Starting phenix.real_space_refine on Sat Apr 6 07:31:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/04_2024/8izf_35863_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/04_2024/8izf_35863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/04_2024/8izf_35863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/04_2024/8izf_35863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/04_2024/8izf_35863_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/04_2024/8izf_35863_updated.pdb" } resolution = 3.85 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= 0.004 sd= 0.052 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 2 5.49 5 S 38 5.16 5 C 5088 2.51 5 N 1202 2.21 5 O 1264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B ARG 25": "NH1" <-> "NH2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ASP 122": "OD1" <-> "OD2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C ASP 248": "OD1" <-> "OD2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "C PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 381": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D TYR 148": "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: 7594 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2670 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1087 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "C" Number of atoms: 2670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2670 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1087 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'6PL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'6PL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 4.67, per 1000 atoms: 0.61 Number of scatterers: 7594 At special positions: 0 Unit cell: (110.416, 101.84, 100.768, 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 2 15.00 O 1264 8.00 N 1202 7.00 C 5088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 102 " - pdb=" SG CYS D 142 " 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: 3.29 Conformation dependent library (CDL) restraints added in 1.2 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 2 sheets defined 62.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 85 through 101 Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 131 through 162 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 168 through 195 Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 240 Processing helix chain 'A' and resid 250 through 268 Processing helix chain 'A' and resid 273 through 297 Proline residue: A 277 - end of helix removed outlier: 3.786A pdb=" N LEU A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 334 removed outlier: 3.947A pdb=" N TYR A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 383 Processing helix chain 'B' and resid 20 through 46 Processing helix chain 'B' and resid 49 through 52 No H-bonds generated for 'chain 'B' and resid 49 through 52' Processing helix chain 'B' and resid 77 through 91 Processing helix chain 'B' and resid 132 through 141 removed outlier: 5.301A pdb=" N GLU B 136 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 85 through 101 Processing helix chain 'C' and resid 110 through 114 Processing helix chain 'C' and resid 131 through 162 Proline residue: C 157 - end of helix Processing helix chain 'C' and resid 168 through 195 Proline residue: C 188 - end of helix Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 218 through 240 Processing helix chain 'C' and resid 250 through 268 Processing helix chain 'C' and resid 273 through 297 Proline residue: C 277 - end of helix removed outlier: 3.786A pdb=" N LEU C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 334 removed outlier: 3.946A pdb=" N TYR C 320 " --> pdb=" O TYR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 383 Processing helix chain 'D' and resid 20 through 46 Processing helix chain 'D' and resid 49 through 52 No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 77 through 91 Processing helix chain 'D' and resid 132 through 141 removed outlier: 5.300A pdb=" N GLU D 136 " --> pdb=" O THR D 133 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 53 through 59 removed outlier: 3.616A pdb=" N VAL B 129 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 53 through 59 removed outlier: 3.616A pdb=" N VAL D 129 " --> pdb=" O ILE D 65 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1308 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: 1.99 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1096 1.32 - 1.44: 2532 1.44 - 1.57: 4158 1.57 - 1.70: 2 1.70 - 1.83: 58 Bond restraints: 7846 Sorted by residual: bond pdb=" C31 6PL D 201 " pdb=" O2 6PL D 201 " ideal model delta sigma weight residual 1.330 1.430 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C31 6PL B 201 " pdb=" O2 6PL B 201 " ideal model delta sigma weight residual 1.330 1.430 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C11 6PL D 201 " pdb=" O3 6PL D 201 " ideal model delta sigma weight residual 1.327 1.426 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C11 6PL B 201 " pdb=" O3 6PL B 201 " ideal model delta sigma weight residual 1.327 1.426 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" CA PHE A 343 " pdb=" CB PHE A 343 " ideal model delta sigma weight residual 1.530 1.462 0.068 1.69e-02 3.50e+03 1.62e+01 ... (remaining 7841 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.38: 129 105.38 - 112.59: 3941 112.59 - 119.79: 2706 119.79 - 126.99: 3766 126.99 - 134.19: 110 Bond angle restraints: 10652 Sorted by residual: angle pdb=" N PHE C 343 " pdb=" CA PHE C 343 " pdb=" C PHE C 343 " ideal model delta sigma weight residual 110.80 130.12 -19.32 2.13e+00 2.20e-01 8.23e+01 angle pdb=" N PHE A 343 " pdb=" CA PHE A 343 " pdb=" C PHE A 343 " ideal model delta sigma weight residual 110.80 130.08 -19.28 2.13e+00 2.20e-01 8.20e+01 angle pdb=" N LYS C 247 " pdb=" CA LYS C 247 " pdb=" C LYS C 247 " ideal model delta sigma weight residual 110.24 98.33 11.91 1.41e+00 5.03e-01 7.13e+01 angle pdb=" N LYS A 247 " pdb=" CA LYS A 247 " pdb=" C LYS A 247 " ideal model delta sigma weight residual 110.24 98.35 11.89 1.41e+00 5.03e-01 7.11e+01 angle pdb=" N MET A 140 " pdb=" CA MET A 140 " pdb=" C MET A 140 " ideal model delta sigma weight residual 111.36 103.42 7.94 1.09e+00 8.42e-01 5.31e+01 ... (remaining 10647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 3954 18.05 - 36.09: 412 36.09 - 54.14: 100 54.14 - 72.19: 16 72.19 - 90.24: 16 Dihedral angle restraints: 4498 sinusoidal: 1834 harmonic: 2664 Sorted by residual: dihedral pdb=" CA GLU D 118 " pdb=" C GLU D 118 " pdb=" N ASP D 119 " pdb=" CA ASP D 119 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLU B 118 " pdb=" C GLU B 118 " pdb=" N ASP B 119 " pdb=" CA ASP B 119 " ideal model delta harmonic sigma weight residual 180.00 158.70 21.30 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA CYS B 53 " pdb=" CB CYS B 53 " pdb=" SG CYS B 53 " pdb=" SG CYS B 75 " ideal model delta sinusoidal sigma weight residual -73.00 2.17 -75.17 1 2.00e+01 2.50e-03 1.79e+01 ... (remaining 4495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1107 0.118 - 0.236: 27 0.236 - 0.354: 2 0.354 - 0.472: 0 0.472 - 0.590: 2 Chirality restraints: 1138 Sorted by residual: chirality pdb=" CA PHE C 343 " pdb=" N PHE C 343 " pdb=" C PHE C 343 " pdb=" CB PHE C 343 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.71e+00 chirality pdb=" CA PHE A 343 " pdb=" N PHE A 343 " pdb=" C PHE A 343 " pdb=" CB PHE A 343 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" CA LYS C 247 " pdb=" N LYS C 247 " pdb=" C LYS C 247 " pdb=" CB LYS C 247 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 1135 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 139 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.49e+01 pdb=" C TYR A 139 " 0.067 2.00e-02 2.50e+03 pdb=" O TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" N MET A 140 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 139 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C TYR C 139 " -0.067 2.00e-02 2.50e+03 pdb=" O TYR C 139 " 0.026 2.00e-02 2.50e+03 pdb=" N MET C 140 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 77 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS D 77 " 0.057 2.00e-02 2.50e+03 pdb=" O LYS D 77 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG D 78 " -0.019 2.00e-02 2.50e+03 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 69 2.54 - 3.13: 6486 3.13 - 3.72: 12034 3.72 - 4.31: 15574 4.31 - 4.90: 25353 Nonbonded interactions: 59516 Sorted by model distance: nonbonded pdb=" O ILE B 103 " pdb=" OH TYR D 148 " model vdw 1.945 2.440 nonbonded pdb=" OH TYR B 148 " pdb=" O ILE D 103 " model vdw 1.952 2.440 nonbonded pdb=" O LYS A 244 " pdb=" O PRO A 245 " model vdw 2.010 3.040 nonbonded pdb=" O LYS C 244 " pdb=" O PRO C 245 " model vdw 2.011 3.040 nonbonded pdb=" OG SER A 186 " pdb=" OD2 ASP A 283 " model vdw 2.168 2.440 ... (remaining 59511 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 'A' selection = chain 'C' } ncs_group { reference = chain 'B' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.800 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.690 Find NCS groups from input model: 0.390 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 7846 Z= 0.380 Angle : 1.095 19.322 10652 Z= 0.624 Chirality : 0.057 0.590 1138 Planarity : 0.006 0.063 1296 Dihedral : 16.149 90.235 2778 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.48 % Favored : 89.84 % Rotamer: Outliers : 2.73 % Allowed : 1.74 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.27), residues: 886 helix: 0.25 (0.20), residues: 562 sheet: -1.68 (0.58), residues: 58 loop : -3.81 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 50 HIS 0.008 0.001 HIS A 249 PHE 0.020 0.002 PHE A 271 TYR 0.032 0.002 TYR C 279 ARG 0.011 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 294 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 TRP cc_start: 0.8276 (p-90) cc_final: 0.7844 (p-90) REVERT: A 168 HIS cc_start: 0.7148 (OUTLIER) cc_final: 0.6197 (m90) REVERT: A 174 MET cc_start: 0.8632 (mmt) cc_final: 0.8164 (mmt) REVERT: A 182 TYR cc_start: 0.7918 (p90) cc_final: 0.7554 (t80) REVERT: A 236 CYS cc_start: 0.8676 (p) cc_final: 0.8464 (p) REVERT: A 251 GLU cc_start: 0.7857 (pm20) cc_final: 0.7460 (pm20) REVERT: A 289 LEU cc_start: 0.8881 (tp) cc_final: 0.8583 (tt) REVERT: A 334 ARG cc_start: 0.7006 (tmt170) cc_final: 0.6782 (tpt170) REVERT: A 343 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7782 (t80) REVERT: A 346 GLN cc_start: 0.8589 (mp10) cc_final: 0.8219 (mp10) REVERT: C 84 TRP cc_start: 0.8268 (p-90) cc_final: 0.7829 (p-90) REVERT: C 168 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6175 (m90) REVERT: C 174 MET cc_start: 0.8753 (mmt) cc_final: 0.8269 (mmt) REVERT: C 236 CYS cc_start: 0.8675 (p) cc_final: 0.8460 (p) REVERT: C 251 GLU cc_start: 0.7866 (pm20) cc_final: 0.7509 (pm20) REVERT: C 334 ARG cc_start: 0.6939 (tmt170) cc_final: 0.6230 (ttt180) REVERT: C 343 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7799 (t80) REVERT: C 346 GLN cc_start: 0.8577 (mp10) cc_final: 0.8175 (mp10) REVERT: D 65 ILE cc_start: 0.9318 (pt) cc_final: 0.9083 (pt) outliers start: 22 outliers final: 4 residues processed: 306 average time/residue: 0.1753 time to fit residues: 73.1937 Evaluate side-chains 212 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 204 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 0.0970 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7846 Z= 0.195 Angle : 0.699 12.505 10652 Z= 0.357 Chirality : 0.042 0.156 1138 Planarity : 0.005 0.055 1296 Dihedral : 9.632 58.349 1084 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 4.84 % Allowed : 15.14 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.28), residues: 886 helix: 0.97 (0.21), residues: 536 sheet: -1.63 (0.57), residues: 58 loop : -3.64 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 68 HIS 0.005 0.001 HIS A 82 PHE 0.033 0.002 PHE A 158 TYR 0.029 0.002 TYR C 182 ARG 0.003 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 250 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.8117 (m-80) cc_final: 0.7896 (m-80) REVERT: A 140 MET cc_start: 0.8449 (tpp) cc_final: 0.8210 (tpp) REVERT: A 168 HIS cc_start: 0.7285 (OUTLIER) cc_final: 0.6480 (m90) REVERT: A 203 ASN cc_start: 0.8373 (t0) cc_final: 0.8172 (t0) REVERT: A 282 MET cc_start: 0.8095 (mmm) cc_final: 0.7888 (mmm) REVERT: A 334 ARG cc_start: 0.6689 (tmt170) cc_final: 0.6437 (tpt170) REVERT: A 343 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7923 (t80) REVERT: B 78 ARG cc_start: 0.8334 (ttp-170) cc_final: 0.8061 (ttp-170) REVERT: B 104 ILE cc_start: 0.8972 (tp) cc_final: 0.8768 (mm) REVERT: C 168 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6488 (m90) REVERT: C 282 MET cc_start: 0.8108 (mmm) cc_final: 0.7905 (mmm) REVERT: C 334 ARG cc_start: 0.6654 (tmt170) cc_final: 0.6155 (ttt180) REVERT: C 343 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7877 (t80) REVERT: D 28 PHE cc_start: 0.8686 (t80) cc_final: 0.8482 (t80) REVERT: D 65 ILE cc_start: 0.9189 (pt) cc_final: 0.8953 (pt) outliers start: 39 outliers final: 27 residues processed: 267 average time/residue: 0.1714 time to fit residues: 63.9814 Evaluate side-chains 245 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 214 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 339 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 126 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 0.0060 chunk 64 optimal weight: 1.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 241 GLN A 332 GLN ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN C 82 HIS ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN C 332 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7846 Z= 0.197 Angle : 0.665 9.903 10652 Z= 0.340 Chirality : 0.042 0.223 1138 Planarity : 0.005 0.052 1296 Dihedral : 9.056 58.199 1082 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 5.71 % Allowed : 19.48 % Favored : 74.81 % 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: -0.95 (0.28), residues: 886 helix: 0.93 (0.21), residues: 544 sheet: -1.57 (0.62), residues: 58 loop : -3.68 (0.31), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 68 HIS 0.008 0.001 HIS C 82 PHE 0.026 0.001 PHE A 158 TYR 0.020 0.002 TYR C 279 ARG 0.003 0.000 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 250 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 151 MET cc_start: 0.8282 (tpp) cc_final: 0.7803 (tpt) REVERT: A 168 HIS cc_start: 0.7339 (m170) cc_final: 0.6790 (m90) REVERT: A 174 MET cc_start: 0.8434 (mmt) cc_final: 0.7591 (mmt) REVERT: A 203 ASN cc_start: 0.8215 (t0) cc_final: 0.7982 (t0) REVERT: A 224 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7101 (t80) REVERT: A 248 ASP cc_start: 0.7613 (t70) cc_final: 0.6340 (t70) REVERT: A 323 LEU cc_start: 0.8571 (mm) cc_final: 0.8350 (tp) REVERT: A 334 ARG cc_start: 0.6624 (tmt170) cc_final: 0.6065 (ttt180) REVERT: A 343 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7859 (t80) REVERT: A 357 VAL cc_start: 0.7691 (t) cc_final: 0.7380 (p) REVERT: B 28 PHE cc_start: 0.8481 (t80) cc_final: 0.8265 (t80) REVERT: B 38 GLU cc_start: 0.8028 (tp30) cc_final: 0.7763 (tp30) REVERT: B 104 ILE cc_start: 0.8976 (tp) cc_final: 0.8747 (mm) REVERT: C 139 TYR cc_start: 0.8087 (m-80) cc_final: 0.7848 (m-80) REVERT: C 151 MET cc_start: 0.8307 (tpp) cc_final: 0.7784 (tpt) REVERT: C 168 HIS cc_start: 0.7311 (m170) cc_final: 0.6772 (m90) REVERT: C 174 MET cc_start: 0.8418 (mmt) cc_final: 0.7546 (mmt) REVERT: C 334 ARG cc_start: 0.6636 (tmt170) cc_final: 0.6058 (ttt180) REVERT: C 343 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7900 (t80) REVERT: C 357 VAL cc_start: 0.7639 (t) cc_final: 0.7397 (p) REVERT: D 28 PHE cc_start: 0.8645 (t80) cc_final: 0.8345 (t80) REVERT: D 38 GLU cc_start: 0.8021 (tp30) cc_final: 0.7817 (tp30) outliers start: 46 outliers final: 31 residues processed: 273 average time/residue: 0.1634 time to fit residues: 62.4009 Evaluate side-chains 245 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 211 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 339 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 126 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 241 GLN A 332 GLN ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN C 332 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7846 Z= 0.205 Angle : 0.668 10.006 10652 Z= 0.341 Chirality : 0.042 0.199 1138 Planarity : 0.005 0.049 1296 Dihedral : 8.384 59.920 1078 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 5.96 % Allowed : 22.70 % Favored : 71.34 % 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: -0.95 (0.27), residues: 886 helix: 0.82 (0.21), residues: 554 sheet: -1.04 (0.64), residues: 54 loop : -3.65 (0.31), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 72 HIS 0.009 0.001 HIS A 82 PHE 0.030 0.001 PHE C 158 TYR 0.026 0.001 TYR A 182 ARG 0.006 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 225 time to evaluate : 0.892 Fit side-chains REVERT: A 168 HIS cc_start: 0.7353 (m170) cc_final: 0.6787 (m90) REVERT: A 174 MET cc_start: 0.8478 (mmt) cc_final: 0.8250 (mmp) REVERT: A 203 ASN cc_start: 0.8185 (t0) cc_final: 0.7930 (t0) REVERT: A 224 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.6987 (t80) REVERT: A 248 ASP cc_start: 0.7386 (t70) cc_final: 0.6957 (t0) REVERT: A 250 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7225 (t0) REVERT: A 251 GLU cc_start: 0.7516 (pm20) cc_final: 0.7219 (pm20) REVERT: A 323 LEU cc_start: 0.8594 (mm) cc_final: 0.8368 (tp) REVERT: A 332 GLN cc_start: 0.7654 (mt0) cc_final: 0.7038 (mt0) REVERT: A 334 ARG cc_start: 0.6692 (tmt170) cc_final: 0.5834 (ttt180) REVERT: A 343 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7808 (t80) REVERT: A 357 VAL cc_start: 0.7708 (t) cc_final: 0.7487 (p) REVERT: B 38 GLU cc_start: 0.8060 (tp30) cc_final: 0.7810 (tp30) REVERT: B 67 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8914 (tt) REVERT: C 168 HIS cc_start: 0.7273 (m170) cc_final: 0.6743 (m90) REVERT: C 174 MET cc_start: 0.8483 (mmt) cc_final: 0.8235 (mmp) REVERT: C 224 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.6970 (t80) REVERT: C 233 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: C 332 GLN cc_start: 0.7705 (mt0) cc_final: 0.7043 (mt0) REVERT: C 334 ARG cc_start: 0.6665 (tmt170) cc_final: 0.5769 (ttt180) REVERT: C 343 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7846 (t80) REVERT: D 28 PHE cc_start: 0.8639 (t80) cc_final: 0.8396 (t80) REVERT: D 67 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8928 (tt) outliers start: 48 outliers final: 34 residues processed: 254 average time/residue: 0.1581 time to fit residues: 58.0452 Evaluate side-chains 259 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 217 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 339 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 4.9990 chunk 1 optimal weight: 0.0570 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.3980 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN C 241 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7846 Z= 0.182 Angle : 0.657 9.358 10652 Z= 0.335 Chirality : 0.041 0.165 1138 Planarity : 0.005 0.048 1296 Dihedral : 7.876 59.277 1078 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 5.83 % Allowed : 22.83 % Favored : 71.34 % 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: -0.81 (0.28), residues: 886 helix: 0.91 (0.22), residues: 552 sheet: -1.47 (0.63), residues: 58 loop : -3.44 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 72 HIS 0.004 0.001 HIS A 319 PHE 0.030 0.001 PHE C 158 TYR 0.019 0.001 TYR D 42 ARG 0.003 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 232 time to evaluate : 1.007 Fit side-chains REVERT: A 140 MET cc_start: 0.8531 (tpp) cc_final: 0.8274 (tpp) REVERT: A 168 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6818 (m90) REVERT: A 174 MET cc_start: 0.8533 (mmt) cc_final: 0.8241 (mmt) REVERT: A 203 ASN cc_start: 0.8046 (t0) cc_final: 0.7807 (t0) REVERT: A 251 GLU cc_start: 0.7350 (pm20) cc_final: 0.6959 (pm20) REVERT: A 334 ARG cc_start: 0.6530 (tmt170) cc_final: 0.5692 (ttt180) REVERT: A 343 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7841 (t80) REVERT: A 357 VAL cc_start: 0.7664 (t) cc_final: 0.7425 (p) REVERT: C 168 HIS cc_start: 0.7201 (OUTLIER) cc_final: 0.6750 (m90) REVERT: C 174 MET cc_start: 0.8586 (mmt) cc_final: 0.8298 (mmp) REVERT: C 224 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.6951 (t80) REVERT: C 233 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: C 248 ASP cc_start: 0.7357 (t70) cc_final: 0.6727 (t0) REVERT: C 251 GLU cc_start: 0.7458 (pm20) cc_final: 0.7255 (pm20) REVERT: C 334 ARG cc_start: 0.6564 (tmt170) cc_final: 0.5712 (ttt180) REVERT: C 343 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7847 (t80) REVERT: D 28 PHE cc_start: 0.8647 (t80) cc_final: 0.8412 (t80) outliers start: 47 outliers final: 34 residues processed: 257 average time/residue: 0.1472 time to fit residues: 54.4204 Evaluate side-chains 257 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 217 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7846 Z= 0.193 Angle : 0.661 9.400 10652 Z= 0.337 Chirality : 0.042 0.164 1138 Planarity : 0.005 0.048 1296 Dihedral : 7.616 57.894 1078 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 5.71 % Allowed : 24.69 % Favored : 69.60 % 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: -0.68 (0.28), residues: 886 helix: 1.01 (0.22), residues: 552 sheet: -1.50 (0.61), residues: 58 loop : -3.36 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 72 HIS 0.003 0.001 HIS C 319 PHE 0.032 0.001 PHE A 158 TYR 0.027 0.001 TYR A 182 ARG 0.003 0.000 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 229 time to evaluate : 0.869 Fit side-chains REVERT: A 168 HIS cc_start: 0.7283 (OUTLIER) cc_final: 0.6875 (m90) REVERT: A 224 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.6920 (t80) REVERT: A 251 GLU cc_start: 0.7272 (pm20) cc_final: 0.6983 (pm20) REVERT: A 334 ARG cc_start: 0.6500 (tmt170) cc_final: 0.5709 (ttt180) REVERT: A 357 VAL cc_start: 0.7654 (t) cc_final: 0.7444 (p) REVERT: C 140 MET cc_start: 0.8492 (tpp) cc_final: 0.8228 (tpp) REVERT: C 168 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6894 (m90) REVERT: C 224 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.6898 (t80) REVERT: C 233 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8558 (tm-30) REVERT: C 248 ASP cc_start: 0.7276 (t70) cc_final: 0.6418 (t0) REVERT: C 251 GLU cc_start: 0.7349 (pm20) cc_final: 0.7075 (pm20) REVERT: C 323 LEU cc_start: 0.8620 (mm) cc_final: 0.8419 (tp) REVERT: C 334 ARG cc_start: 0.6685 (tmt170) cc_final: 0.5573 (ttt180) REVERT: D 28 PHE cc_start: 0.8614 (t80) cc_final: 0.8387 (t80) outliers start: 46 outliers final: 34 residues processed: 256 average time/residue: 0.1533 time to fit residues: 56.4861 Evaluate side-chains 258 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 220 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 84 optimal weight: 0.1980 chunk 53 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 52 HIS B 139 GLN C 241 GLN D 52 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7846 Z= 0.188 Angle : 0.687 9.069 10652 Z= 0.349 Chirality : 0.042 0.173 1138 Planarity : 0.005 0.047 1296 Dihedral : 7.155 56.826 1074 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 5.58 % Allowed : 24.94 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.28), residues: 886 helix: 1.06 (0.22), residues: 550 sheet: -1.34 (0.59), residues: 56 loop : -3.35 (0.32), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 68 HIS 0.002 0.001 HIS C 82 PHE 0.037 0.002 PHE A 158 TYR 0.020 0.001 TYR A 211 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 238 time to evaluate : 0.815 Fit side-chains REVERT: A 168 HIS cc_start: 0.7213 (OUTLIER) cc_final: 0.6904 (m90) REVERT: A 224 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.6914 (t80) REVERT: A 251 GLU cc_start: 0.7164 (pm20) cc_final: 0.6870 (pm20) REVERT: A 334 ARG cc_start: 0.6493 (tmt170) cc_final: 0.5567 (ttt180) REVERT: B 65 ILE cc_start: 0.9178 (pt) cc_final: 0.8916 (pt) REVERT: C 168 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6873 (m90) REVERT: C 224 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.6908 (t80) REVERT: C 233 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8177 (tm-30) REVERT: C 248 ASP cc_start: 0.7251 (t70) cc_final: 0.6280 (t0) REVERT: C 251 GLU cc_start: 0.7364 (pm20) cc_final: 0.7025 (pm20) REVERT: C 334 ARG cc_start: 0.6573 (tmt170) cc_final: 0.5550 (ttt180) REVERT: D 28 PHE cc_start: 0.8626 (t80) cc_final: 0.8378 (t80) outliers start: 45 outliers final: 32 residues processed: 263 average time/residue: 0.1538 time to fit residues: 57.5106 Evaluate side-chains 253 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 217 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 0.0670 chunk 7 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN D 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7846 Z= 0.185 Angle : 0.718 12.965 10652 Z= 0.357 Chirality : 0.042 0.167 1138 Planarity : 0.005 0.047 1296 Dihedral : 6.998 56.245 1074 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 5.09 % Allowed : 27.05 % Favored : 67.87 % 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: -0.57 (0.28), residues: 886 helix: 1.08 (0.22), residues: 548 sheet: -0.82 (0.59), residues: 52 loop : -3.33 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 68 HIS 0.003 0.001 HIS B 52 PHE 0.028 0.001 PHE A 373 TYR 0.029 0.002 TYR A 182 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 228 time to evaluate : 0.860 Fit side-chains REVERT: A 168 HIS cc_start: 0.7155 (OUTLIER) cc_final: 0.6903 (m90) REVERT: A 224 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.6920 (t80) REVERT: A 251 GLU cc_start: 0.7187 (pm20) cc_final: 0.6869 (pm20) REVERT: A 334 ARG cc_start: 0.6558 (tmt170) cc_final: 0.5554 (ttt180) REVERT: C 224 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.6960 (t80) REVERT: C 248 ASP cc_start: 0.7182 (t70) cc_final: 0.6250 (t0) REVERT: C 251 GLU cc_start: 0.7330 (pm20) cc_final: 0.6984 (pm20) REVERT: C 334 ARG cc_start: 0.6624 (tmt170) cc_final: 0.5445 (ttt180) REVERT: D 28 PHE cc_start: 0.8516 (t80) cc_final: 0.8279 (t80) REVERT: D 118 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7415 (tm-30) outliers start: 41 outliers final: 35 residues processed: 251 average time/residue: 0.1596 time to fit residues: 56.1841 Evaluate side-chains 258 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 220 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 0.0570 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN D 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7846 Z= 0.195 Angle : 0.706 9.537 10652 Z= 0.356 Chirality : 0.043 0.240 1138 Planarity : 0.005 0.047 1296 Dihedral : 6.902 55.690 1074 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.71 % Allowed : 27.42 % Favored : 67.87 % 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: -0.49 (0.28), residues: 886 helix: 1.11 (0.22), residues: 550 sheet: -1.10 (0.59), residues: 56 loop : -3.20 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 68 HIS 0.002 0.001 HIS B 52 PHE 0.029 0.001 PHE A 373 TYR 0.020 0.001 TYR C 211 ARG 0.005 0.000 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 231 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 224 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.6976 (t80) REVERT: A 251 GLU cc_start: 0.7197 (pm20) cc_final: 0.6853 (pm20) REVERT: A 334 ARG cc_start: 0.6587 (tmt170) cc_final: 0.5416 (ttt180) REVERT: B 118 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7577 (tm-30) REVERT: C 224 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.6976 (t80) REVERT: C 248 ASP cc_start: 0.7184 (t70) cc_final: 0.6265 (t0) REVERT: C 251 GLU cc_start: 0.7355 (pm20) cc_final: 0.6957 (pm20) REVERT: C 334 ARG cc_start: 0.6579 (tmt170) cc_final: 0.5459 (ttt180) REVERT: D 28 PHE cc_start: 0.8500 (t80) cc_final: 0.8257 (t80) outliers start: 38 outliers final: 33 residues processed: 249 average time/residue: 0.1574 time to fit residues: 55.7900 Evaluate side-chains 259 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 224 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 80 optimal weight: 0.0770 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7846 Z= 0.196 Angle : 0.718 9.689 10652 Z= 0.362 Chirality : 0.042 0.170 1138 Planarity : 0.005 0.047 1296 Dihedral : 6.822 55.459 1074 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.47 % Allowed : 28.91 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.28), residues: 886 helix: 1.09 (0.22), residues: 552 sheet: -1.20 (0.59), residues: 56 loop : -3.28 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 68 HIS 0.002 0.001 HIS D 117 PHE 0.029 0.001 PHE A 373 TYR 0.036 0.002 TYR A 182 ARG 0.005 0.000 ARG A 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 235 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 224 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.6963 (t80) REVERT: A 248 ASP cc_start: 0.7338 (t0) cc_final: 0.6418 (t0) REVERT: A 251 GLU cc_start: 0.7190 (pm20) cc_final: 0.6816 (pm20) REVERT: A 334 ARG cc_start: 0.6531 (tmt170) cc_final: 0.5427 (ttt180) REVERT: C 176 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8575 (mm110) REVERT: C 224 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.6959 (t80) REVERT: C 248 ASP cc_start: 0.7253 (t70) cc_final: 0.6362 (t0) REVERT: C 251 GLU cc_start: 0.7327 (pm20) cc_final: 0.6945 (pm20) REVERT: C 334 ARG cc_start: 0.6508 (tmt170) cc_final: 0.5407 (ttt180) REVERT: D 28 PHE cc_start: 0.8635 (t80) cc_final: 0.8397 (t80) outliers start: 36 outliers final: 31 residues processed: 250 average time/residue: 0.1650 time to fit residues: 58.3460 Evaluate side-chains 257 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 224 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.128230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.104399 restraints weight = 18730.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.107638 restraints weight = 10193.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.109872 restraints weight = 6959.488| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7846 Z= 0.201 Angle : 0.716 9.679 10652 Z= 0.363 Chirality : 0.042 0.193 1138 Planarity : 0.005 0.053 1296 Dihedral : 6.775 55.208 1074 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.47 % Allowed : 29.28 % Favored : 66.25 % 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: -0.53 (0.28), residues: 886 helix: 1.21 (0.22), residues: 542 sheet: -1.25 (0.60), residues: 56 loop : -3.38 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 68 HIS 0.002 0.001 HIS B 52 PHE 0.030 0.001 PHE A 373 TYR 0.035 0.002 TYR A 182 ARG 0.004 0.000 ARG D 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1949.21 seconds wall clock time: 36 minutes 20.32 seconds (2180.32 seconds total)