1189 TYR cc_start: 0.6212 (m-80) cc_final: 0.5500 (m-80) outliers start: 45 outliers final: 26 residues processed: 125 average time/residue: 0.2549 time to fit residues: 46.0212 Evaluate side-chains 106 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 76 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 841 GLU Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1192 THR Chi-restraints excluded: chain A residue 1269 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 65 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN ** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 GLN ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12419 Z= 0.199 Angle : 0.557 10.602 17103 Z= 0.283 Chirality : 0.040 0.216 1947 Planarity : 0.004 0.047 1859 Dihedral : 17.953 174.385 2394 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.84 % Favored : 95.08 % Rotamer: Outliers : 3.72 % Allowed : 12.79 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1261 helix: 1.38 (0.20), residues: 667 sheet: -0.43 (0.48), residues: 111 loop : -0.11 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 926 HIS 0.007 0.001 HIS A1225 PHE 0.026 0.002 PHE A 651 TYR 0.021 0.001 TYR A 768 ARG 0.003 0.000 ARG A 853 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 78 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.4965 (mmm) cc_final: 0.4398 (ttm) REVERT: A 266 MET cc_start: 0.8357 (tpp) cc_final: 0.8010 (tpp) REVERT: A 306 LYS cc_start: 0.7006 (tppt) cc_final: 0.6510 (ttpp) REVERT: A 311 ARG cc_start: 0.7216 (ppt90) cc_final: 0.6910 (mtp180) REVERT: A 321 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5844 (mm) REVERT: A 369 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7209 (mtt90) REVERT: A 423 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7631 (pp) REVERT: A 834 MET cc_start: 0.8163 (tpp) cc_final: 0.7933 (tpt) REVERT: A 841 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8285 (tp30) REVERT: A 992 LYS cc_start: 0.8258 (mtpp) cc_final: 0.7815 (pptt) REVERT: A 997 LYS cc_start: 0.8499 (tptt) cc_final: 0.7736 (ttpp) REVERT: A 1063 LYS cc_start: 0.7864 (mppt) cc_final: 0.7482 (mmtp) REVERT: A 1119 MET cc_start: 0.8377 (mmm) cc_final: 0.8154 (mmm) REVERT: A 1189 TYR cc_start: 0.6127 (m-80) cc_final: 0.5386 (m-80) outliers start: 43 outliers final: 27 residues processed: 115 average time/residue: 0.2711 time to fit residues: 45.1784 Evaluate side-chains 105 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 74 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 841 GLU Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1156 SER Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1192 THR Chi-restraints excluded: chain A residue 1269 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 0.0870 chunk 31 optimal weight: 8.9990 chunk 128 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 594 HIS A 659 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12419 Z= 0.210 Angle : 0.561 10.722 17103 Z= 0.284 Chirality : 0.040 0.215 1947 Planarity : 0.004 0.040 1859 Dihedral : 17.946 173.568 2394 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.47 % Favored : 94.45 % Rotamer: Outliers : 3.63 % Allowed : 13.40 % Favored : 82.97 % 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: 0.92 (0.25), residues: 1261 helix: 1.38 (0.20), residues: 667 sheet: -0.46 (0.47), residues: 111 loop : -0.09 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 926 HIS 0.007 0.001 HIS A1225 PHE 0.026 0.002 PHE A 651 TYR 0.022 0.001 TYR A 768 ARG 0.003 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 79 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.4948 (mmm) cc_final: 0.4386 (ttm) REVERT: A 251 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8389 (mtmt) REVERT: A 266 MET cc_start: 0.8347 (tpp) cc_final: 0.7955 (tpp) REVERT: A 272 MET cc_start: 0.8379 (ppp) cc_final: 0.8077 (ppp) REVERT: A 306 LYS cc_start: 0.7014 (tppt) cc_final: 0.6522 (ttpp) REVERT: A 311 ARG cc_start: 0.7260 (ppt90) cc_final: 0.6836 (mtp-110) REVERT: A 321 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5893 (mm) REVERT: A 369 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7220 (mtt90) REVERT: A 423 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7658 (pp) REVERT: A 834 MET cc_start: 0.8123 (tpp) cc_final: 0.7902 (tpt) REVERT: A 841 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8276 (tp30) REVERT: A 992 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7844 (pptt) REVERT: A 997 LYS cc_start: 0.8488 (tptt) cc_final: 0.7680 (ttpp) REVERT: A 1063 LYS cc_start: 0.7917 (mppt) cc_final: 0.7529 (mmtp) REVERT: A 1119 MET cc_start: 0.8408 (mmm) cc_final: 0.8201 (mmm) outliers start: 42 outliers final: 27 residues processed: 116 average time/residue: 0.2594 time to fit residues: 43.7368 Evaluate side-chains 107 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 75 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 841 GLU Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1156 SER Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1192 THR Chi-restraints excluded: chain A residue 1269 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.9990 chunk 14 optimal weight: 40.0000 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 30.0000 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 659 GLN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 12419 Z= 0.327 Angle : 0.616 10.821 17103 Z= 0.314 Chirality : 0.042 0.222 1947 Planarity : 0.004 0.038 1859 Dihedral : 18.114 170.555 2394 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.08 % Favored : 94.85 % Rotamer: Outliers : 3.80 % Allowed : 14.00 % Favored : 82.20 % 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: 0.65 (0.25), residues: 1261 helix: 1.12 (0.20), residues: 678 sheet: -0.58 (0.46), residues: 116 loop : -0.17 (0.32), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1219 HIS 0.008 0.001 HIS A1225 PHE 0.027 0.002 PHE A 651 TYR 0.025 0.002 TYR A 768 ARG 0.003 0.000 ARG A1052 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 70 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.4957 (mmm) cc_final: 0.4305 (ttm) REVERT: A 266 MET cc_start: 0.8348 (tpp) cc_final: 0.7970 (tpp) REVERT: A 272 MET cc_start: 0.8386 (ppp) cc_final: 0.8074 (ppp) REVERT: A 306 LYS cc_start: 0.7107 (tppt) cc_final: 0.6565 (ttpp) REVERT: A 311 ARG cc_start: 0.7381 (ppt90) cc_final: 0.7023 (mtp-110) REVERT: A 369 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7379 (mtt-85) REVERT: A 423 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7670 (pp) REVERT: A 834 MET cc_start: 0.8244 (tpp) cc_final: 0.7909 (tpt) REVERT: A 992 LYS cc_start: 0.8376 (mtpp) cc_final: 0.8018 (pttp) REVERT: A 1063 LYS cc_start: 0.7943 (mppt) cc_final: 0.7562 (mmtm) REVERT: A 1119 MET cc_start: 0.8498 (mmm) cc_final: 0.8291 (mmm) outliers start: 44 outliers final: 29 residues processed: 107 average time/residue: 0.2682 time to fit residues: 42.1490 Evaluate side-chains 98 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 67 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1156 SER Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1192 THR Chi-restraints excluded: chain A residue 1269 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 659 GLN ** A 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12419 Z= 0.167 Angle : 0.556 10.674 17103 Z= 0.283 Chirality : 0.040 0.211 1947 Planarity : 0.004 0.038 1859 Dihedral : 18.035 170.895 2394 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 2.85 % Allowed : 15.13 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1261 helix: 1.24 (0.20), residues: 676 sheet: -0.62 (0.46), residues: 116 loop : -0.15 (0.32), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 926 HIS 0.007 0.001 HIS A1225 PHE 0.027 0.002 PHE A 651 TYR 0.018 0.001 TYR A 768 ARG 0.003 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 78 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.4932 (mmm) cc_final: 0.4328 (ttm) REVERT: A 266 MET cc_start: 0.8345 (tpp) cc_final: 0.7938 (tpp) REVERT: A 272 MET cc_start: 0.8344 (ppp) cc_final: 0.8081 (ppp) REVERT: A 306 LYS cc_start: 0.6972 (tppt) cc_final: 0.6516 (ttpp) REVERT: A 311 ARG cc_start: 0.7323 (ppt90) cc_final: 0.6943 (mtp-110) REVERT: A 369 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7234 (mtt-85) REVERT: A 373 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8945 (mt) REVERT: A 423 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7683 (pp) REVERT: A 834 MET cc_start: 0.8116 (tpp) cc_final: 0.7885 (tpt) REVERT: A 992 LYS cc_start: 0.8353 (mtpp) cc_final: 0.7980 (pttp) REVERT: A 997 LYS cc_start: 0.8484 (tptt) cc_final: 0.7707 (ttpp) REVERT: A 1039 ILE cc_start: 0.8968 (mt) cc_final: 0.8709 (mt) REVERT: A 1063 LYS cc_start: 0.7967 (mppt) cc_final: 0.7577 (mmtp) REVERT: A 1229 MET cc_start: 0.7995 (mmt) cc_final: 0.7732 (mmt) outliers start: 33 outliers final: 25 residues processed: 106 average time/residue: 0.2668 time to fit residues: 40.9774 Evaluate side-chains 105 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 77 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1156 SER Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1192 THR Chi-restraints excluded: chain A residue 1269 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 119 optimal weight: 0.0670 chunk 71 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 659 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12419 Z= 0.161 Angle : 0.532 10.697 17103 Z= 0.270 Chirality : 0.039 0.206 1947 Planarity : 0.004 0.038 1859 Dihedral : 17.952 171.529 2394 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.76 % Favored : 95.16 % Rotamer: Outliers : 2.33 % Allowed : 15.56 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1261 helix: 1.44 (0.21), residues: 668 sheet: -0.58 (0.47), residues: 116 loop : -0.19 (0.32), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1158 HIS 0.008 0.001 HIS A1225 PHE 0.027 0.002 PHE A 651 TYR 0.017 0.001 TYR A 768 ARG 0.002 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 86 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.4860 (mmm) cc_final: 0.4299 (ttm) REVERT: A 251 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8377 (mtmt) REVERT: A 266 MET cc_start: 0.8351 (tpp) cc_final: 0.7926 (tpp) REVERT: A 272 MET cc_start: 0.8397 (ppp) cc_final: 0.8104 (ppp) REVERT: A 306 LYS cc_start: 0.6997 (tppt) cc_final: 0.6553 (ttpp) REVERT: A 311 ARG cc_start: 0.7305 (ppt90) cc_final: 0.7048 (mtp-110) REVERT: A 321 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.6034 (mm) REVERT: A 369 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7147 (mtt90) REVERT: A 373 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8942 (mt) REVERT: A 834 MET cc_start: 0.8046 (tpp) cc_final: 0.7840 (tpt) REVERT: A 992 LYS cc_start: 0.8355 (mtpp) cc_final: 0.7996 (pttp) REVERT: A 1039 ILE cc_start: 0.8860 (mt) cc_final: 0.8561 (mt) REVERT: A 1229 MET cc_start: 0.8001 (mmt) cc_final: 0.7723 (mmt) outliers start: 27 outliers final: 18 residues processed: 108 average time/residue: 0.2791 time to fit residues: 43.2995 Evaluate side-chains 99 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1192 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 659 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12419 Z= 0.162 Angle : 0.531 10.702 17103 Z= 0.270 Chirality : 0.039 0.206 1947 Planarity : 0.004 0.039 1859 Dihedral : 17.961 173.091 2394 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.92 % Rotamer: Outliers : 2.16 % Allowed : 15.99 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1261 helix: 1.40 (0.21), residues: 673 sheet: -0.52 (0.47), residues: 116 loop : -0.13 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1219 HIS 0.005 0.001 HIS A1225 PHE 0.027 0.002 PHE A 651 TYR 0.013 0.001 TYR A 768 ARG 0.003 0.000 ARG A 344 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.4845 (mmm) cc_final: 0.4287 (ttm) REVERT: A 251 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8409 (mtmt) REVERT: A 266 MET cc_start: 0.8327 (tpp) cc_final: 0.7910 (tpp) REVERT: A 272 MET cc_start: 0.8371 (ppp) cc_final: 0.8091 (ppp) REVERT: A 306 LYS cc_start: 0.6997 (tppt) cc_final: 0.6553 (ttpp) REVERT: A 311 ARG cc_start: 0.7313 (ppt90) cc_final: 0.7060 (mtp-110) REVERT: A 321 LEU cc_start: 0.6296 (OUTLIER) cc_final: 0.6026 (mm) REVERT: A 423 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7596 (pp) REVERT: A 834 MET cc_start: 0.8057 (tpp) cc_final: 0.7853 (tpt) REVERT: A 992 LYS cc_start: 0.8445 (mtpp) cc_final: 0.8156 (ptmm) REVERT: A 1039 ILE cc_start: 0.8843 (mt) cc_final: 0.8535 (mt) outliers start: 25 outliers final: 19 residues processed: 103 average time/residue: 0.2623 time to fit residues: 39.6158 Evaluate side-chains 99 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 594 HIS Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1192 THR Chi-restraints excluded: chain A residue 1269 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 15 optimal weight: 40.0000 chunk 29 optimal weight: 0.0770 chunk 105 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 13 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 659 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.162884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.117127 restraints weight = 22294.471| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.51 r_work: 0.3267 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12419 Z= 0.235 Angle : 0.554 10.862 17103 Z= 0.282 Chirality : 0.040 0.212 1947 Planarity : 0.004 0.038 1859 Dihedral : 18.022 173.501 2394 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.76 % Favored : 95.16 % Rotamer: Outliers : 2.42 % Allowed : 15.56 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1261 helix: 1.37 (0.21), residues: 667 sheet: -0.49 (0.47), residues: 116 loop : -0.13 (0.32), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 926 HIS 0.014 0.001 HIS A1225 PHE 0.027 0.002 PHE A 651 TYR 0.016 0.001 TYR A 768 ARG 0.002 0.000 ARG A 344 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2659.14 seconds wall clock time: 49 minutes 42.30 seconds (2982.30 seconds total)