Starting phenix.real_space_refine on Thu Feb 15 04:40:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8att_15662/02_2024/8att_15662_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8att_15662/02_2024/8att_15662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8att_15662/02_2024/8att_15662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8att_15662/02_2024/8att_15662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8att_15662/02_2024/8att_15662_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8att_15662/02_2024/8att_15662_updated.pdb" } resolution = 3.44 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= 0.001 sd= 0.011 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 59 5.49 5 S 36 5.16 5 C 6931 2.51 5 N 1921 2.21 5 O 2177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 527": "OE1" <-> "OE2" Residue "A PHE 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 962": "OE1" <-> "OE2" Residue "A PHE 1209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1331": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11124 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2785 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 320} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 7184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7184 Classifications: {'peptide': 906} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 43, 'TRANS': 862} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "N" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "T" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 505 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' DC:plan2': 1, ' DG:plan': 1, ' DG:plan2': 1, ' DC:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.38, per 1000 atoms: 0.57 Number of scatterers: 11124 At special positions: 0 Unit cell: (104.76, 109.61, 119.31, 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 36 16.00 P 59 15.00 O 2177 8.00 N 1921 7.00 C 6931 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: 4.47 Conformation dependent library (CDL) restraints added in 1.8 seconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2354 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 10 sheets defined 51.5% alpha, 7.8% beta 22 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 38 through 41 No H-bonds generated for 'chain 'B' and resid 38 through 41' Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 59 through 68 Processing helix chain 'B' and resid 80 through 89 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.828A pdb=" N LYS B 214 " --> pdb=" O ASN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 256 through 266 Processing helix chain 'B' and resid 274 through 280 removed outlier: 4.048A pdb=" N MET B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP B 279 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N SER B 280 " --> pdb=" O THR B 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 280' Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 308 through 320 Processing helix chain 'A' and resid 408 through 419 removed outlier: 3.706A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 441 removed outlier: 3.618A pdb=" N TRP A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 476 Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 488 through 502 removed outlier: 3.840A pdb=" N LEU A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Proline residue: A 498 - end of helix removed outlier: 3.563A pdb=" N THR A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU A 502 " --> pdb=" O PRO A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 518 Processing helix chain 'A' and resid 531 through 557 Processing helix chain 'A' and resid 594 through 609 Processing helix chain 'A' and resid 653 through 659 removed outlier: 3.739A pdb=" N GLN A 658 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 667 removed outlier: 3.773A pdb=" N ILE A 665 " --> pdb=" O GLU A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 716 Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 738 through 750 Processing helix chain 'A' and resid 776 through 812 Processing helix chain 'A' and resid 843 through 847 Processing helix chain 'A' and resid 858 through 873 removed outlier: 4.657A pdb=" N LEU A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 899 removed outlier: 3.909A pdb=" N HIS A 890 " --> pdb=" O PHE A 886 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLN A 892 " --> pdb=" O GLU A 888 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP A 893 " --> pdb=" O SER A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 929 Processing helix chain 'A' and resid 933 through 935 No H-bonds generated for 'chain 'A' and resid 933 through 935' Processing helix chain 'A' and resid 949 through 958 Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 978 through 996 removed outlier: 4.448A pdb=" N GLU A 995 " --> pdb=" O GLU A 991 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LYS A 996 " --> pdb=" O ILE A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1006 removed outlier: 4.859A pdb=" N ASP A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1020 removed outlier: 4.053A pdb=" N THR A1019 " --> pdb=" O GLN A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1038 Processing helix chain 'A' and resid 1048 through 1065 removed outlier: 3.720A pdb=" N TYR A1053 " --> pdb=" O ASP A1049 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A1064 " --> pdb=" O SER A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1084 Processing helix chain 'A' and resid 1150 through 1180 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1198 through 1213 Processing helix chain 'A' and resid 1217 through 1228 Processing helix chain 'A' and resid 1243 through 1259 removed outlier: 3.630A pdb=" N LYS A1247 " --> pdb=" O ASP A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1265 through 1280 Processing helix chain 'A' and resid 1284 through 1292 Processing helix chain 'A' and resid 1296 through 1302 Processing helix chain 'A' and resid 1306 through 1309 No H-bonds generated for 'chain 'A' and resid 1306 through 1309' Processing helix chain 'A' and resid 1340 through 1345 removed outlier: 3.542A pdb=" N LEU A1343 " --> pdb=" O VAL A1340 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 72 through 76 removed outlier: 3.561A pdb=" N LEU B 133 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS B 167 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ALA B 136 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 169 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL B 138 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TRP B 171 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU B 246 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU B 204 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASP B 248 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N THR B 202 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 528 through 530 Processing sheet with id= C, first strand: chain 'A' and resid 613 through 620 removed outlier: 3.685A pdb=" N ALA A 625 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 817 through 819 Processing sheet with id= E, first strand: chain 'A' and resid 822 through 824 Processing sheet with id= F, first strand: chain 'A' and resid 942 through 945 removed outlier: 3.667A pdb=" N THR A1193 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A1185 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1086 through 1088 Processing sheet with id= H, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id= I, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 3.511A pdb=" N ILE A1139 " --> pdb=" O LYS A1128 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1236 through 1238 447 hydrogen bonds defined for protein. 1311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3347 1.34 - 1.46: 2025 1.46 - 1.57: 5952 1.57 - 1.69: 108 1.69 - 1.81: 61 Bond restraints: 11493 Sorted by residual: bond pdb=" O3' DG N 126 " pdb=" P DA N 127 " ideal model delta sigma weight residual 1.607 1.475 0.132 1.50e-02 4.44e+03 7.76e+01 bond pdb=" O3' DA N 129 " pdb=" P DA N 130 " ideal model delta sigma weight residual 1.607 1.504 0.103 1.50e-02 4.44e+03 4.75e+01 bond pdb=" C4' DG N 108 " pdb=" O4' DG N 108 " ideal model delta sigma weight residual 1.450 1.552 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O3' DT N 128 " pdb=" P DA N 129 " ideal model delta sigma weight residual 1.607 1.678 -0.071 1.50e-02 4.44e+03 2.21e+01 bond pdb=" O3' DA N 125 " pdb=" P DG N 126 " ideal model delta sigma weight residual 1.607 1.677 -0.070 1.50e-02 4.44e+03 2.18e+01 ... (remaining 11488 not shown) Histogram of bond angle deviations from ideal: 95.71 - 103.38: 210 103.38 - 111.04: 4682 111.04 - 118.70: 4752 118.70 - 126.37: 5788 126.37 - 134.03: 363 Bond angle restraints: 15795 Sorted by residual: angle pdb=" C5' DG N 108 " pdb=" C4' DG N 108 " pdb=" O4' DG N 108 " ideal model delta sigma weight residual 109.40 127.10 -17.70 1.50e+00 4.44e-01 1.39e+02 angle pdb=" C3' DG N 126 " pdb=" O3' DG N 126 " pdb=" P DA N 127 " ideal model delta sigma weight residual 120.20 107.37 12.83 1.50e+00 4.44e-01 7.31e+01 angle pdb=" C5' DT T 16 " pdb=" C4' DT T 16 " pdb=" O4' DT T 16 " ideal model delta sigma weight residual 109.40 121.15 -11.75 1.50e+00 4.44e-01 6.13e+01 angle pdb=" C4' DA T 19 " pdb=" C3' DA T 19 " pdb=" O3' DA T 19 " ideal model delta sigma weight residual 110.00 120.31 -10.31 1.50e+00 4.44e-01 4.72e+01 angle pdb=" CA PRO A 621 " pdb=" N PRO A 621 " pdb=" CD PRO A 621 " ideal model delta sigma weight residual 112.00 102.99 9.01 1.40e+00 5.10e-01 4.14e+01 ... (remaining 15790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.43: 6258 26.43 - 52.87: 483 52.87 - 79.30: 82 79.30 - 105.73: 5 105.73 - 132.17: 1 Dihedral angle restraints: 6829 sinusoidal: 3194 harmonic: 3635 Sorted by residual: dihedral pdb=" C4' GTP C 201 " pdb=" C5' GTP C 201 " pdb=" O5' GTP C 201 " pdb=" PA GTP C 201 " ideal model delta sinusoidal sigma weight residual 260.87 128.71 132.17 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 3.46 101.14 1 2.00e+01 2.50e-03 2.86e+01 dihedral pdb=" C5' GTP C 201 " pdb=" O5' GTP C 201 " pdb=" PA GTP C 201 " pdb=" O3A GTP C 201 " ideal model delta sinusoidal sigma weight residual 69.27 5.26 64.01 1 2.00e+01 2.50e-03 1.35e+01 ... (remaining 6826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1697 0.127 - 0.254: 28 0.254 - 0.381: 2 0.381 - 0.508: 8 0.508 - 0.635: 10 Chirality restraints: 1745 Sorted by residual: chirality pdb=" P DC T 24 " pdb=" OP1 DC T 24 " pdb=" OP2 DC T 24 " pdb=" O5' DC T 24 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DA N 122 " pdb=" OP1 DA N 122 " pdb=" OP2 DA N 122 " pdb=" O5' DA N 122 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.52e+00 chirality pdb=" P DG T 22 " pdb=" OP1 DG T 22 " pdb=" OP2 DG T 22 " pdb=" O5' DG T 22 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.57 2.00e-01 2.50e+01 8.03e+00 ... (remaining 1742 not shown) Planarity restraints: 1822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 620 " 0.068 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO A 621 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 431 " -0.018 2.00e-02 2.50e+03 1.38e-02 4.74e+00 pdb=" CG TRP A 431 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 431 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 431 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 431 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 431 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 431 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 431 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 431 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 431 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1019 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C THR A1019 " -0.033 2.00e-02 2.50e+03 pdb=" O THR A1019 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN A1020 " 0.011 2.00e-02 2.50e+03 ... (remaining 1819 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 256 2.68 - 3.24: 10785 3.24 - 3.79: 17978 3.79 - 4.35: 23676 4.35 - 4.90: 37611 Nonbonded interactions: 90306 Sorted by model distance: nonbonded pdb=" OG SER A1186 " pdb=" O SER A1190 " model vdw 2.127 2.440 nonbonded pdb=" OG1 THR A1132 " pdb=" O GLN A1135 " model vdw 2.134 2.440 nonbonded pdb=" OG1 THR B 307 " pdb=" OE1 GLU B 310 " model vdw 2.210 2.440 nonbonded pdb=" NZ LYS B 21 " pdb=" O LYS B 240 " model vdw 2.227 2.520 nonbonded pdb=" OG SER A 703 " pdb=" OE1 GLN A 706 " model vdw 2.232 2.440 ... (remaining 90301 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.070 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: 1.150 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 35.290 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 : 0.005 0.132 11493 Z= 0.275 Angle : 0.806 17.700 15795 Z= 0.451 Chirality : 0.070 0.635 1745 Planarity : 0.005 0.097 1822 Dihedral : 17.712 132.167 4475 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.63 % 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 (0.24), residues: 1238 helix: 1.64 (0.21), residues: 685 sheet: -0.20 (0.50), residues: 106 loop : -0.88 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 431 HIS 0.005 0.001 HIS A1213 PHE 0.024 0.001 PHE A1338 TYR 0.012 0.001 TYR A 496 ARG 0.003 0.000 ARG A1063 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ASN cc_start: 0.8252 (p0) cc_final: 0.7887 (p0) REVERT: A 544 MET cc_start: 0.7622 (mmt) cc_final: 0.7396 (mmt) REVERT: A 657 ARG cc_start: 0.8021 (ttm-80) cc_final: 0.7801 (ptm160) REVERT: A 763 GLU cc_start: 0.6832 (pt0) cc_final: 0.6549 (pt0) REVERT: A 976 GLN cc_start: 0.6396 (mt0) cc_final: 0.5625 (tp-100) REVERT: A 1157 LEU cc_start: 0.6675 (tp) cc_final: 0.6426 (tp) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.2220 time to fit residues: 53.7661 Evaluate side-chains 131 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.0030 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 HIS ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11493 Z= 0.214 Angle : 0.572 8.203 15795 Z= 0.305 Chirality : 0.041 0.156 1745 Planarity : 0.004 0.041 1822 Dihedral : 19.265 128.363 2005 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.29 % Allowed : 7.82 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1238 helix: 1.67 (0.20), residues: 686 sheet: 0.02 (0.52), residues: 96 loop : -0.68 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 431 HIS 0.005 0.001 HIS A1213 PHE 0.012 0.001 PHE A1041 TYR 0.032 0.002 TYR B 161 ARG 0.003 0.000 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 ILE cc_start: 0.8594 (mp) cc_final: 0.8318 (mm) REVERT: B 334 MET cc_start: 0.6332 (mmt) cc_final: 0.6052 (mmm) REVERT: A 544 MET cc_start: 0.7657 (mmt) cc_final: 0.7447 (mmt) REVERT: A 976 GLN cc_start: 0.6613 (mt0) cc_final: 0.5744 (tp-100) REVERT: A 1070 HIS cc_start: 0.6939 (t-90) cc_final: 0.6598 (t70) outliers start: 14 outliers final: 11 residues processed: 155 average time/residue: 0.2159 time to fit residues: 49.5236 Evaluate side-chains 153 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 142 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1125 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS A 660 ASN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11493 Z= 0.263 Angle : 0.579 7.843 15795 Z= 0.305 Chirality : 0.041 0.155 1745 Planarity : 0.004 0.045 1822 Dihedral : 19.420 125.577 2005 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.48 % Allowed : 10.67 % Favored : 86.84 % 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: 0.85 (0.24), residues: 1238 helix: 1.58 (0.20), residues: 687 sheet: -0.63 (0.48), residues: 112 loop : -0.69 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 431 HIS 0.009 0.001 HIS A 943 PHE 0.018 0.002 PHE A1338 TYR 0.020 0.002 TYR A 954 ARG 0.002 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 334 MET cc_start: 0.6438 (mmt) cc_final: 0.6121 (mmm) REVERT: A 553 LYS cc_start: 0.6230 (pptt) cc_final: 0.5893 (pptt) REVERT: A 976 GLN cc_start: 0.6853 (mt0) cc_final: 0.5959 (tp-100) REVERT: A 1070 HIS cc_start: 0.7293 (t-90) cc_final: 0.6961 (t70) REVERT: A 1250 ARG cc_start: 0.8154 (mmp80) cc_final: 0.7860 (mmp-170) REVERT: A 1300 PHE cc_start: 0.6739 (m-80) cc_final: 0.5880 (m-80) outliers start: 27 outliers final: 17 residues processed: 159 average time/residue: 0.2143 time to fit residues: 50.6028 Evaluate side-chains 152 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 20.0000 chunk 87 optimal weight: 0.0770 chunk 60 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 78 optimal weight: 30.0000 chunk 116 optimal weight: 40.0000 chunk 123 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 overall best weight: 6.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11493 Z= 0.331 Angle : 0.612 8.617 15795 Z= 0.323 Chirality : 0.042 0.160 1745 Planarity : 0.004 0.047 1822 Dihedral : 19.465 123.587 2005 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.50 % Allowed : 13.34 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.24), residues: 1238 helix: 1.41 (0.20), residues: 681 sheet: -0.55 (0.49), residues: 108 loop : -0.86 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 431 HIS 0.006 0.001 HIS A 652 PHE 0.021 0.002 PHE A1338 TYR 0.029 0.002 TYR B 161 ARG 0.007 0.000 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: B 255 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7580 (p0) REVERT: A 553 LYS cc_start: 0.6240 (pptt) cc_final: 0.5934 (pptt) REVERT: A 976 GLN cc_start: 0.6852 (mt0) cc_final: 0.5865 (tp-100) REVERT: A 1070 HIS cc_start: 0.7579 (t-90) cc_final: 0.7267 (t70) REVERT: A 1300 PHE cc_start: 0.6791 (m-80) cc_final: 0.5885 (m-80) outliers start: 38 outliers final: 31 residues processed: 159 average time/residue: 0.2209 time to fit residues: 51.7819 Evaluate side-chains 159 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 0.0060 chunk 111 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11493 Z= 0.170 Angle : 0.545 7.958 15795 Z= 0.284 Chirality : 0.039 0.143 1745 Planarity : 0.004 0.043 1822 Dihedral : 19.126 121.649 2005 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.94 % Allowed : 15.09 % Favored : 81.97 % 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: 0.96 (0.25), residues: 1238 helix: 1.68 (0.21), residues: 686 sheet: -0.48 (0.48), residues: 112 loop : -0.69 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 431 HIS 0.005 0.001 HIS A1213 PHE 0.022 0.001 PHE A1338 TYR 0.030 0.002 TYR B 161 ARG 0.004 0.000 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.7894 (tt0) cc_final: 0.7173 (tt0) REVERT: B 255 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7582 (p0) REVERT: A 553 LYS cc_start: 0.6226 (pptt) cc_final: 0.6016 (pptt) REVERT: A 976 GLN cc_start: 0.6653 (mt0) cc_final: 0.5586 (tp-100) REVERT: A 1070 HIS cc_start: 0.7552 (t-90) cc_final: 0.7177 (t70) REVERT: A 1300 PHE cc_start: 0.6755 (m-80) cc_final: 0.5815 (m-80) outliers start: 32 outliers final: 23 residues processed: 157 average time/residue: 0.2295 time to fit residues: 53.4539 Evaluate side-chains 159 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 123 optimal weight: 0.0170 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11493 Z= 0.236 Angle : 0.574 8.995 15795 Z= 0.298 Chirality : 0.040 0.151 1745 Planarity : 0.004 0.042 1822 Dihedral : 19.112 119.547 2005 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.22 % Allowed : 15.55 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1238 helix: 1.66 (0.21), residues: 681 sheet: -0.37 (0.49), residues: 108 loop : -0.74 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 431 HIS 0.004 0.001 HIS A1213 PHE 0.022 0.001 PHE A1338 TYR 0.043 0.002 TYR B 161 ARG 0.002 0.000 ARG A1250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.7939 (tt0) cc_final: 0.7218 (tt0) REVERT: B 255 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7645 (p0) REVERT: A 553 LYS cc_start: 0.6244 (pptt) cc_final: 0.6026 (pptt) REVERT: A 1070 HIS cc_start: 0.7593 (t-90) cc_final: 0.7250 (t70) REVERT: A 1250 ARG cc_start: 0.8497 (mmm160) cc_final: 0.7869 (tpp80) REVERT: A 1300 PHE cc_start: 0.6841 (m-80) cc_final: 0.5893 (m-80) outliers start: 35 outliers final: 29 residues processed: 156 average time/residue: 0.2299 time to fit residues: 52.7557 Evaluate side-chains 160 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 50.0000 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11493 Z= 0.289 Angle : 0.605 8.829 15795 Z= 0.314 Chirality : 0.041 0.182 1745 Planarity : 0.004 0.043 1822 Dihedral : 19.191 118.315 2005 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.68 % Allowed : 15.82 % Favored : 80.50 % 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 (0.24), residues: 1238 helix: 1.52 (0.20), residues: 681 sheet: -0.43 (0.48), residues: 108 loop : -0.81 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 431 HIS 0.004 0.001 HIS A 652 PHE 0.025 0.002 PHE A1338 TYR 0.019 0.002 TYR B 83 ARG 0.002 0.000 ARG A1206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.7970 (tt0) cc_final: 0.7225 (tt0) REVERT: B 255 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7629 (p0) REVERT: A 673 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7653 (pp) REVERT: A 1070 HIS cc_start: 0.7679 (t-90) cc_final: 0.7318 (t70) REVERT: A 1250 ARG cc_start: 0.8483 (mmm160) cc_final: 0.8226 (mmm160) REVERT: A 1300 PHE cc_start: 0.6883 (m-80) cc_final: 0.5894 (m-80) outliers start: 40 outliers final: 33 residues processed: 156 average time/residue: 0.2376 time to fit residues: 54.7294 Evaluate side-chains 159 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 124 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 11 optimal weight: 0.0970 chunk 96 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11493 Z= 0.223 Angle : 0.580 8.528 15795 Z= 0.302 Chirality : 0.040 0.163 1745 Planarity : 0.004 0.041 1822 Dihedral : 19.103 116.726 2005 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.50 % Allowed : 16.10 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1238 helix: 1.56 (0.20), residues: 679 sheet: -0.40 (0.48), residues: 108 loop : -0.76 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 431 HIS 0.003 0.001 HIS A1213 PHE 0.025 0.001 PHE A1338 TYR 0.019 0.002 TYR B 83 ARG 0.002 0.000 ARG A 827 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.7935 (tt0) cc_final: 0.7184 (tt0) REVERT: B 255 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7626 (p0) REVERT: A 673 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7630 (pp) REVERT: A 824 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8061 (mp) REVERT: A 1070 HIS cc_start: 0.7668 (t-90) cc_final: 0.7247 (t70) REVERT: A 1250 ARG cc_start: 0.8480 (mmm160) cc_final: 0.8208 (mmm160) REVERT: A 1300 PHE cc_start: 0.6883 (m-80) cc_final: 0.5887 (m-80) outliers start: 38 outliers final: 31 residues processed: 159 average time/residue: 0.2209 time to fit residues: 52.3256 Evaluate side-chains 162 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 114 optimal weight: 0.0370 chunk 69 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 overall best weight: 5.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11493 Z= 0.298 Angle : 0.622 10.659 15795 Z= 0.321 Chirality : 0.041 0.169 1745 Planarity : 0.004 0.043 1822 Dihedral : 19.170 115.752 2005 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.68 % Allowed : 16.19 % Favored : 80.13 % 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: 0.61 (0.24), residues: 1238 helix: 1.42 (0.20), residues: 678 sheet: -0.45 (0.48), residues: 108 loop : -0.89 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 431 HIS 0.004 0.001 HIS A 953 PHE 0.025 0.002 PHE A1338 TYR 0.018 0.002 TYR B 83 ARG 0.003 0.000 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.7951 (tt0) cc_final: 0.7194 (tt0) REVERT: B 255 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7592 (p0) REVERT: A 673 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7739 (pp) REVERT: A 824 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8041 (mp) REVERT: A 1250 ARG cc_start: 0.8505 (mmm160) cc_final: 0.8252 (mmm160) REVERT: A 1300 PHE cc_start: 0.6898 (m-80) cc_final: 0.5878 (m-80) outliers start: 40 outliers final: 33 residues processed: 157 average time/residue: 0.2212 time to fit residues: 50.7739 Evaluate side-chains 161 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 125 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 0.0570 chunk 84 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11493 Z= 0.160 Angle : 0.581 11.916 15795 Z= 0.296 Chirality : 0.039 0.146 1745 Planarity : 0.004 0.042 1822 Dihedral : 18.912 112.961 2005 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.48 % Allowed : 17.57 % Favored : 79.94 % 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 (0.24), residues: 1238 helix: 1.61 (0.20), residues: 683 sheet: -0.29 (0.49), residues: 108 loop : -0.72 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 431 HIS 0.004 0.001 HIS A1213 PHE 0.024 0.001 PHE A1338 TYR 0.018 0.001 TYR B 83 ARG 0.003 0.000 ARG A 827 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 TYR cc_start: 0.7319 (m-10) cc_final: 0.6897 (m-10) REVERT: B 72 GLN cc_start: 0.7916 (tt0) cc_final: 0.7175 (tt0) REVERT: B 255 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7312 (p0) REVERT: A 673 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7631 (pp) REVERT: A 824 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8027 (mp) REVERT: A 871 ASN cc_start: 0.7509 (m110) cc_final: 0.7297 (m-40) REVERT: A 1300 PHE cc_start: 0.6933 (m-80) cc_final: 0.5966 (m-80) outliers start: 27 outliers final: 22 residues processed: 163 average time/residue: 0.2113 time to fit residues: 50.9900 Evaluate side-chains 160 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.175059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134255 restraints weight = 17180.182| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.46 r_work: 0.3646 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11493 Z= 0.168 Angle : 0.584 11.337 15795 Z= 0.297 Chirality : 0.039 0.159 1745 Planarity : 0.004 0.041 1822 Dihedral : 18.818 110.924 2005 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.58 % Allowed : 17.85 % Favored : 79.58 % 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: 0.97 (0.25), residues: 1238 helix: 1.67 (0.20), residues: 682 sheet: -0.22 (0.48), residues: 108 loop : -0.71 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 431 HIS 0.004 0.001 HIS A1213 PHE 0.025 0.001 PHE A1338 TYR 0.044 0.002 TYR B 161 ARG 0.004 0.000 ARG A1240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2279.25 seconds wall clock time: 42 minutes 26.47 seconds (2546.47 seconds total)