Starting phenix.real_space_refine on Sun Apr 7 09:39:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8se9_40407/04_2024/8se9_40407_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8se9_40407/04_2024/8se9_40407.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8se9_40407/04_2024/8se9_40407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8se9_40407/04_2024/8se9_40407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8se9_40407/04_2024/8se9_40407_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8se9_40407/04_2024/8se9_40407_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= 0.023 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 1 5.49 5 S 38 5.16 5 C 6480 2.51 5 N 1790 2.21 5 O 1886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10195 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7693 Classifications: {'peptide': 989} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 923} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 633 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "C" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1243 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133} Chain: "D" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 5.37, per 1000 atoms: 0.53 Number of scatterers: 10195 At special positions: 0 Unit cell: (91.652, 105.816, 117.481, 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 38 16.00 P 1 15.00 O 1886 8.00 N 1790 7.00 C 6480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS C 86 " distance=2.03 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: 3.96 Conformation dependent library (CDL) restraints added in 1.8 seconds 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 12 sheets defined 36.5% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 25 through 32 removed outlier: 3.533A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 31 " --> pdb=" O MET A 27 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 87 through 98 removed outlier: 3.919A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.837A pdb=" N ASP A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 141 Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 267 through 270 No H-bonds generated for 'chain 'A' and resid 267 through 270' Processing helix chain 'A' and resid 281 through 304 Processing helix chain 'A' and resid 313 through 325 Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 416 through 419 No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 442 through 454 Processing helix chain 'A' and resid 477 through 479 No H-bonds generated for 'chain 'A' and resid 477 through 479' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 518 through 520 No H-bonds generated for 'chain 'A' and resid 518 through 520' Processing helix chain 'A' and resid 526 through 529 No H-bonds generated for 'chain 'A' and resid 526 through 529' Processing helix chain 'A' and resid 542 through 555 Processing helix chain 'A' and resid 586 through 592 Processing helix chain 'A' and resid 598 through 600 No H-bonds generated for 'chain 'A' and resid 598 through 600' Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 645 through 653 Processing helix chain 'A' and resid 671 through 681 removed outlier: 4.771A pdb=" N HIS A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 691 Processing helix chain 'A' and resid 723 through 739 removed outlier: 3.638A pdb=" N TYR A 727 " --> pdb=" O THR A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 755 Processing helix chain 'A' and resid 761 through 769 removed outlier: 6.153A pdb=" N ALA A 766 " --> pdb=" O GLN A 763 " (cutoff:3.500A) Proline residue: A 767 - end of helix Processing helix chain 'A' and resid 783 through 797 Processing helix chain 'A' and resid 817 through 831 removed outlier: 3.515A pdb=" N VAL A 821 " --> pdb=" O HIS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 843 Processing helix chain 'A' and resid 854 through 873 removed outlier: 3.678A pdb=" N LYS A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 880 No H-bonds generated for 'chain 'A' and resid 878 through 880' Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 928 through 938 Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 971 through 979 Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 137 through 139 No H-bonds generated for 'chain 'B' and resid 137 through 139' Processing helix chain 'C' and resid 3 through 16 removed outlier: 3.616A pdb=" N LYS C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 101 through 113 Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 133 through 147 Processing helix chain 'D' and resid 104 through 115 removed outlier: 4.677A pdb=" N GLN D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN D 110 " --> pdb=" O HIS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 139 No H-bonds generated for 'chain 'D' and resid 137 through 139' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 38 removed outlier: 6.936A pdb=" N VAL A 121 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N SER A 38 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 123 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS A 145 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU A 124 " --> pdb=" O CYS A 145 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU A 147 " --> pdb=" O LEU A 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.630A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 166 through 168 Processing sheet with id= D, first strand: chain 'A' and resid 178 through 180 removed outlier: 3.511A pdb=" N THR A 254 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU A 208 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 464 through 467 Processing sheet with id= F, first strand: chain 'A' and resid 534 through 537 removed outlier: 7.357A pdb=" N ALA A 537 " --> pdb=" O PRO A 558 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU A 560 " --> pdb=" O ALA A 537 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 559 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 904 through 906 Processing sheet with id= H, first strand: chain 'A' and resid 917 through 920 Processing sheet with id= I, first strand: chain 'A' and resid 945 through 948 removed outlier: 6.238A pdb=" N HIS A 948 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU A 952 " --> pdb=" O HIS A 948 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 93 through 98 Processing sheet with id= K, first strand: chain 'C' and resid 34 through 39 Processing sheet with id= L, first strand: chain 'D' and resid 122 through 125 removed outlier: 4.230A pdb=" N TRP D 123 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN D 151 " --> pdb=" O TRP D 123 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 4.28 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: 3379 1.34 - 1.46: 1342 1.46 - 1.57: 5665 1.57 - 1.69: 4 1.69 - 1.81: 57 Bond restraints: 10447 Sorted by residual: bond pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.415 1.624 -0.209 1.50e-02 4.44e+03 1.94e+02 bond pdb=" C1' AMP B1101 " pdb=" C2' AMP B1101 " ideal model delta sigma weight residual 1.526 1.363 0.163 1.50e-02 4.44e+03 1.17e+02 bond pdb=" C4' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 1.454 1.294 0.160 1.50e-02 4.44e+03 1.13e+02 bond pdb=" C6 AMP B1101 " pdb=" N6 AMP B1101 " ideal model delta sigma weight residual 1.355 1.499 -0.144 2.00e-02 2.50e+03 5.15e+01 bond pdb=" C4 AMP B1101 " pdb=" C5 AMP B1101 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.30e+01 ... (remaining 10442 not shown) Histogram of bond angle deviations from ideal: 94.58 - 102.59: 36 102.59 - 110.60: 3292 110.60 - 118.61: 5178 118.61 - 126.62: 5507 126.62 - 134.63: 211 Bond angle restraints: 14224 Sorted by residual: angle pdb=" N9 AMP B1101 " pdb=" C1' AMP B1101 " pdb=" O4' AMP B1101 " ideal model delta sigma weight residual 108.20 94.58 13.62 1.50e+00 4.44e-01 8.24e+01 angle pdb=" C2' AMP B1101 " pdb=" C1' AMP B1101 " pdb=" N9 AMP B1101 " ideal model delta sigma weight residual 114.00 126.43 -12.43 1.50e+00 4.44e-01 6.87e+01 angle pdb=" C1' AMP B1101 " pdb=" C2' AMP B1101 " pdb=" C3' AMP B1101 " ideal model delta sigma weight residual 101.50 106.56 -5.06 1.00e+00 1.00e+00 2.56e+01 angle pdb=" O2P AMP B1101 " pdb=" P AMP B1101 " pdb=" O3P AMP B1101 " ideal model delta sigma weight residual 119.90 106.91 12.99 3.00e+00 1.11e-01 1.87e+01 angle pdb=" C GLY A 187 " pdb=" N SER A 188 " pdb=" CA SER A 188 " ideal model delta sigma weight residual 121.80 132.20 -10.40 2.44e+00 1.68e-01 1.82e+01 ... (remaining 14219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5885 17.67 - 35.35: 323 35.35 - 53.02: 65 53.02 - 70.70: 14 70.70 - 88.37: 8 Dihedral angle restraints: 6295 sinusoidal: 2548 harmonic: 3747 Sorted by residual: dihedral pdb=" CA SER A 188 " pdb=" C SER A 188 " pdb=" N PRO A 189 " pdb=" CA PRO A 189 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLN A 923 " pdb=" C GLN A 923 " pdb=" N PRO A 924 " pdb=" CA PRO A 924 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" C1' AMP B1101 " pdb=" C4' AMP B1101 " pdb=" O4' AMP B1101 " pdb=" C5' AMP B1101 " ideal model delta sinusoidal sigma weight residual -123.00 -145.10 22.10 1 8.00e+00 1.56e-02 1.10e+01 ... (remaining 6292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 987 0.029 - 0.058: 416 0.058 - 0.087: 106 0.087 - 0.116: 69 0.116 - 0.145: 10 Chirality restraints: 1588 Sorted by residual: chirality pdb=" C2' AMP B1101 " pdb=" C1' AMP B1101 " pdb=" C3' AMP B1101 " pdb=" O2' AMP B1101 " both_signs ideal model delta sigma weight residual False -2.52 -2.37 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 945 " pdb=" N ILE A 945 " pdb=" C ILE A 945 " pdb=" CB ILE A 945 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 1585 not shown) Planarity restraints: 1865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 517 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 518 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 188 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO A 189 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 923 " -0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO A 924 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 924 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 924 " -0.015 5.00e-02 4.00e+02 ... (remaining 1862 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 1485 2.76 - 3.47: 14222 3.47 - 4.19: 22936 4.19 - 4.90: 41521 Nonbonded interactions: 80165 Sorted by model distance: nonbonded pdb=" NZ LYS C 121 " pdb=" C GLY D 157 " model vdw 1.330 3.350 nonbonded pdb=" OE1 GLU A 925 " pdb=" OG1 THR A 972 " model vdw 2.204 2.440 nonbonded pdb=" O TYR A 514 " pdb=" OH TYR A 524 " model vdw 2.219 2.440 nonbonded pdb=" NZ LYS C 121 " pdb=" O GLY D 157 " model vdw 2.230 2.520 nonbonded pdb=" OH TYR C 46 " pdb=" O TYR C 75 " model vdw 2.235 2.440 ... (remaining 80160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 82 through 157) selection = chain 'D' } 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 10.000 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 29.510 Find NCS groups from input model: 0.320 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 0.209 10447 Z= 0.302 Angle : 0.583 13.618 14224 Z= 0.292 Chirality : 0.038 0.145 1588 Planarity : 0.004 0.048 1865 Dihedral : 11.987 88.369 3868 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.41 % Favored : 96.43 % Rotamer: Outliers : 2.00 % Allowed : 7.45 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.48 (0.24), residues: 1289 helix: 1.53 (0.24), residues: 457 sheet: -0.62 (0.40), residues: 171 loop : -0.21 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 95 HIS 0.002 0.001 HIS A 275 PHE 0.008 0.001 PHE A 146 TYR 0.008 0.001 TYR C 61 ARG 0.002 0.000 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 225 PRO cc_start: 0.8058 (Cg_exo) cc_final: 0.7802 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7357 (tm-30) cc_final: 0.6964 (tm-30) REVERT: A 373 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8519 (mm) REVERT: A 508 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7171 (mt0) REVERT: A 531 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7513 (ptp-110) REVERT: A 638 THR cc_start: 0.3737 (OUTLIER) cc_final: 0.3268 (m) REVERT: A 738 MET cc_start: 0.3515 (ppp) cc_final: 0.0513 (mmm) REVERT: C 5 MET cc_start: 0.8894 (tpt) cc_final: 0.8506 (tpt) REVERT: C 43 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7496 (tm-30) REVERT: C 70 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: D 99 ARG cc_start: 0.8030 (mmp-170) cc_final: 0.7529 (mmm160) outliers start: 22 outliers final: 10 residues processed: 152 average time/residue: 0.2581 time to fit residues: 53.5501 Evaluate side-chains 119 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.4980 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 10.0000 chunk 74 optimal weight: 0.0070 chunk 116 optimal weight: 0.5980 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 140 HIS A 199 ASN A 634 GLN A 637 HIS ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 GLN ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 HIS A 939 HIS A1009 HIS ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS B 110 GLN C 103 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10447 Z= 0.138 Angle : 0.525 10.360 14224 Z= 0.247 Chirality : 0.038 0.161 1588 Planarity : 0.004 0.048 1865 Dihedral : 5.708 58.211 1432 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 2.09 % Allowed : 10.73 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1289 helix: 1.75 (0.24), residues: 457 sheet: -0.62 (0.39), residues: 176 loop : -0.18 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 677 HIS 0.007 0.000 HIS A 682 PHE 0.016 0.001 PHE A 481 TYR 0.010 0.001 TYR A1010 ARG 0.005 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8652 (mp) REVERT: A 225 PRO cc_start: 0.7950 (Cg_exo) cc_final: 0.7687 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7357 (tm-30) cc_final: 0.7071 (tm-30) REVERT: A 373 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8524 (mm) REVERT: A 508 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7132 (mt0) REVERT: A 531 ARG cc_start: 0.7911 (mtm110) cc_final: 0.7552 (ptp-110) REVERT: A 568 TRP cc_start: 0.8805 (m100) cc_final: 0.8528 (m100) REVERT: A 638 THR cc_start: 0.3583 (OUTLIER) cc_final: 0.3188 (m) REVERT: A 738 MET cc_start: 0.3538 (ppp) cc_final: 0.0595 (mmm) REVERT: B 140 TYR cc_start: 0.7682 (m-80) cc_final: 0.7134 (m-10) REVERT: C 5 MET cc_start: 0.8873 (tpt) cc_final: 0.8476 (tpt) REVERT: C 70 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: D 99 ARG cc_start: 0.8031 (mmp-170) cc_final: 0.7514 (mmm160) outliers start: 23 outliers final: 7 residues processed: 131 average time/residue: 0.2561 time to fit residues: 46.5066 Evaluate side-chains 118 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 103 optimal weight: 0.0970 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 0.0670 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10447 Z= 0.245 Angle : 0.549 10.357 14224 Z= 0.255 Chirality : 0.039 0.128 1588 Planarity : 0.004 0.050 1865 Dihedral : 5.347 58.831 1423 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 2.64 % Allowed : 11.82 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.52 (0.24), residues: 1289 helix: 1.69 (0.24), residues: 459 sheet: -0.56 (0.39), residues: 170 loop : -0.31 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 677 HIS 0.004 0.001 HIS A 682 PHE 0.012 0.001 PHE A 481 TYR 0.008 0.001 TYR A1010 ARG 0.005 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8759 (mp) REVERT: A 225 PRO cc_start: 0.8032 (Cg_exo) cc_final: 0.7758 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7344 (tm-30) cc_final: 0.7060 (tm-30) REVERT: A 373 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8581 (mm) REVERT: A 508 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7154 (mt0) REVERT: A 531 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7534 (ptp-110) REVERT: A 638 THR cc_start: 0.3651 (OUTLIER) cc_final: 0.3255 (m) REVERT: A 738 MET cc_start: 0.3659 (ppp) cc_final: 0.0764 (mmm) REVERT: C 5 MET cc_start: 0.8901 (tpt) cc_final: 0.8505 (tpt) REVERT: C 70 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: D 99 ARG cc_start: 0.8037 (mmp-170) cc_final: 0.7523 (mmm160) outliers start: 29 outliers final: 15 residues processed: 128 average time/residue: 0.2407 time to fit residues: 43.2451 Evaluate side-chains 125 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 7.9990 chunk 87 optimal weight: 0.2980 chunk 60 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 116 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10447 Z= 0.225 Angle : 0.536 10.352 14224 Z= 0.249 Chirality : 0.038 0.125 1588 Planarity : 0.004 0.050 1865 Dihedral : 5.454 59.604 1423 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.82 % Rotamer: Outliers : 2.73 % Allowed : 12.73 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.48 (0.24), residues: 1289 helix: 1.65 (0.24), residues: 458 sheet: -0.60 (0.38), residues: 170 loop : -0.32 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 677 HIS 0.003 0.001 HIS A 682 PHE 0.013 0.001 PHE A 481 TYR 0.008 0.001 TYR A1010 ARG 0.005 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8837 (mp) REVERT: A 225 PRO cc_start: 0.8080 (Cg_exo) cc_final: 0.7806 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7375 (tm-30) cc_final: 0.7095 (tm-30) REVERT: A 373 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8563 (mm) REVERT: A 508 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7151 (mt0) REVERT: A 531 ARG cc_start: 0.7880 (mtm110) cc_final: 0.7484 (ptp-110) REVERT: A 638 THR cc_start: 0.3529 (OUTLIER) cc_final: 0.3128 (m) REVERT: A 713 GLN cc_start: 0.9035 (tt0) cc_final: 0.8739 (pp30) REVERT: A 738 MET cc_start: 0.3673 (ppp) cc_final: 0.0843 (mmm) REVERT: B 140 TYR cc_start: 0.8127 (m-80) cc_final: 0.7870 (m-10) REVERT: C 5 MET cc_start: 0.8869 (tpt) cc_final: 0.8490 (tpt) REVERT: C 70 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: D 99 ARG cc_start: 0.8011 (mmp-170) cc_final: 0.7504 (mmm160) REVERT: D 110 GLN cc_start: 0.1568 (OUTLIER) cc_final: 0.0885 (mp10) outliers start: 30 outliers final: 19 residues processed: 128 average time/residue: 0.2400 time to fit residues: 43.0299 Evaluate side-chains 128 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 1 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.0030 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10447 Z= 0.166 Angle : 0.525 10.372 14224 Z= 0.241 Chirality : 0.038 0.149 1588 Planarity : 0.004 0.049 1865 Dihedral : 5.354 59.178 1423 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 2.09 % Allowed : 14.00 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.24), residues: 1289 helix: 1.73 (0.24), residues: 459 sheet: -0.54 (0.40), residues: 164 loop : -0.25 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 677 HIS 0.003 0.000 HIS A 682 PHE 0.016 0.001 PHE A 481 TYR 0.008 0.001 TYR A1010 ARG 0.005 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8765 (mp) REVERT: A 225 PRO cc_start: 0.8087 (Cg_exo) cc_final: 0.7818 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7354 (tm-30) cc_final: 0.7076 (tm-30) REVERT: A 373 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8531 (mm) REVERT: A 508 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7385 (pt0) REVERT: A 531 ARG cc_start: 0.7898 (mtm110) cc_final: 0.7479 (ptp-110) REVERT: A 638 THR cc_start: 0.3579 (OUTLIER) cc_final: 0.3195 (m) REVERT: A 695 ASN cc_start: 0.5635 (OUTLIER) cc_final: 0.5419 (t0) REVERT: A 713 GLN cc_start: 0.9035 (tt0) cc_final: 0.8741 (pp30) REVERT: A 718 ASP cc_start: 0.1069 (OUTLIER) cc_final: -0.0455 (t70) REVERT: A 738 MET cc_start: 0.3698 (ppp) cc_final: 0.0884 (mmm) REVERT: A 1010 TYR cc_start: 0.8496 (t80) cc_final: 0.8177 (t80) REVERT: C 5 MET cc_start: 0.8823 (tpt) cc_final: 0.8377 (tpt) REVERT: C 70 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: D 99 ARG cc_start: 0.8034 (mmp-170) cc_final: 0.7529 (mmm160) REVERT: D 110 GLN cc_start: 0.1616 (OUTLIER) cc_final: 0.0921 (mp10) outliers start: 23 outliers final: 11 residues processed: 121 average time/residue: 0.2562 time to fit residues: 43.1352 Evaluate side-chains 120 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10447 Z= 0.232 Angle : 0.542 10.356 14224 Z= 0.252 Chirality : 0.039 0.147 1588 Planarity : 0.004 0.051 1865 Dihedral : 5.456 59.788 1423 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 2.73 % Allowed : 14.18 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1289 helix: 1.64 (0.24), residues: 464 sheet: -0.54 (0.39), residues: 170 loop : -0.27 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 677 HIS 0.002 0.001 HIS A 291 PHE 0.012 0.001 PHE A 481 TYR 0.019 0.001 TYR B 140 ARG 0.006 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8840 (mp) REVERT: A 225 PRO cc_start: 0.8104 (Cg_exo) cc_final: 0.7839 (Cg_endo) REVERT: A 273 GLN cc_start: 0.7340 (tm-30) cc_final: 0.7066 (tm-30) REVERT: A 473 GLU cc_start: 0.7672 (pm20) cc_final: 0.7193 (tp30) REVERT: A 508 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7274 (pt0) REVERT: A 531 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7444 (ptp-110) REVERT: A 568 TRP cc_start: 0.8878 (m100) cc_final: 0.8568 (m100) REVERT: A 638 THR cc_start: 0.3648 (OUTLIER) cc_final: 0.3208 (m) REVERT: A 677 TRP cc_start: 0.5756 (t60) cc_final: 0.5479 (t60) REVERT: A 695 ASN cc_start: 0.5660 (OUTLIER) cc_final: 0.5412 (t0) REVERT: A 713 GLN cc_start: 0.9035 (tt0) cc_final: 0.8740 (pp30) REVERT: A 718 ASP cc_start: 0.1045 (OUTLIER) cc_final: -0.0336 (t70) REVERT: A 738 MET cc_start: 0.3745 (ppp) cc_final: 0.0968 (mmm) REVERT: C 5 MET cc_start: 0.8840 (tpt) cc_final: 0.8390 (tpt) REVERT: C 70 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: D 99 ARG cc_start: 0.8035 (mmp-170) cc_final: 0.7532 (mmm160) REVERT: D 110 GLN cc_start: 0.1772 (OUTLIER) cc_final: 0.1110 (mp10) outliers start: 30 outliers final: 17 residues processed: 123 average time/residue: 0.2532 time to fit residues: 43.3289 Evaluate side-chains 122 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 75 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10447 Z= 0.278 Angle : 0.562 10.322 14224 Z= 0.262 Chirality : 0.040 0.181 1588 Planarity : 0.004 0.051 1865 Dihedral : 5.482 59.067 1421 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 2.73 % Allowed : 14.91 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.46 (0.24), residues: 1289 helix: 1.57 (0.24), residues: 464 sheet: -0.57 (0.39), residues: 170 loop : -0.31 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 677 HIS 0.003 0.001 HIS A 291 PHE 0.013 0.001 PHE A 481 TYR 0.012 0.001 TYR B 140 ARG 0.004 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8839 (mp) REVERT: A 225 PRO cc_start: 0.8152 (Cg_exo) cc_final: 0.7831 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6665 (ttm170) cc_final: 0.6195 (ttp-110) REVERT: A 273 GLN cc_start: 0.7270 (tm-30) cc_final: 0.6988 (tm-30) REVERT: A 508 GLN cc_start: 0.7602 (mm-40) cc_final: 0.7277 (pt0) REVERT: A 568 TRP cc_start: 0.8875 (m100) cc_final: 0.8568 (m100) REVERT: A 638 THR cc_start: 0.3537 (OUTLIER) cc_final: 0.3163 (m) REVERT: A 677 TRP cc_start: 0.5813 (t60) cc_final: 0.5583 (t60) REVERT: A 695 ASN cc_start: 0.5567 (OUTLIER) cc_final: 0.5233 (t0) REVERT: A 713 GLN cc_start: 0.9075 (tt0) cc_final: 0.8803 (pp30) REVERT: A 718 ASP cc_start: 0.1159 (OUTLIER) cc_final: -0.0272 (t70) REVERT: A 738 MET cc_start: 0.3740 (ppp) cc_final: 0.1033 (mmm) REVERT: C 5 MET cc_start: 0.8779 (tpt) cc_final: 0.8344 (tpt) REVERT: C 43 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7618 (tm-30) REVERT: C 70 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: D 110 GLN cc_start: 0.2216 (OUTLIER) cc_final: 0.1664 (mp10) outliers start: 30 outliers final: 16 residues processed: 125 average time/residue: 0.2394 time to fit residues: 42.2600 Evaluate side-chains 122 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 0.0870 chunk 84 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 112 optimal weight: 0.2980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10447 Z= 0.200 Angle : 0.546 10.298 14224 Z= 0.252 Chirality : 0.038 0.182 1588 Planarity : 0.004 0.051 1865 Dihedral : 5.410 59.395 1421 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.03 % Favored : 96.90 % Rotamer: Outliers : 2.18 % Allowed : 15.55 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.55 (0.24), residues: 1289 helix: 1.65 (0.24), residues: 464 sheet: -0.51 (0.39), residues: 170 loop : -0.27 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 677 HIS 0.003 0.000 HIS A 908 PHE 0.009 0.001 PHE A 481 TYR 0.008 0.001 TYR A1010 ARG 0.006 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8823 (mp) REVERT: A 225 PRO cc_start: 0.8127 (Cg_exo) cc_final: 0.7836 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6677 (ttm170) cc_final: 0.6238 (ttp-110) REVERT: A 273 GLN cc_start: 0.7344 (tm-30) cc_final: 0.7065 (tm-30) REVERT: A 508 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7257 (pt0) REVERT: A 638 THR cc_start: 0.3573 (OUTLIER) cc_final: 0.3204 (m) REVERT: A 677 TRP cc_start: 0.5853 (t60) cc_final: 0.5627 (t60) REVERT: A 695 ASN cc_start: 0.5617 (OUTLIER) cc_final: 0.5260 (t0) REVERT: A 713 GLN cc_start: 0.9080 (tt0) cc_final: 0.8804 (pp30) REVERT: A 718 ASP cc_start: 0.1085 (OUTLIER) cc_final: -0.0330 (t70) REVERT: A 738 MET cc_start: 0.3739 (ppp) cc_final: 0.1036 (mmm) REVERT: C 43 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7639 (tm-30) REVERT: C 70 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8137 (m-80) REVERT: D 99 ARG cc_start: 0.7261 (mmp-170) cc_final: 0.6649 (mmp-170) REVERT: D 110 GLN cc_start: 0.2248 (OUTLIER) cc_final: 0.1701 (mp10) outliers start: 24 outliers final: 18 residues processed: 116 average time/residue: 0.2498 time to fit residues: 40.6062 Evaluate side-chains 123 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 HIS C 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10447 Z= 0.195 Angle : 0.545 10.308 14224 Z= 0.251 Chirality : 0.038 0.146 1588 Planarity : 0.004 0.051 1865 Dihedral : 5.363 59.662 1421 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 2.55 % Allowed : 15.27 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.24), residues: 1289 helix: 1.70 (0.24), residues: 464 sheet: -0.50 (0.40), residues: 164 loop : -0.25 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 677 HIS 0.003 0.000 HIS A 908 PHE 0.009 0.001 PHE A 481 TYR 0.008 0.001 TYR C 61 ARG 0.002 0.000 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8820 (mp) REVERT: A 225 PRO cc_start: 0.8141 (Cg_exo) cc_final: 0.7868 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6586 (ttm170) cc_final: 0.6375 (ttm170) REVERT: A 273 GLN cc_start: 0.7355 (tm-30) cc_final: 0.7079 (tm-30) REVERT: A 473 GLU cc_start: 0.7657 (pm20) cc_final: 0.7209 (tp30) REVERT: A 508 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7114 (mt0) REVERT: A 638 THR cc_start: 0.3613 (OUTLIER) cc_final: 0.3233 (m) REVERT: A 677 TRP cc_start: 0.5861 (t60) cc_final: 0.5649 (t60) REVERT: A 695 ASN cc_start: 0.5564 (OUTLIER) cc_final: 0.5184 (t0) REVERT: A 713 GLN cc_start: 0.9076 (tt0) cc_final: 0.8802 (pp30) REVERT: A 718 ASP cc_start: 0.1079 (OUTLIER) cc_final: -0.0330 (t70) REVERT: A 738 MET cc_start: 0.3654 (ppp) cc_final: 0.1029 (mmm) REVERT: A 1010 TYR cc_start: 0.8506 (t80) cc_final: 0.8206 (t80) REVERT: C 43 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7602 (tm-30) REVERT: C 70 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: D 99 ARG cc_start: 0.7230 (mmp-170) cc_final: 0.6807 (mmp80) REVERT: D 110 GLN cc_start: 0.2266 (OUTLIER) cc_final: 0.1757 (mp10) outliers start: 28 outliers final: 19 residues processed: 121 average time/residue: 0.2501 time to fit residues: 42.2794 Evaluate side-chains 126 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 110 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.0000 chunk 57 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10447 Z= 0.293 Angle : 0.584 10.294 14224 Z= 0.272 Chirality : 0.040 0.130 1588 Planarity : 0.004 0.052 1865 Dihedral : 5.541 58.120 1421 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.35 % Rotamer: Outliers : 2.27 % Allowed : 15.64 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.42 (0.24), residues: 1289 helix: 1.55 (0.24), residues: 464 sheet: -0.66 (0.39), residues: 171 loop : -0.33 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 677 HIS 0.003 0.001 HIS A 291 PHE 0.012 0.001 PHE A 481 TYR 0.008 0.001 TYR C 61 ARG 0.005 0.000 ARG C 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8884 (mp) REVERT: A 225 PRO cc_start: 0.8137 (Cg_exo) cc_final: 0.7874 (Cg_endo) REVERT: A 231 ARG cc_start: 0.6601 (ttm170) cc_final: 0.6374 (ttm170) REVERT: A 273 GLN cc_start: 0.7276 (tm-30) cc_final: 0.6995 (tm-30) REVERT: A 508 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7239 (pt0) REVERT: A 638 THR cc_start: 0.3610 (OUTLIER) cc_final: 0.3247 (m) REVERT: A 677 TRP cc_start: 0.5906 (t60) cc_final: 0.5701 (t60) REVERT: A 695 ASN cc_start: 0.5590 (OUTLIER) cc_final: 0.5182 (t0) REVERT: A 713 GLN cc_start: 0.9090 (tt0) cc_final: 0.8809 (pp30) REVERT: A 718 ASP cc_start: 0.1176 (OUTLIER) cc_final: -0.0286 (t70) REVERT: A 738 MET cc_start: 0.3729 (ppp) cc_final: 0.1094 (mmm) REVERT: C 43 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7556 (tm-30) REVERT: C 70 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: D 99 ARG cc_start: 0.7258 (mmp-170) cc_final: 0.6881 (mmp80) outliers start: 25 outliers final: 18 residues processed: 115 average time/residue: 0.2501 time to fit residues: 41.2879 Evaluate side-chains 118 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 149 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 chunk 28 optimal weight: 0.0980 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.199218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128957 restraints weight = 12373.528| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.38 r_work: 0.3280 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10447 Z= 0.156 Angle : 0.536 10.301 14224 Z= 0.246 Chirality : 0.038 0.129 1588 Planarity : 0.004 0.050 1865 Dihedral : 5.149 59.407 1418 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 1.82 % Allowed : 15.91 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1289 helix: 1.75 (0.24), residues: 464 sheet: -0.49 (0.40), residues: 164 loop : -0.26 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 677 HIS 0.002 0.000 HIS A 887 PHE 0.009 0.001 PHE A 76 TYR 0.010 0.001 TYR A1010 ARG 0.007 0.000 ARG C 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2565.12 seconds wall clock time: 47 minutes 9.90 seconds (2829.90 seconds total)