Starting phenix.real_space_refine on Thu May 9 03:38:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/05_2024/8uw3_42637_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/05_2024/8uw3_42637.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/05_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_42637/05_2024/8uw3_42637_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/05_2024/8uw3_42637_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/05_2024/8uw3_42637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/05_2024/8uw3_42637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/05_2024/8uw3_42637_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uw3_42637/05_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-dev-5322/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: 7.21, per 1000 atoms: 0.60 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: 6.07 Conformation dependent library (CDL) restraints added in 2.0 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: 6.59 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: 5.24 Time building geometry restraints manager: 6.44 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: 7289 35.68 - 71.36: 260 71.36 - 107.04: 33 107.04 - 142.72: 5 142.72 - 178.41: 2 Dihedral angle restraints: 7589 sinusoidal: 3844 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 7586 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: 1.390 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: 3.700 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 42.410 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.070 ------------------------------------------------------------------------------- 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 : 17.216 178.405 5149 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 : 1.371 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: 0.3384 time to fit residues: 69.6584 Evaluate side-chains 94 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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: 0.7647 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12419 Z= 0.216 Angle : 0.618 10.606 17103 Z= 0.315 Chirality : 0.042 0.203 1947 Planarity : 0.004 0.036 1859 Dihedral : 18.876 168.090 2437 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 3.28 % Allowed : 9.08 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1261 helix: 1.20 (0.20), residues: 671 sheet: -0.13 (0.50), residues: 110 loop : -0.05 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1158 HIS 0.004 0.001 HIS A1142 PHE 0.027 0.002 PHE A 651 TYR 0.014 0.001 TYR A1112 ARG 0.005 0.000 ARG A 588 *********************** 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 : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.5068 (mmm) cc_final: 0.4241 (ttm) REVERT: A 266 MET cc_start: 0.8403 (tpp) cc_final: 0.8107 (tpp) REVERT: A 306 LYS cc_start: 0.7075 (tppt) cc_final: 0.6426 (ttpp) REVERT: A 321 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5452 (mm) REVERT: A 369 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7338 (mtt90) REVERT: A 423 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7694 (pp) REVERT: A 834 MET cc_start: 0.8256 (tpp) cc_final: 0.8012 (tpt) REVERT: A 892 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7732 (mp-120) REVERT: A 992 LYS cc_start: 0.8305 (mtpp) cc_final: 0.7848 (pptt) REVERT: A 997 LYS cc_start: 0.8527 (tptt) cc_final: 0.7870 (ttpp) REVERT: A 1063 LYS cc_start: 0.7911 (mppt) cc_final: 0.7612 (mmtm) REVERT: A 1066 ASN cc_start: 0.8203 (t0) cc_final: 0.7536 (p0) REVERT: A 1110 MET cc_start: 0.9033 (mmp) cc_final: 0.8819 (mmm) REVERT: A 1119 MET cc_start: 0.8269 (mmm) cc_final: 0.7536 (mmm) REVERT: A 1148 LYS cc_start: 0.8577 (pttt) cc_final: 0.8297 (ptmm) REVERT: A 1189 TYR cc_start: 0.6307 (m-80) cc_final: 0.5513 (m-80) outliers start: 38 outliers final: 17 residues processed: 128 average time/residue: 0.3041 time to fit residues: 54.5194 Evaluate side-chains 101 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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: 1.9990 chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 893 ASN ** A1225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 12419 Z= 0.386 Angle : 0.681 10.813 17103 Z= 0.347 Chirality : 0.044 0.229 1947 Planarity : 0.005 0.042 1859 Dihedral : 18.848 175.025 2432 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.47 % Favored : 94.45 % Rotamer: Outliers : 4.84 % Allowed : 11.15 % 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: 0.44 (0.24), residues: 1261 helix: 0.86 (0.20), residues: 669 sheet: -0.50 (0.47), residues: 115 loop : -0.16 (0.32), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 799 HIS 0.006 0.001 HIS A 52 PHE 0.035 0.002 PHE A 700 TYR 0.015 0.002 TYR A1112 ARG 0.008 0.001 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 130 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 74 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.5141 (mmm) cc_final: 0.4287 (ptp) REVERT: A 272 MET cc_start: 0.8393 (ppp) cc_final: 0.8062 (ppp) REVERT: A 306 LYS cc_start: 0.7124 (tppt) cc_final: 0.6528 (ttpp) REVERT: A 369 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7517 (mtt-85) REVERT: A 423 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7723 (pp) REVERT: A 834 MET cc_start: 0.8287 (tpp) cc_final: 0.8039 (tpt) REVERT: A 892 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.7988 (mp-120) REVERT: A 992 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8019 (ptmm) REVERT: A 997 LYS cc_start: 0.8514 (tptt) cc_final: 0.7756 (ttpp) REVERT: A 1063 LYS cc_start: 0.7970 (mppt) cc_final: 0.7643 (mmtm) REVERT: A 1110 MET cc_start: 0.9072 (mmp) cc_final: 0.8847 (mmm) REVERT: A 1148 LYS cc_start: 0.8634 (pttt) cc_final: 0.8357 (ptmm) outliers start: 56 outliers final: 23 residues processed: 120 average time/residue: 0.2728 time to fit residues: 47.2182 Evaluate side-chains 94 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 68 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 517 ILE Chi-restraints excluded: chain A residue 539 ASP 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 777 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 815 MET 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 973 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 13 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 128 optimal weight: 30.0000 chunk 63 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 HIS A 659 GLN A 893 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12419 Z= 0.228 Angle : 0.598 11.567 17103 Z= 0.304 Chirality : 0.041 0.208 1947 Planarity : 0.004 0.040 1859 Dihedral : 18.716 173.400 2427 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 4.15 % Allowed : 12.45 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1261 helix: 1.06 (0.20), residues: 670 sheet: -0.61 (0.46), residues: 115 loop : -0.15 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1158 HIS 0.008 0.001 HIS A1225 PHE 0.029 0.002 PHE A 651 TYR 0.015 0.001 TYR A 768 ARG 0.002 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 126 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 78 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: A 143 MET cc_start: 0.5095 (mmm) cc_final: 0.4189 (ptp) REVERT: A 266 MET cc_start: 0.8281 (tpp) cc_final: 0.7754 (tpp) REVERT: A 306 LYS cc_start: 0.7051 (tppt) cc_final: 0.6545 (ttpp) REVERT: A 311 ARG cc_start: 0.7283 (ppt90) cc_final: 0.6763 (mtm180) REVERT: A 369 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7377 (mtt-85) REVERT: A 423 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7741 (pp) REVERT: A 834 MET cc_start: 0.8229 (tpp) cc_final: 0.7967 (tpt) REVERT: A 862 SER cc_start: 0.8643 (p) cc_final: 0.8364 (t) REVERT: A 892 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7962 (mp-120) REVERT: A 992 LYS cc_start: 0.8342 (mtpp) cc_final: 0.7962 (pttp) REVERT: A 997 LYS cc_start: 0.8576 (tptt) cc_final: 0.7802 (ttpp) REVERT: A 1063 LYS cc_start: 0.7934 (mppt) cc_final: 0.7578 (mmtm) outliers start: 48 outliers final: 26 residues processed: 116 average time/residue: 0.2590 time to fit residues: 43.7750 Evaluate side-chains 103 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 74 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR 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 515 ILE Chi-restraints excluded: chain A residue 517 ILE 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 892 GLN Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 912 TYR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 959 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 0.0040 chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 109 optimal weight: 0.0970 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 65 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN A 851 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2485 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= 0.201 Angle : 0.572 10.758 17103 Z= 0.290 Chirality : 0.041 0.211 1947 Planarity : 0.004 0.053 1859 Dihedral : 18.615 173.078 2427 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.08 % Favored : 94.85 % Rotamer: Outliers : 3.80 % Allowed : 13.92 % Favored : 82.28 % 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: 0.69 (0.25), residues: 1261 helix: 1.19 (0.20), residues: 670 sheet: -0.66 (0.46), residues: 116 loop : -0.16 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 926 HIS 0.007 0.001 HIS A1225 PHE 0.028 0.002 PHE A 651 TYR 0.018 0.001 TYR A 415 ARG 0.005 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 125 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 81 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: A 143 MET cc_start: 0.5205 (mmm) cc_final: 0.4363 (ttm) REVERT: A 229 ASP cc_start: 0.6293 (OUTLIER) cc_final: 0.5997 (p0) REVERT: A 266 MET cc_start: 0.8345 (tpp) cc_final: 0.7825 (tpp) REVERT: A 272 MET cc_start: 0.8359 (ppp) cc_final: 0.8072 (ppp) REVERT: A 306 LYS cc_start: 0.7022 (tppt) cc_final: 0.6554 (ttpp) REVERT: A 311 ARG cc_start: 0.7243 (ppt90) cc_final: 0.6832 (mtp-110) REVERT: A 369 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7268 (mtt-85) REVERT: A 423 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7685 (pp) REVERT: A 834 MET cc_start: 0.8186 (tpp) cc_final: 0.7859 (tpt) REVERT: A 892 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8026 (mp-120) REVERT: A 992 LYS cc_start: 0.8341 (mtpp) cc_final: 0.7960 (pttp) REVERT: A 997 LYS cc_start: 0.8561 (tptt) cc_final: 0.7748 (ttpp) REVERT: A 1063 LYS cc_start: 0.7929 (mppt) cc_final: 0.7554 (mmtm) REVERT: A 1119 MET cc_start: 0.8367 (mmm) cc_final: 0.8040 (mmm) REVERT: A 1189 TYR cc_start: 0.6259 (m-80) cc_final: 0.5399 (m-80) outliers start: 44 outliers final: 26 residues processed: 117 average time/residue: 0.2730 time to fit residues: 46.8757 Evaluate side-chains 102 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 72 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 249 THR 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 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 892 GLN Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 941 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 128 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN A 980 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 12419 Z= 0.385 Angle : 0.646 11.140 17103 Z= 0.329 Chirality : 0.043 0.224 1947 Planarity : 0.004 0.039 1859 Dihedral : 18.771 170.462 2427 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer: Outliers : 4.32 % Allowed : 14.26 % Favored : 81.42 % 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: 0.54 (0.24), residues: 1261 helix: 1.02 (0.20), residues: 670 sheet: -0.54 (0.47), residues: 116 loop : -0.20 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1158 HIS 0.008 0.001 HIS A1225 PHE 0.030 0.002 PHE A 367 TYR 0.025 0.002 TYR A 768 ARG 0.003 0.000 ARG A1052 *********************** 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 116 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 66 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.6182 (OUTLIER) cc_final: 0.5840 (p0) REVERT: A 266 MET cc_start: 0.8302 (tpp) cc_final: 0.7945 (tpp) REVERT: A 272 MET cc_start: 0.8414 (ppp) cc_final: 0.8082 (ppp) REVERT: A 306 LYS cc_start: 0.7096 (tppt) cc_final: 0.6560 (ttpp) REVERT: A 311 ARG cc_start: 0.7352 (ppt90) cc_final: 0.6899 (mtp-110) REVERT: A 369 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7403 (mtt-85) REVERT: A 373 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8943 (mt) REVERT: A 423 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7763 (pp) REVERT: A 834 MET cc_start: 0.8267 (tpp) cc_final: 0.8010 (tpt) REVERT: A 892 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.7947 (mp-120) REVERT: A 992 LYS cc_start: 0.8435 (mtpp) cc_final: 0.8001 (pttp) REVERT: A 1063 LYS cc_start: 0.8011 (mppt) cc_final: 0.7639 (mmtm) REVERT: A 1119 MET cc_start: 0.8458 (mmm) cc_final: 0.8222 (mmm) outliers start: 50 outliers final: 33 residues processed: 111 average time/residue: 0.2581 time to fit residues: 42.0492 Evaluate side-chains 101 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 63 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 249 THR 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 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 430 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 596 ILE 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 756 GLU 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 892 GLN Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 940 TRP Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 959 ILE 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 1253 ILE 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: 1.9990 chunk 14 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 128 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.7685 moved from start: 0.2842 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= 0.207 Angle : 0.576 10.926 17103 Z= 0.291 Chirality : 0.041 0.212 1947 Planarity : 0.004 0.039 1859 Dihedral : 18.700 170.585 2427 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 3.72 % Allowed : 14.95 % Favored : 81.33 % 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: 0.56 (0.24), residues: 1261 helix: 1.15 (0.20), residues: 673 sheet: -0.69 (0.46), residues: 116 loop : -0.36 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1158 HIS 0.006 0.001 HIS A1225 PHE 0.029 0.002 PHE A 651 TYR 0.020 0.001 TYR A 768 ARG 0.003 0.000 ARG A 344 *********************** 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 119 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 76 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.4777 (mmm) cc_final: 0.3773 (ptp) REVERT: A 229 ASP cc_start: 0.6284 (OUTLIER) cc_final: 0.5946 (p0) REVERT: A 266 MET cc_start: 0.8336 (tpp) cc_final: 0.7894 (tpp) REVERT: A 272 MET cc_start: 0.8391 (ppp) cc_final: 0.8063 (ppp) REVERT: A 306 LYS cc_start: 0.6999 (tppt) cc_final: 0.6577 (ttpp) REVERT: A 311 ARG cc_start: 0.7338 (ppt90) cc_final: 0.6904 (mtp-110) REVERT: A 369 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7263 (mtt-85) REVERT: A 834 MET cc_start: 0.8149 (tpp) cc_final: 0.7804 (tpt) REVERT: A 892 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8010 (mp-120) REVERT: A 992 LYS cc_start: 0.8395 (mtpp) cc_final: 0.7999 (pttp) REVERT: A 997 LYS cc_start: 0.8505 (tptt) cc_final: 0.7756 (ttpp) REVERT: A 1063 LYS cc_start: 0.7979 (mppt) cc_final: 0.7546 (mmtp) outliers start: 43 outliers final: 25 residues processed: 111 average time/residue: 0.2812 time to fit residues: 45.2810 Evaluate side-chains 100 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 249 THR 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 515 ILE Chi-restraints excluded: chain A residue 517 ILE 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 892 GLN Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 941 LEU 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: 5.9990 chunk 51 optimal weight: 0.0370 chunk 76 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 581 ASN A 659 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12419 Z= 0.161 Angle : 0.546 10.836 17103 Z= 0.277 Chirality : 0.040 0.215 1947 Planarity : 0.004 0.040 1859 Dihedral : 18.654 171.805 2427 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 3.20 % Allowed : 15.56 % Favored : 81.24 % 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: 0.67 (0.25), residues: 1261 helix: 1.28 (0.20), residues: 673 sheet: -0.80 (0.46), residues: 114 loop : -0.34 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 926 HIS 0.008 0.001 HIS A1225 PHE 0.028 0.002 PHE A 651 TYR 0.022 0.001 TYR A 768 ARG 0.004 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 121 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 84 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.4870 (mmm) cc_final: 0.3681 (ttm) REVERT: A 229 ASP cc_start: 0.6262 (OUTLIER) cc_final: 0.5933 (p0) REVERT: A 266 MET cc_start: 0.8362 (tpp) cc_final: 0.7840 (tpp) REVERT: A 272 MET cc_start: 0.8342 (ppp) cc_final: 0.8055 (ppp) REVERT: A 306 LYS cc_start: 0.6973 (tppt) cc_final: 0.6588 (ttpp) REVERT: A 311 ARG cc_start: 0.7301 (ppt90) cc_final: 0.6937 (mtp-110) REVERT: A 369 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7140 (mtt-85) REVERT: A 423 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7695 (pp) REVERT: A 834 MET cc_start: 0.8092 (tpp) cc_final: 0.7862 (tpt) REVERT: A 992 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8180 (ptmm) REVERT: A 997 LYS cc_start: 0.8482 (tptt) cc_final: 0.7733 (ttpp) REVERT: A 1063 LYS cc_start: 0.7876 (mppt) cc_final: 0.7513 (mmtp) outliers start: 37 outliers final: 22 residues processed: 117 average time/residue: 0.2860 time to fit residues: 47.9625 Evaluate side-chains 98 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 73 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 302 LEU 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 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 910 HIS Chi-restraints excluded: chain A residue 941 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.0870 chunk 122 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 71 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 892 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12419 Z= 0.149 Angle : 0.540 10.618 17103 Z= 0.274 Chirality : 0.039 0.211 1947 Planarity : 0.004 0.040 1859 Dihedral : 18.583 171.650 2424 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.08 % Favored : 94.85 % Rotamer: Outliers : 2.33 % Allowed : 17.11 % Favored : 80.55 % 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: 0.73 (0.25), residues: 1261 helix: 1.32 (0.20), residues: 670 sheet: -0.73 (0.47), residues: 114 loop : -0.30 (0.31), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1219 HIS 0.010 0.001 HIS A1225 PHE 0.028 0.002 PHE A 651 TYR 0.017 0.001 TYR A 768 ARG 0.003 0.000 ARG A 747 *********************** 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 102 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 75 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.4867 (mmm) cc_final: 0.3798 (ptp) REVERT: A 229 ASP cc_start: 0.6314 (OUTLIER) cc_final: 0.5993 (p0) REVERT: A 266 MET cc_start: 0.8355 (tpp) cc_final: 0.7898 (tpp) REVERT: A 272 MET cc_start: 0.8356 (ppp) cc_final: 0.8095 (ppp) REVERT: A 306 LYS cc_start: 0.6976 (tppt) cc_final: 0.6595 (ttpp) REVERT: A 311 ARG cc_start: 0.7309 (ppt90) cc_final: 0.7018 (mtp-110) REVERT: A 369 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7119 (mtt90) REVERT: A 423 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7590 (pp) REVERT: A 834 MET cc_start: 0.8068 (tpp) cc_final: 0.7856 (tpt) REVERT: A 992 LYS cc_start: 0.8487 (mtpp) cc_final: 0.8183 (ptmm) REVERT: A 1063 LYS cc_start: 0.7906 (mppt) cc_final: 0.7531 (mmtp) REVERT: A 1229 MET cc_start: 0.7991 (mmt) cc_final: 0.7699 (mmt) outliers start: 27 outliers final: 22 residues processed: 98 average time/residue: 0.2727 time to fit residues: 38.7907 Evaluate side-chains 101 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 302 LEU 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 760 THR Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 968 ASN Chi-restraints excluded: chain A residue 1046 ASP 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: 1.9990 chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 105 optimal weight: 0.4980 chunk 10 optimal weight: 10.0000 chunk 81 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 980 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12419 Z= 0.154 Angle : 0.528 10.412 17103 Z= 0.269 Chirality : 0.039 0.211 1947 Planarity : 0.004 0.040 1859 Dihedral : 18.532 171.681 2424 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 2.51 % Allowed : 16.59 % Favored : 80.90 % 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: 0.80 (0.25), residues: 1261 helix: 1.38 (0.20), residues: 670 sheet: -0.65 (0.48), residues: 114 loop : -0.29 (0.31), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 926 HIS 0.009 0.001 HIS A1225 PHE 0.027 0.001 PHE A 651 TYR 0.016 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 109 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 80 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.4845 (mmm) cc_final: 0.3744 (ptp) REVERT: A 229 ASP cc_start: 0.6334 (OUTLIER) cc_final: 0.6011 (p0) REVERT: A 266 MET cc_start: 0.8362 (tpp) cc_final: 0.7891 (tpp) REVERT: A 272 MET cc_start: 0.8377 (ppp) cc_final: 0.8109 (ppp) REVERT: A 306 LYS cc_start: 0.6979 (tppt) cc_final: 0.6585 (ttpp) REVERT: A 311 ARG cc_start: 0.7313 (ppt90) cc_final: 0.7015 (mtp-110) REVERT: A 352 THR cc_start: 0.8083 (m) cc_final: 0.7717 (p) REVERT: A 423 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7620 (pp) REVERT: A 834 MET cc_start: 0.8079 (tpp) cc_final: 0.7863 (tpt) REVERT: A 992 LYS cc_start: 0.8474 (mtpp) cc_final: 0.8175 (ptmm) REVERT: A 1063 LYS cc_start: 0.7927 (mppt) cc_final: 0.7547 (mmtp) REVERT: A 1076 MET cc_start: 0.7697 (mtm) cc_final: 0.7477 (mtm) outliers start: 29 outliers final: 22 residues processed: 105 average time/residue: 0.2806 time to fit residues: 43.3636 Evaluate side-chains 98 residues out of total 1159 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 74 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 321 LEU 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 477 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 517 ILE 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 941 LEU Chi-restraints excluded: chain A residue 968 ASN Chi-restraints excluded: chain A residue 1046 ASP 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 32 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 105 optimal weight: 0.0770 chunk 44 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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 = 0.4319 r_free = 0.4319 target = 0.164320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.118031 restraints weight = 22315.964| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.43 r_work: 0.3336 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12419 Z= 0.173 Angle : 0.540 10.535 17103 Z= 0.275 Chirality : 0.039 0.212 1947 Planarity : 0.004 0.040 1859 Dihedral : 18.512 172.315 2424 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer: Outliers : 2.51 % Allowed : 16.94 % Favored : 80.55 % 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: 1.45 (0.20), residues: 662 sheet: -0.61 (0.48), residues: 114 loop : -0.33 (0.31), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1219 HIS 0.007 0.001 HIS A1225 PHE 0.027 0.002 PHE A 651 TYR 0.016 0.001 TYR A 768 ARG 0.003 0.000 ARG A 344 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.98 seconds wall clock time: 51 minutes 24.00 seconds (3084.00 seconds total)