Starting phenix.real_space_refine on Thu Feb 15 20:33:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkf_33250/02_2024/7xkf_33250_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkf_33250/02_2024/7xkf_33250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkf_33250/02_2024/7xkf_33250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkf_33250/02_2024/7xkf_33250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkf_33250/02_2024/7xkf_33250_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkf_33250/02_2024/7xkf_33250_updated.pdb" } resolution = 2.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5427 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5087 2.51 5 N 1372 2.21 5 O 1454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "R GLU 646": "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: 7961 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1856 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2107 Unusual residues: {'AND': 1} Classifications: {'peptide': 261, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 256, None: 1} Not linked: pdbres="ARG R 883 " pdbres="AND R1001 " Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 5.04, per 1000 atoms: 0.63 Number of scatterers: 7961 At special positions: 0 Unit cell: (103.887, 109.242, 95.319, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1454 8.00 N 1372 7.00 C 5087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 686 " - pdb=" SG CYS R 770 " 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=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.4 seconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 10 sheets defined 36.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 11 through 38 removed outlier: 3.552A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 57 No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.893A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.520A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 617 through 644 Processing helix chain 'R' and resid 646 through 648 No H-bonds generated for 'chain 'R' and resid 646 through 648' Processing helix chain 'R' and resid 652 through 676 Processing helix chain 'R' and resid 683 through 715 Processing helix chain 'R' and resid 726 through 748 Proline residue: R 738 - end of helix Processing helix chain 'R' and resid 750 through 752 No H-bonds generated for 'chain 'R' and resid 750 through 752' Processing helix chain 'R' and resid 777 through 782 Processing helix chain 'R' and resid 784 through 808 Processing helix chain 'R' and resid 821 through 834 Processing helix chain 'R' and resid 836 through 844 removed outlier: 3.533A pdb=" N PHE R 840 " --> pdb=" O THR R 837 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE R 843 " --> pdb=" O PHE R 840 " (cutoff:3.500A) Processing helix chain 'R' and resid 850 through 861 Processing helix chain 'R' and resid 863 through 871 Processing helix chain 'R' and resid 876 through 882 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 6.917A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.631A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.934A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.802A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 220 through 223 removed outlier: 5.354A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.875A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.376A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.080A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1053 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: 2.66 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1283 1.31 - 1.44: 2278 1.44 - 1.56: 4493 1.56 - 1.69: 8 1.69 - 1.81: 66 Bond restraints: 8128 Sorted by residual: bond pdb=" C5 AND R1001 " pdb=" C6 AND R1001 " ideal model delta sigma weight residual 1.332 1.680 -0.348 2.00e-02 2.50e+03 3.02e+02 bond pdb=" C15 AND R1001 " pdb=" C16 AND R1001 " ideal model delta sigma weight residual 1.535 1.740 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C14 AND R1001 " pdb=" C15 AND R1001 " ideal model delta sigma weight residual 1.529 1.680 -0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" C13 AND R1001 " pdb=" C17 AND R1001 " ideal model delta sigma weight residual 1.514 1.661 -0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C11 AND R1001 " pdb=" C12 AND R1001 " ideal model delta sigma weight residual 1.531 1.638 -0.107 2.00e-02 2.50e+03 2.87e+01 ... (remaining 8123 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.24: 126 106.24 - 113.20: 4365 113.20 - 120.15: 2874 120.15 - 127.11: 3573 127.11 - 134.07: 75 Bond angle restraints: 11013 Sorted by residual: angle pdb=" C ALA N 101 " pdb=" N PRO N 102 " pdb=" CA PRO N 102 " ideal model delta sigma weight residual 120.03 124.44 -4.41 9.90e-01 1.02e+00 1.99e+01 angle pdb=" CA PRO G 53 " pdb=" N PRO G 53 " pdb=" CD PRO G 53 " ideal model delta sigma weight residual 112.00 106.26 5.74 1.40e+00 5.10e-01 1.68e+01 angle pdb=" N ALA B 140 " pdb=" CA ALA B 140 " pdb=" C ALA B 140 " ideal model delta sigma weight residual 108.49 115.17 -6.68 1.65e+00 3.67e-01 1.64e+01 angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 113.53 119.12 -5.59 1.39e+00 5.18e-01 1.62e+01 angle pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta sigma weight residual 119.05 123.35 -4.30 1.11e+00 8.12e-01 1.50e+01 ... (remaining 11008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4249 17.29 - 34.57: 460 34.57 - 51.86: 103 51.86 - 69.14: 22 69.14 - 86.43: 6 Dihedral angle restraints: 4840 sinusoidal: 1920 harmonic: 2920 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 6.57 86.43 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CB CYS R 686 " pdb=" SG CYS R 686 " pdb=" SG CYS R 770 " pdb=" CB CYS R 770 " ideal model delta sinusoidal sigma weight residual -86.00 -125.04 39.04 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 4837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1093 0.069 - 0.139: 145 0.139 - 0.208: 3 0.208 - 0.277: 1 0.277 - 0.346: 1 Chirality restraints: 1243 Sorted by residual: chirality pdb=" C13 AND R1001 " pdb=" C12 AND R1001 " pdb=" C14 AND R1001 " pdb=" C17 AND R1001 " both_signs ideal model delta sigma weight residual False -2.72 -2.37 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C9 AND R1001 " pdb=" C10 AND R1001 " pdb=" C11 AND R1001 " pdb=" C8 AND R1001 " both_signs ideal model delta sigma weight residual False -2.46 -2.73 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" C PRO N 100 " pdb=" CB PRO N 100 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1240 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG N 98 " 0.024 2.00e-02 2.50e+03 4.84e-02 2.34e+01 pdb=" C ARG N 98 " -0.084 2.00e-02 2.50e+03 pdb=" O ARG N 98 " 0.032 2.00e-02 2.50e+03 pdb=" N CYS N 99 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.076 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO G 53 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN N 13 " -0.030 5.00e-02 4.00e+02 4.63e-02 3.44e+00 pdb=" N PRO N 14 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.026 5.00e-02 4.00e+02 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 121 2.62 - 3.19: 7187 3.19 - 3.76: 12393 3.76 - 4.33: 17516 4.33 - 4.90: 29070 Nonbonded interactions: 66287 Sorted by model distance: nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.055 2.440 nonbonded pdb=" OD1 ASN A 278 " pdb=" OG SER A 352 " model vdw 2.210 2.440 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.215 2.520 nonbonded pdb=" CA ASN A 279 " pdb=" OD2 ASP N 106 " model vdw 2.217 3.470 nonbonded pdb=" O SER A 251 " pdb=" NZ LYS A 300 " model vdw 2.222 2.520 ... (remaining 66282 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 3.930 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.120 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.007 0.348 8128 Z= 0.369 Angle : 0.678 7.729 11013 Z= 0.378 Chirality : 0.046 0.346 1243 Planarity : 0.006 0.112 1394 Dihedral : 15.092 85.281 2945 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.06 % Allowed : 17.22 % Favored : 81.72 % 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: 0.77 (0.27), residues: 988 helix: 2.40 (0.26), residues: 375 sheet: -0.04 (0.33), residues: 229 loop : -1.07 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.011 0.001 HIS A 357 PHE 0.012 0.001 PHE R 634 TYR 0.012 0.001 TYR N 60 ARG 0.014 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 159 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8813 (mm110) cc_final: 0.8095 (pt0) REVERT: A 381 ASP cc_start: 0.8517 (t70) cc_final: 0.8103 (t70) REVERT: G 13 ARG cc_start: 0.8406 (mtm110) cc_final: 0.7964 (mtm110) outliers start: 9 outliers final: 7 residues processed: 166 average time/residue: 1.3967 time to fit residues: 243.6861 Evaluate side-chains 133 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 824 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 0.0970 chunk 88 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8128 Z= 0.184 Angle : 0.518 5.263 11013 Z= 0.278 Chirality : 0.041 0.143 1243 Planarity : 0.004 0.064 1394 Dihedral : 5.142 58.948 1163 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.42 % Allowed : 19.58 % Favored : 77.00 % 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: 0.88 (0.27), residues: 988 helix: 2.54 (0.26), residues: 372 sheet: 0.04 (0.33), residues: 225 loop : -1.05 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.001 PHE R 671 TYR 0.010 0.001 TYR A 339 ARG 0.007 0.001 ARG R 650 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 0.988 Fit side-chains REVERT: A 12 GLN cc_start: 0.8255 (mm110) cc_final: 0.7897 (pt0) REVERT: A 38 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8135 (mmt90) REVERT: B 23 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8697 (tppt) REVERT: B 61 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8494 (ppp) REVERT: R 646 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7229 (tm-30) outliers start: 29 outliers final: 10 residues processed: 151 average time/residue: 1.3421 time to fit residues: 213.6862 Evaluate side-chains 141 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8128 Z= 0.172 Angle : 0.512 8.015 11013 Z= 0.271 Chirality : 0.041 0.143 1243 Planarity : 0.004 0.053 1394 Dihedral : 4.223 36.378 1155 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.54 % Allowed : 20.28 % Favored : 76.18 % 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 (0.27), residues: 988 helix: 2.55 (0.26), residues: 374 sheet: 0.04 (0.33), residues: 226 loop : -1.00 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.001 PHE R 671 TYR 0.010 0.001 TYR A 339 ARG 0.008 0.001 ARG R 650 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 0.915 Fit side-chains REVERT: A 12 GLN cc_start: 0.8329 (mm110) cc_final: 0.7913 (pt0) REVERT: A 13 ARG cc_start: 0.8167 (mpt180) cc_final: 0.7856 (mtm-85) REVERT: A 209 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: B 10 GLU cc_start: 0.8534 (tp30) cc_final: 0.8275 (tp30) REVERT: B 23 LYS cc_start: 0.8965 (mmmm) cc_final: 0.8706 (tppt) REVERT: B 61 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8524 (ppp) REVERT: R 646 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7320 (tm-30) REVERT: R 822 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8481 (tp-100) outliers start: 30 outliers final: 14 residues processed: 156 average time/residue: 1.3366 time to fit residues: 219.8428 Evaluate side-chains 144 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 680 TYR Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 78 optimal weight: 7.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 668 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8128 Z= 0.172 Angle : 0.519 6.791 11013 Z= 0.277 Chirality : 0.040 0.138 1243 Planarity : 0.004 0.048 1394 Dihedral : 4.515 59.407 1155 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.13 % Allowed : 20.52 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 (0.27), residues: 988 helix: 2.51 (0.26), residues: 376 sheet: 0.05 (0.34), residues: 226 loop : -0.97 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE R 671 TYR 0.010 0.001 TYR A 339 ARG 0.013 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 0.949 Fit side-chains REVERT: A 12 GLN cc_start: 0.8307 (mm110) cc_final: 0.7921 (pt0) REVERT: A 13 ARG cc_start: 0.8162 (mpt180) cc_final: 0.7921 (mpp-170) REVERT: A 38 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8110 (mmt90) REVERT: A 209 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: B 10 GLU cc_start: 0.8609 (tp30) cc_final: 0.8250 (tp30) REVERT: B 23 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8708 (tppt) REVERT: B 61 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8500 (ppp) REVERT: B 127 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8644 (ptpt) REVERT: B 234 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.7247 (t80) REVERT: R 623 ILE cc_start: 0.9214 (mt) cc_final: 0.8872 (tp) REVERT: R 646 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7235 (tm-30) outliers start: 35 outliers final: 15 residues processed: 154 average time/residue: 1.2542 time to fit residues: 204.2424 Evaluate side-chains 147 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 0.0060 chunk 85 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 849 ASN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8128 Z= 0.222 Angle : 0.529 6.055 11013 Z= 0.282 Chirality : 0.041 0.145 1243 Planarity : 0.004 0.047 1394 Dihedral : 4.209 35.847 1153 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.01 % Allowed : 21.70 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 (0.27), residues: 988 helix: 2.52 (0.26), residues: 376 sheet: 0.03 (0.33), residues: 228 loop : -1.01 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 676 HIS 0.007 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.012 0.001 TYR A 339 ARG 0.014 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 0.983 Fit side-chains REVERT: A 12 GLN cc_start: 0.8275 (mm110) cc_final: 0.7827 (pt0) REVERT: A 13 ARG cc_start: 0.8160 (mpt180) cc_final: 0.7749 (mpp-170) REVERT: A 38 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8158 (mmt90) REVERT: B 10 GLU cc_start: 0.8628 (tp30) cc_final: 0.8210 (tp30) REVERT: B 23 LYS cc_start: 0.8993 (mmmm) cc_final: 0.8719 (tppt) REVERT: B 61 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8454 (ppp) REVERT: B 127 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8658 (ptpt) REVERT: B 234 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.7217 (t80) REVERT: R 646 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7273 (tm-30) outliers start: 34 outliers final: 18 residues processed: 156 average time/residue: 1.3184 time to fit residues: 217.3069 Evaluate side-chains 153 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 680 TYR Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 0.0170 chunk 49 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8128 Z= 0.215 Angle : 0.548 7.126 11013 Z= 0.290 Chirality : 0.042 0.143 1243 Planarity : 0.004 0.047 1394 Dihedral : 4.199 35.366 1153 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.48 % Allowed : 21.58 % Favored : 73.94 % 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: 0.83 (0.27), residues: 988 helix: 2.46 (0.26), residues: 375 sheet: 0.01 (0.33), residues: 228 loop : -1.05 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 676 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE R 856 TYR 0.012 0.001 TYR A 339 ARG 0.010 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 133 time to evaluate : 0.956 Fit side-chains REVERT: A 12 GLN cc_start: 0.8322 (mm110) cc_final: 0.7854 (pt0) REVERT: A 13 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7759 (mpp-170) REVERT: A 38 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8151 (mmt90) REVERT: A 209 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: B 10 GLU cc_start: 0.8629 (tp30) cc_final: 0.8203 (tp30) REVERT: B 23 LYS cc_start: 0.9000 (mmmm) cc_final: 0.8721 (tppt) REVERT: B 61 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8453 (ppp) REVERT: B 234 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.7172 (t80) REVERT: N 11 LEU cc_start: 0.9373 (tm) cc_final: 0.9115 (mm) REVERT: R 623 ILE cc_start: 0.9181 (mt) cc_final: 0.8835 (OUTLIER) REVERT: R 646 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7187 (tm-30) REVERT: R 768 ASP cc_start: 0.5195 (p0) cc_final: 0.4858 (m-30) REVERT: R 803 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7690 (mt0) REVERT: R 822 GLN cc_start: 0.8732 (tp40) cc_final: 0.8233 (tp40) outliers start: 38 outliers final: 20 residues processed: 158 average time/residue: 1.3218 time to fit residues: 220.3202 Evaluate side-chains 148 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 803 GLN Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 848 VAL Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8128 Z= 0.202 Angle : 0.549 7.924 11013 Z= 0.292 Chirality : 0.041 0.140 1243 Planarity : 0.004 0.046 1394 Dihedral : 4.188 34.779 1153 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.25 % Allowed : 22.17 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.79 (0.27), residues: 988 helix: 2.42 (0.26), residues: 375 sheet: -0.03 (0.33), residues: 228 loop : -1.06 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 676 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE R 856 TYR 0.011 0.001 TYR A 339 ARG 0.015 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 0.989 Fit side-chains REVERT: A 12 GLN cc_start: 0.8294 (mm110) cc_final: 0.7937 (pt0) REVERT: A 13 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7954 (mpp-170) REVERT: A 38 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8115 (mmt90) REVERT: A 209 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7733 (mm-30) REVERT: B 10 GLU cc_start: 0.8593 (tp30) cc_final: 0.8203 (tp30) REVERT: B 23 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8747 (tppt) REVERT: B 61 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8450 (ppp) REVERT: B 234 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.7151 (t80) REVERT: N 11 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9138 (mm) REVERT: R 623 ILE cc_start: 0.9200 (mt) cc_final: 0.8838 (OUTLIER) REVERT: R 646 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7185 (tm-30) REVERT: R 803 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7679 (mt0) outliers start: 36 outliers final: 20 residues processed: 150 average time/residue: 1.3499 time to fit residues: 213.3648 Evaluate side-chains 148 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 803 GLN Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 848 VAL Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8128 Z= 0.283 Angle : 0.592 8.551 11013 Z= 0.316 Chirality : 0.043 0.150 1243 Planarity : 0.004 0.051 1394 Dihedral : 4.372 36.628 1153 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.77 % Allowed : 23.11 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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: 0.71 (0.27), residues: 988 helix: 2.30 (0.27), residues: 375 sheet: -0.02 (0.33), residues: 228 loop : -1.08 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 676 HIS 0.008 0.001 HIS A 357 PHE 0.012 0.001 PHE R 856 TYR 0.013 0.001 TYR A 339 ARG 0.012 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 0.933 Fit side-chains REVERT: A 12 GLN cc_start: 0.8299 (mm110) cc_final: 0.7813 (pt0) REVERT: A 13 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7741 (mpp-170) REVERT: A 38 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8155 (mmt90) REVERT: A 209 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7765 (mm-30) REVERT: B 10 GLU cc_start: 0.8670 (tp30) cc_final: 0.8280 (tp30) REVERT: B 61 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8440 (ppp) REVERT: B 234 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.7250 (t80) REVERT: R 646 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7174 (tm-30) REVERT: R 803 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7701 (mt0) outliers start: 32 outliers final: 20 residues processed: 147 average time/residue: 1.3758 time to fit residues: 213.2031 Evaluate side-chains 150 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 803 GLN Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 848 VAL Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 90 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8128 Z= 0.299 Angle : 0.606 8.269 11013 Z= 0.324 Chirality : 0.043 0.162 1243 Planarity : 0.004 0.054 1394 Dihedral : 4.471 36.831 1153 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.01 % Allowed : 23.23 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 (0.27), residues: 988 helix: 2.19 (0.27), residues: 375 sheet: -0.04 (0.33), residues: 228 loop : -1.11 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 676 HIS 0.008 0.001 HIS A 357 PHE 0.013 0.001 PHE R 856 TYR 0.014 0.001 TYR A 339 ARG 0.014 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 1.008 Fit side-chains REVERT: A 12 GLN cc_start: 0.8252 (mm110) cc_final: 0.7922 (pt0) REVERT: A 38 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8172 (mmt90) REVERT: A 209 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7696 (mm-30) REVERT: B 10 GLU cc_start: 0.8687 (tp30) cc_final: 0.8283 (tp30) REVERT: B 61 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8416 (ppp) REVERT: B 234 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.7320 (t80) REVERT: G 13 ARG cc_start: 0.8344 (mtm110) cc_final: 0.8062 (mtm110) REVERT: R 646 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7236 (tm-30) outliers start: 34 outliers final: 22 residues processed: 143 average time/residue: 1.3353 time to fit residues: 201.2985 Evaluate side-chains 149 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 848 VAL Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8128 Z= 0.232 Angle : 0.592 8.878 11013 Z= 0.316 Chirality : 0.042 0.180 1243 Planarity : 0.004 0.059 1394 Dihedral : 4.402 36.195 1153 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.83 % Allowed : 24.29 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 (0.27), residues: 988 helix: 2.18 (0.27), residues: 375 sheet: -0.07 (0.33), residues: 228 loop : -1.09 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 676 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE R 865 TYR 0.012 0.001 TYR A 339 ARG 0.014 0.001 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 0.963 Fit side-chains REVERT: A 12 GLN cc_start: 0.8260 (mm110) cc_final: 0.7912 (pt0) REVERT: A 13 ARG cc_start: 0.8196 (mpt180) cc_final: 0.7891 (mpt180) REVERT: A 38 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8169 (mmt90) REVERT: A 209 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: B 10 GLU cc_start: 0.8681 (tp30) cc_final: 0.8325 (tp30) REVERT: B 61 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8431 (ppp) REVERT: B 234 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.7211 (t80) REVERT: R 646 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7202 (tm-30) outliers start: 24 outliers final: 17 residues processed: 148 average time/residue: 1.3659 time to fit residues: 213.6836 Evaluate side-chains 140 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 711 MET Chi-restraints excluded: chain R residue 782 VAL Chi-restraints excluded: chain R residue 824 LEU Chi-restraints excluded: chain R residue 848 VAL Chi-restraints excluded: chain R residue 872 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 0.0030 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 279 ASN ** R 860 ASN ** 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 = 0.3389 r_free = 0.3389 target = 0.092473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.069205 restraints weight = 14315.428| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.87 r_work: 0.2816 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8128 Z= 0.193 Angle : 0.576 7.852 11013 Z= 0.308 Chirality : 0.041 0.176 1243 Planarity : 0.004 0.058 1394 Dihedral : 4.258 34.959 1153 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.83 % Allowed : 24.41 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % 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 (0.27), residues: 988 helix: 2.13 (0.27), residues: 375 sheet: -0.11 (0.33), residues: 225 loop : -1.13 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 676 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE R 865 TYR 0.010 0.001 TYR A 339 ARG 0.014 0.001 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3820.20 seconds wall clock time: 68 minutes 26.78 seconds (4106.78 seconds total)