Starting phenix.real_space_refine on Mon Mar 11 02:31:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evp_31339/03_2024/7evp_31339.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evp_31339/03_2024/7evp_31339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evp_31339/03_2024/7evp_31339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evp_31339/03_2024/7evp_31339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evp_31339/03_2024/7evp_31339.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evp_31339/03_2024/7evp_31339.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.097 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 4184 2.51 5 N 1064 2.21 5 O 1350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 25": "NH1" <-> "NH2" Residue "A PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 25": "NH1" <-> "NH2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6616 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2944 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 360} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 364 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "B" Number of atoms: 2944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2944 Classifications: {'peptide': 377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 360} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 364 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Time building chain proxies: 4.15, per 1000 atoms: 0.63 Number of scatterers: 6616 At special positions: 0 Unit cell: (107.42, 97.58, 66.42, 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 18 16.00 O 1350 8.00 N 1064 7.00 C 4184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.4 seconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 18 sheets defined 25.2% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 removed outlier: 4.225A pdb=" N THR A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.745A pdb=" N VAL A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.557A pdb=" N GLN A 123 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 151 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 252 through 256 removed outlier: 3.538A pdb=" N LEU A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 256 " --> pdb=" O THR A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.773A pdb=" N ILE A 275 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.746A pdb=" N ARG A 283 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 284 " --> pdb=" O LEU A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 331 through 340 removed outlier: 3.578A pdb=" N ALA A 337 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 25 Processing helix chain 'C' and resid 32 through 54 removed outlier: 3.615A pdb=" N LEU C 36 " --> pdb=" O TYR C 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 16 removed outlier: 4.225A pdb=" N THR B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 88 removed outlier: 3.745A pdb=" N VAL B 84 " --> pdb=" O GLY B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.557A pdb=" N GLN B 123 " --> pdb=" O ASP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.538A pdb=" N LEU B 255 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE B 256 " --> pdb=" O THR B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.773A pdb=" N ILE B 275 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.746A pdb=" N ARG B 283 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 284 " --> pdb=" O LEU B 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 284' Processing helix chain 'B' and resid 331 through 340 removed outlier: 3.578A pdb=" N ALA B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 25 Processing helix chain 'D' and resid 32 through 54 removed outlier: 3.614A pdb=" N LEU D 36 " --> pdb=" O TYR D 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 72 removed outlier: 6.321A pdb=" N GLU A 3 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 59 removed outlier: 4.961A pdb=" N SER A 48 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLY A 33 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 62 removed outlier: 3.537A pdb=" N GLU A 65 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=AA6, first strand: chain 'A' and resid 199 through 204 removed outlier: 3.562A pdb=" N VAL A 187 " --> pdb=" O THR A 368 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 360 " --> pdb=" O GLU A 347 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 262 " --> pdb=" O PHE A 350 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 199 through 204 removed outlier: 3.562A pdb=" N VAL A 187 " --> pdb=" O THR A 368 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 360 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 289 through 291 Processing sheet with id=AA9, first strand: chain 'A' and resid 298 through 299 Processing sheet with id=AB1, first strand: chain 'A' and resid 302 through 305 Processing sheet with id=AB2, first strand: chain 'B' and resid 70 through 72 removed outlier: 6.321A pdb=" N GLU B 3 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 59 removed outlier: 4.961A pdb=" N SER B 48 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLY B 33 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AB5, first strand: chain 'B' and resid 61 through 62 removed outlier: 3.537A pdb=" N GLU B 65 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 199 through 204 removed outlier: 3.562A pdb=" N VAL B 187 " --> pdb=" O THR B 368 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 360 " --> pdb=" O GLU B 347 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 262 " --> pdb=" O PHE B 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 199 through 204 removed outlier: 3.562A pdb=" N VAL B 187 " --> pdb=" O THR B 368 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 360 " --> pdb=" O GLU B 347 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AB9, first strand: chain 'B' and resid 298 through 299 310 hydrogen bonds defined for protein. 840 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: 1.98 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1687 1.33 - 1.45: 1095 1.45 - 1.57: 3902 1.57 - 1.68: 0 1.68 - 1.80: 34 Bond restraints: 6718 Sorted by residual: bond pdb=" CG LEU B 370 " pdb=" CD1 LEU B 370 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.19e+00 bond pdb=" CG LEU A 370 " pdb=" CD1 LEU A 370 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.19e+00 bond pdb=" CA ILE B 107 " pdb=" CB ILE B 107 " ideal model delta sigma weight residual 1.540 1.521 0.019 1.36e-02 5.41e+03 2.03e+00 bond pdb=" CA ILE A 107 " pdb=" CB ILE A 107 " ideal model delta sigma weight residual 1.540 1.521 0.019 1.36e-02 5.41e+03 2.03e+00 bond pdb=" CG LEU A 359 " pdb=" CD2 LEU A 359 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 ... (remaining 6713 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.06: 144 106.06 - 112.99: 3701 112.99 - 119.92: 2283 119.92 - 126.86: 2914 126.86 - 133.79: 58 Bond angle restraints: 9100 Sorted by residual: angle pdb=" C MET A 354 " pdb=" N LYS A 355 " pdb=" CA LYS A 355 " ideal model delta sigma weight residual 122.56 127.94 -5.38 1.58e+00 4.01e-01 1.16e+01 angle pdb=" C MET B 354 " pdb=" N LYS B 355 " pdb=" CA LYS B 355 " ideal model delta sigma weight residual 122.56 127.94 -5.38 1.58e+00 4.01e-01 1.16e+01 angle pdb=" C PRO B 306 " pdb=" N GLU B 307 " pdb=" CA GLU B 307 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C PRO A 306 " pdb=" N GLU A 307 " pdb=" CA GLU A 307 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" CG1 ILE A 374 " pdb=" CB ILE A 374 " pdb=" CG2 ILE A 374 " ideal model delta sigma weight residual 110.70 102.04 8.66 3.00e+00 1.11e-01 8.33e+00 ... (remaining 9095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.84: 3632 10.84 - 21.68: 388 21.68 - 32.52: 64 32.52 - 43.36: 26 43.36 - 54.20: 8 Dihedral angle restraints: 4118 sinusoidal: 1672 harmonic: 2446 Sorted by residual: dihedral pdb=" CA ALA B 282 " pdb=" C ALA B 282 " pdb=" N ARG B 283 " pdb=" CA ARG B 283 " ideal model delta harmonic sigma weight residual 180.00 148.64 31.36 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA ALA A 282 " pdb=" C ALA A 282 " pdb=" N ARG A 283 " pdb=" CA ARG A 283 " ideal model delta harmonic sigma weight residual 180.00 148.64 31.36 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CA ASN A 151 " pdb=" C ASN A 151 " pdb=" N PHE A 152 " pdb=" CA PHE A 152 " ideal model delta harmonic sigma weight residual 180.00 160.70 19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 4115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 615 0.045 - 0.091: 317 0.091 - 0.136: 114 0.136 - 0.181: 14 0.181 - 0.226: 8 Chirality restraints: 1068 Sorted by residual: chirality pdb=" CG LEU C 36 " pdb=" CB LEU C 36 " pdb=" CD1 LEU C 36 " pdb=" CD2 LEU C 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU D 36 " pdb=" CB LEU D 36 " pdb=" CD1 LEU D 36 " pdb=" CD2 LEU D 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE B 374 " pdb=" CA ILE B 374 " pdb=" CG1 ILE B 374 " pdb=" CG2 ILE B 374 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1065 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 168 " 0.013 2.00e-02 2.50e+03 1.26e-02 3.96e+00 pdb=" CG TRP B 168 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 168 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 168 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 168 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 168 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 168 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 168 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 168 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 168 " 0.013 2.00e-02 2.50e+03 1.26e-02 3.96e+00 pdb=" CG TRP A 168 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 168 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 168 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 168 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 168 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 168 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 168 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 168 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 168 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 282 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.59e+00 pdb=" C ALA A 282 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA A 282 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 283 " 0.011 2.00e-02 2.50e+03 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2099 2.84 - 3.36: 6096 3.36 - 3.87: 10574 3.87 - 4.39: 12402 4.39 - 4.90: 21631 Nonbonded interactions: 52802 Sorted by model distance: nonbonded pdb=" OG SER B 216 " pdb=" OD1 ASN B 218 " model vdw 2.328 2.440 nonbonded pdb=" OG SER A 216 " pdb=" OD1 ASN A 218 " model vdw 2.328 2.440 nonbonded pdb=" OE2 GLU C 48 " pdb=" NZ LYS D 20 " model vdw 2.370 2.520 nonbonded pdb=" NZ LYS C 20 " pdb=" OE2 GLU D 48 " model vdw 2.406 2.520 nonbonded pdb=" O ASN A 16 " pdb=" NZ LYS A 20 " model vdw 2.418 2.520 ... (remaining 52797 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 'B' } ncs_group { reference = chain 'C' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 3.830 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 22.090 Find NCS groups from input model: 0.320 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 : 0.008 0.052 6718 Z= 0.511 Angle : 0.868 8.660 9100 Z= 0.464 Chirality : 0.060 0.226 1068 Planarity : 0.006 0.047 1186 Dihedral : 9.798 54.203 2530 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.26 % Allowed : 3.44 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -5.27 (0.22), residues: 832 helix: -3.56 (0.22), residues: 226 sheet: -3.63 (0.24), residues: 298 loop : -2.87 (0.29), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.007 TRP B 168 HIS 0.010 0.002 HIS C 19 PHE 0.029 0.004 PHE B 11 TYR 0.019 0.003 TYR C 32 ARG 0.007 0.001 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7595 (ttmt) cc_final: 0.7231 (tttm) REVERT: A 44 ILE cc_start: 0.7399 (pt) cc_final: 0.7186 (pt) REVERT: A 106 LEU cc_start: 0.7356 (mp) cc_final: 0.6824 (pp) REVERT: A 131 SER cc_start: 0.8802 (m) cc_final: 0.8592 (p) REVERT: A 149 GLN cc_start: 0.7718 (mt0) cc_final: 0.7367 (mt0) REVERT: A 158 GLU cc_start: 0.7791 (mp0) cc_final: 0.7275 (tm-30) REVERT: A 171 GLN cc_start: 0.8408 (pt0) cc_final: 0.8094 (mt0) REVERT: A 206 LYS cc_start: 0.8342 (ptpp) cc_final: 0.8079 (ptpp) REVERT: A 243 ARG cc_start: 0.7343 (ttp80) cc_final: 0.6568 (ttm110) REVERT: A 246 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7647 (mm-30) REVERT: A 263 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7378 (ttmm) REVERT: A 270 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7505 (mt-10) REVERT: A 349 GLU cc_start: 0.8176 (pt0) cc_final: 0.7951 (pt0) REVERT: B 7 LYS cc_start: 0.7595 (ttmt) cc_final: 0.7229 (tttm) REVERT: B 44 ILE cc_start: 0.7404 (pt) cc_final: 0.7183 (pt) REVERT: B 106 LEU cc_start: 0.7363 (mp) cc_final: 0.6827 (pp) REVERT: B 131 SER cc_start: 0.8805 (m) cc_final: 0.8598 (p) REVERT: B 149 GLN cc_start: 0.7724 (mt0) cc_final: 0.7369 (mt0) REVERT: B 158 GLU cc_start: 0.7785 (mp0) cc_final: 0.7272 (tm-30) REVERT: B 171 GLN cc_start: 0.8407 (pt0) cc_final: 0.8099 (mt0) REVERT: B 206 LYS cc_start: 0.8345 (ptpp) cc_final: 0.8083 (ptpp) REVERT: B 243 ARG cc_start: 0.7340 (ttp80) cc_final: 0.6572 (ttm110) REVERT: B 246 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7645 (mm-30) REVERT: B 262 ILE cc_start: 0.8187 (pt) cc_final: 0.7987 (pt) REVERT: B 263 LYS cc_start: 0.8041 (ttmt) cc_final: 0.7385 (ttmm) REVERT: B 270 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7494 (mt-10) REVERT: B 349 GLU cc_start: 0.8176 (pt0) cc_final: 0.7954 (pt0) outliers start: 2 outliers final: 2 residues processed: 146 average time/residue: 0.1988 time to fit residues: 37.8110 Evaluate side-chains 105 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 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 16 ASN A 102 GLN A 212 ASN C 43 GLN B 16 ASN B 102 GLN B 212 ASN D 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6718 Z= 0.197 Angle : 0.532 5.998 9100 Z= 0.274 Chirality : 0.047 0.144 1068 Planarity : 0.004 0.034 1186 Dihedral : 5.112 22.537 886 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.98 % Allowed : 7.80 % Favored : 90.21 % 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: -4.06 (0.26), residues: 832 helix: -2.33 (0.29), residues: 224 sheet: -2.86 (0.27), residues: 296 loop : -2.44 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 168 HIS 0.004 0.001 HIS D 19 PHE 0.010 0.001 PHE B 357 TYR 0.007 0.001 TYR D 14 ARG 0.002 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7606 (ttmt) cc_final: 0.7212 (tttm) REVERT: A 28 LEU cc_start: 0.7426 (mp) cc_final: 0.7225 (tp) REVERT: A 44 ILE cc_start: 0.7210 (pt) cc_final: 0.6954 (pt) REVERT: A 86 ILE cc_start: 0.7835 (mm) cc_final: 0.7622 (mt) REVERT: A 102 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: A 106 LEU cc_start: 0.7189 (mp) cc_final: 0.6573 (pp) REVERT: A 149 GLN cc_start: 0.7592 (mt0) cc_final: 0.7244 (mt0) REVERT: A 158 GLU cc_start: 0.7752 (mp0) cc_final: 0.7253 (tm-30) REVERT: A 171 GLN cc_start: 0.8430 (pt0) cc_final: 0.7978 (mt0) REVERT: A 206 LYS cc_start: 0.8286 (ptpp) cc_final: 0.8037 (ptpp) REVERT: A 243 ARG cc_start: 0.7207 (ttp80) cc_final: 0.6495 (ttm110) REVERT: A 246 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7632 (mm-30) REVERT: A 263 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7721 (ttmm) REVERT: A 313 GLU cc_start: 0.8082 (mp0) cc_final: 0.7478 (mp0) REVERT: B 7 LYS cc_start: 0.7599 (ttmt) cc_final: 0.7205 (tttm) REVERT: B 28 LEU cc_start: 0.7437 (mp) cc_final: 0.7235 (tp) REVERT: B 44 ILE cc_start: 0.7214 (pt) cc_final: 0.6953 (pt) REVERT: B 86 ILE cc_start: 0.7827 (mm) cc_final: 0.7616 (mt) REVERT: B 102 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7797 (mp10) REVERT: B 106 LEU cc_start: 0.7199 (mp) cc_final: 0.6580 (pp) REVERT: B 149 GLN cc_start: 0.7599 (mt0) cc_final: 0.7252 (mt0) REVERT: B 158 GLU cc_start: 0.7744 (mp0) cc_final: 0.7251 (tm-30) REVERT: B 171 GLN cc_start: 0.8429 (pt0) cc_final: 0.7981 (mt0) REVERT: B 206 LYS cc_start: 0.8286 (ptpp) cc_final: 0.8040 (ptpp) REVERT: B 243 ARG cc_start: 0.7204 (ttp80) cc_final: 0.6499 (ttm110) REVERT: B 246 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7632 (mm-30) REVERT: B 263 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7571 (ttmm) REVERT: B 313 GLU cc_start: 0.8081 (mp0) cc_final: 0.7480 (mp0) outliers start: 15 outliers final: 12 residues processed: 124 average time/residue: 0.1724 time to fit residues: 28.8265 Evaluate side-chains 111 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 367 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 151 ASN B 102 GLN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6718 Z= 0.203 Angle : 0.500 6.390 9100 Z= 0.255 Chirality : 0.046 0.150 1068 Planarity : 0.003 0.024 1186 Dihedral : 4.728 22.271 886 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.23 % Allowed : 8.07 % Favored : 87.70 % 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: -3.50 (0.27), residues: 832 helix: -1.55 (0.31), residues: 224 sheet: -2.77 (0.27), residues: 316 loop : -2.00 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 168 HIS 0.002 0.001 HIS D 19 PHE 0.012 0.001 PHE B 103 TYR 0.006 0.001 TYR B 10 ARG 0.001 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7566 (ttmt) cc_final: 0.7164 (tttm) REVERT: A 44 ILE cc_start: 0.7182 (pt) cc_final: 0.6966 (pt) REVERT: A 102 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7916 (mp10) REVERT: A 106 LEU cc_start: 0.7207 (mp) cc_final: 0.6903 (mm) REVERT: A 149 GLN cc_start: 0.7584 (mt0) cc_final: 0.7257 (mt0) REVERT: A 158 GLU cc_start: 0.7778 (mp0) cc_final: 0.7273 (tm-30) REVERT: A 171 GLN cc_start: 0.8495 (pt0) cc_final: 0.8022 (mt0) REVERT: A 206 LYS cc_start: 0.8211 (ptpp) cc_final: 0.7872 (pttm) REVERT: A 230 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8345 (mm-40) REVERT: A 246 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7862 (mm-30) REVERT: A 263 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7718 (ttmm) REVERT: A 313 GLU cc_start: 0.8087 (mp0) cc_final: 0.7514 (mp0) REVERT: B 7 LYS cc_start: 0.7560 (ttmt) cc_final: 0.7158 (tttm) REVERT: B 44 ILE cc_start: 0.7187 (pt) cc_final: 0.6964 (pt) REVERT: B 102 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7919 (mp10) REVERT: B 106 LEU cc_start: 0.7217 (mp) cc_final: 0.6911 (mm) REVERT: B 149 GLN cc_start: 0.7591 (mt0) cc_final: 0.7263 (mt0) REVERT: B 158 GLU cc_start: 0.7769 (mp0) cc_final: 0.7270 (tm-30) REVERT: B 171 GLN cc_start: 0.8495 (pt0) cc_final: 0.8025 (mt0) REVERT: B 206 LYS cc_start: 0.8212 (ptpp) cc_final: 0.7875 (pttm) REVERT: B 230 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8348 (mm-40) REVERT: B 246 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7862 (mm-30) REVERT: B 263 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7780 (ttmm) REVERT: B 313 GLU cc_start: 0.8088 (mp0) cc_final: 0.7520 (mp0) outliers start: 32 outliers final: 16 residues processed: 120 average time/residue: 0.1646 time to fit residues: 27.3122 Evaluate side-chains 108 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN C 42 GLN B 151 ASN D 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6718 Z= 0.208 Angle : 0.513 6.232 9100 Z= 0.255 Chirality : 0.046 0.144 1068 Planarity : 0.003 0.019 1186 Dihedral : 4.566 22.372 886 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.57 % Allowed : 8.99 % Favored : 87.43 % 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: -3.06 (0.27), residues: 832 helix: -1.01 (0.33), residues: 228 sheet: -2.93 (0.28), residues: 268 loop : -1.70 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 168 HIS 0.006 0.001 HIS D 19 PHE 0.010 0.001 PHE B 357 TYR 0.007 0.001 TYR B 10 ARG 0.001 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 85 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7616 (ttmt) cc_final: 0.7169 (tttm) REVERT: A 44 ILE cc_start: 0.7270 (pt) cc_final: 0.7004 (pt) REVERT: A 106 LEU cc_start: 0.7240 (mp) cc_final: 0.7022 (mt) REVERT: A 158 GLU cc_start: 0.7787 (mp0) cc_final: 0.7283 (tm-30) REVERT: A 171 GLN cc_start: 0.8518 (pt0) cc_final: 0.8015 (mt0) REVERT: A 206 LYS cc_start: 0.8173 (ptpp) cc_final: 0.7820 (pttm) REVERT: A 230 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8398 (mm-40) REVERT: A 246 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7823 (mm-30) REVERT: A 263 LYS cc_start: 0.8251 (ttmt) cc_final: 0.7752 (ttmm) REVERT: A 313 GLU cc_start: 0.8071 (mp0) cc_final: 0.7458 (mp0) REVERT: C 25 MET cc_start: 0.7513 (mtt) cc_final: 0.7191 (mtt) REVERT: B 7 LYS cc_start: 0.7607 (ttmt) cc_final: 0.7161 (tttm) REVERT: B 44 ILE cc_start: 0.7275 (pt) cc_final: 0.7002 (pt) REVERT: B 106 LEU cc_start: 0.7246 (mp) cc_final: 0.7025 (mt) REVERT: B 158 GLU cc_start: 0.7779 (mp0) cc_final: 0.7282 (tm-30) REVERT: B 171 GLN cc_start: 0.8517 (pt0) cc_final: 0.8018 (mt0) REVERT: B 206 LYS cc_start: 0.8176 (ptpp) cc_final: 0.7826 (pttm) REVERT: B 230 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8400 (mm-40) REVERT: B 246 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7823 (mm-30) REVERT: B 263 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7737 (ttmm) REVERT: B 313 GLU cc_start: 0.8070 (mp0) cc_final: 0.7461 (mp0) REVERT: D 25 MET cc_start: 0.7419 (mtt) cc_final: 0.7125 (mtt) outliers start: 27 outliers final: 17 residues processed: 107 average time/residue: 0.1590 time to fit residues: 23.5119 Evaluate side-chains 98 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 67 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 71 optimal weight: 0.0270 chunk 20 optimal weight: 2.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6718 Z= 0.195 Angle : 0.498 6.215 9100 Z= 0.245 Chirality : 0.046 0.145 1068 Planarity : 0.002 0.017 1186 Dihedral : 4.417 22.842 886 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.44 % Allowed : 9.66 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.28), residues: 832 helix: -0.79 (0.34), residues: 232 sheet: -2.89 (0.28), residues: 268 loop : -1.49 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 168 HIS 0.001 0.000 HIS A 183 PHE 0.009 0.001 PHE A 357 TYR 0.010 0.001 TYR C 47 ARG 0.001 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7623 (ttmt) cc_final: 0.7273 (tttm) REVERT: A 44 ILE cc_start: 0.7263 (pt) cc_final: 0.7009 (pt) REVERT: A 106 LEU cc_start: 0.7299 (mp) cc_final: 0.6962 (mm) REVERT: A 158 GLU cc_start: 0.7754 (mp0) cc_final: 0.7305 (tm-30) REVERT: A 171 GLN cc_start: 0.8516 (pt0) cc_final: 0.7985 (mt0) REVERT: A 206 LYS cc_start: 0.8199 (ptpp) cc_final: 0.7823 (pttm) REVERT: A 215 MET cc_start: 0.7937 (mtp) cc_final: 0.7615 (mtm) REVERT: A 230 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8368 (mm-40) REVERT: A 243 ARG cc_start: 0.7091 (ttp80) cc_final: 0.6528 (ttm110) REVERT: A 246 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7826 (mm-30) REVERT: A 263 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7824 (ttmm) REVERT: A 313 GLU cc_start: 0.8094 (mp0) cc_final: 0.7520 (mp0) REVERT: C 25 MET cc_start: 0.7389 (mtt) cc_final: 0.7087 (mtt) REVERT: B 7 LYS cc_start: 0.7619 (ttmt) cc_final: 0.7268 (tttm) REVERT: B 44 ILE cc_start: 0.7268 (pt) cc_final: 0.7008 (pt) REVERT: B 106 LEU cc_start: 0.7303 (mp) cc_final: 0.6962 (mm) REVERT: B 158 GLU cc_start: 0.7747 (mp0) cc_final: 0.7305 (tm-30) REVERT: B 171 GLN cc_start: 0.8515 (pt0) cc_final: 0.7988 (mt0) REVERT: B 206 LYS cc_start: 0.8201 (ptpp) cc_final: 0.7827 (pttm) REVERT: B 215 MET cc_start: 0.7934 (mtp) cc_final: 0.7613 (mtm) REVERT: B 230 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8369 (mm-40) REVERT: B 243 ARG cc_start: 0.7092 (ttp80) cc_final: 0.6534 (ttm110) REVERT: B 246 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7825 (mm-30) REVERT: B 263 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7813 (ttmm) REVERT: B 313 GLU cc_start: 0.8096 (mp0) cc_final: 0.7527 (mp0) REVERT: D 25 MET cc_start: 0.7353 (mtt) cc_final: 0.7047 (mtt) outliers start: 26 outliers final: 21 residues processed: 108 average time/residue: 0.1884 time to fit residues: 27.3209 Evaluate side-chains 107 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.0000 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 151 ASN B 102 GLN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6718 Z= 0.260 Angle : 0.545 6.943 9100 Z= 0.266 Chirality : 0.048 0.151 1068 Planarity : 0.002 0.016 1186 Dihedral : 4.541 24.091 886 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.44 % Allowed : 10.98 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.28), residues: 832 helix: -0.67 (0.35), residues: 228 sheet: -2.60 (0.28), residues: 296 loop : -1.43 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 168 HIS 0.001 0.000 HIS B 183 PHE 0.010 0.001 PHE A 357 TYR 0.007 0.001 TYR A 10 ARG 0.002 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ILE cc_start: 0.7289 (pt) cc_final: 0.7053 (pt) REVERT: A 106 LEU cc_start: 0.7368 (mp) cc_final: 0.7003 (mm) REVERT: A 158 GLU cc_start: 0.7769 (mp0) cc_final: 0.7319 (tm-30) REVERT: A 171 GLN cc_start: 0.8515 (pt0) cc_final: 0.7989 (mt0) REVERT: A 206 LYS cc_start: 0.8223 (ptpp) cc_final: 0.7836 (pttm) REVERT: A 215 MET cc_start: 0.8084 (mtp) cc_final: 0.7702 (mtm) REVERT: A 230 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8278 (mm-40) REVERT: A 243 ARG cc_start: 0.7104 (ttp80) cc_final: 0.6504 (ttm110) REVERT: A 246 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7813 (mm-30) REVERT: A 263 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7751 (ttmm) REVERT: A 313 GLU cc_start: 0.8168 (mp0) cc_final: 0.7579 (mp0) REVERT: C 25 MET cc_start: 0.7457 (mtt) cc_final: 0.7175 (mtt) REVERT: B 44 ILE cc_start: 0.7295 (pt) cc_final: 0.7055 (pt) REVERT: B 106 LEU cc_start: 0.7369 (mp) cc_final: 0.7003 (mm) REVERT: B 158 GLU cc_start: 0.7764 (mp0) cc_final: 0.7319 (tm-30) REVERT: B 171 GLN cc_start: 0.8514 (pt0) cc_final: 0.7992 (mt0) REVERT: B 206 LYS cc_start: 0.8221 (ptpp) cc_final: 0.7839 (pttm) REVERT: B 215 MET cc_start: 0.8081 (mtp) cc_final: 0.7700 (mtm) REVERT: B 230 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8279 (mm-40) REVERT: B 243 ARG cc_start: 0.7104 (ttp80) cc_final: 0.6508 (ttm110) REVERT: B 246 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7804 (mm-30) REVERT: B 263 LYS cc_start: 0.8273 (ttmt) cc_final: 0.7743 (ttmm) REVERT: B 313 GLU cc_start: 0.8168 (mp0) cc_final: 0.7581 (mp0) REVERT: D 25 MET cc_start: 0.7377 (mtt) cc_final: 0.7115 (mtt) outliers start: 26 outliers final: 19 residues processed: 112 average time/residue: 0.1882 time to fit residues: 28.8020 Evaluate side-chains 105 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain D residue 28 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN C 42 GLN B 102 GLN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6718 Z= 0.204 Angle : 0.509 6.668 9100 Z= 0.250 Chirality : 0.047 0.147 1068 Planarity : 0.002 0.016 1186 Dihedral : 4.368 22.753 886 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.57 % Allowed : 11.38 % Favored : 85.05 % 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: -2.53 (0.29), residues: 832 helix: -0.51 (0.35), residues: 228 sheet: -2.79 (0.28), residues: 276 loop : -1.21 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 168 HIS 0.001 0.000 HIS B 183 PHE 0.009 0.001 PHE B 103 TYR 0.007 0.001 TYR A 10 ARG 0.001 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ILE cc_start: 0.7251 (pt) cc_final: 0.7007 (pt) REVERT: A 106 LEU cc_start: 0.7344 (mp) cc_final: 0.6980 (mm) REVERT: A 158 GLU cc_start: 0.7763 (mp0) cc_final: 0.7316 (tm-30) REVERT: A 171 GLN cc_start: 0.8519 (pt0) cc_final: 0.8001 (mt0) REVERT: A 174 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6033 (tp30) REVERT: A 206 LYS cc_start: 0.8220 (ptpp) cc_final: 0.7826 (pttm) REVERT: A 215 MET cc_start: 0.8014 (mtp) cc_final: 0.7595 (mtm) REVERT: A 230 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8266 (mm-40) REVERT: A 243 ARG cc_start: 0.7102 (ttp80) cc_final: 0.6501 (ttm110) REVERT: A 246 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7810 (mm-30) REVERT: A 263 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7814 (ttmm) REVERT: A 313 GLU cc_start: 0.8130 (mp0) cc_final: 0.7537 (mp0) REVERT: C 25 MET cc_start: 0.7362 (mtt) cc_final: 0.7074 (mtt) REVERT: B 44 ILE cc_start: 0.7252 (pt) cc_final: 0.7005 (pt) REVERT: B 106 LEU cc_start: 0.7334 (mp) cc_final: 0.7098 (mt) REVERT: B 158 GLU cc_start: 0.7757 (mp0) cc_final: 0.7316 (tm-30) REVERT: B 171 GLN cc_start: 0.8520 (pt0) cc_final: 0.8006 (mt0) REVERT: B 174 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6030 (tp30) REVERT: B 206 LYS cc_start: 0.8220 (ptpp) cc_final: 0.7831 (pttm) REVERT: B 215 MET cc_start: 0.8012 (mtp) cc_final: 0.7593 (mtm) REVERT: B 230 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8269 (mm-40) REVERT: B 243 ARG cc_start: 0.7102 (ttp80) cc_final: 0.6504 (ttm110) REVERT: B 246 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7809 (mm-30) REVERT: B 263 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7790 (ttmm) REVERT: B 313 GLU cc_start: 0.8128 (mp0) cc_final: 0.7536 (mp0) REVERT: D 25 MET cc_start: 0.7311 (mtt) cc_final: 0.7028 (mtt) outliers start: 27 outliers final: 20 residues processed: 109 average time/residue: 0.1774 time to fit residues: 26.5130 Evaluate side-chains 105 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.0670 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 chunk 75 optimal weight: 0.0870 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN C 42 GLN B 102 GLN B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6718 Z= 0.147 Angle : 0.485 6.103 9100 Z= 0.239 Chirality : 0.046 0.158 1068 Planarity : 0.002 0.015 1186 Dihedral : 4.183 21.625 886 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.31 % Allowed : 11.24 % Favored : 85.45 % 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: -2.43 (0.29), residues: 832 helix: -0.31 (0.35), residues: 232 sheet: -2.71 (0.30), residues: 248 loop : -1.47 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 168 HIS 0.001 0.000 HIS A 273 PHE 0.008 0.001 PHE B 103 TYR 0.007 0.001 TYR A 10 ARG 0.002 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 91 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ILE cc_start: 0.7240 (pt) cc_final: 0.6994 (pt) REVERT: A 106 LEU cc_start: 0.7302 (mp) cc_final: 0.6949 (mm) REVERT: A 158 GLU cc_start: 0.7735 (mp0) cc_final: 0.7328 (tm-30) REVERT: A 171 GLN cc_start: 0.8452 (pt0) cc_final: 0.7989 (mt0) REVERT: A 206 LYS cc_start: 0.8226 (ptpp) cc_final: 0.7881 (mtmm) REVERT: A 230 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8263 (mm-40) REVERT: A 243 ARG cc_start: 0.7083 (ttp80) cc_final: 0.6509 (ttm110) REVERT: A 246 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7811 (mm-30) REVERT: A 263 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7809 (ttmm) REVERT: A 313 GLU cc_start: 0.8077 (mp0) cc_final: 0.7540 (mp0) REVERT: C 25 MET cc_start: 0.7283 (mtt) cc_final: 0.6982 (mtt) REVERT: B 44 ILE cc_start: 0.7243 (pt) cc_final: 0.6994 (pt) REVERT: B 106 LEU cc_start: 0.7367 (mp) cc_final: 0.7012 (mm) REVERT: B 158 GLU cc_start: 0.7732 (mp0) cc_final: 0.7328 (tm-30) REVERT: B 171 GLN cc_start: 0.8454 (pt0) cc_final: 0.7995 (mt0) REVERT: B 206 LYS cc_start: 0.8223 (ptpp) cc_final: 0.7879 (mtmm) REVERT: B 230 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8269 (mm-40) REVERT: B 243 ARG cc_start: 0.7088 (ttp80) cc_final: 0.6517 (ttm110) REVERT: B 246 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7809 (mm-30) REVERT: B 263 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7792 (ttmm) REVERT: B 313 GLU cc_start: 0.8079 (mp0) cc_final: 0.7545 (mp0) REVERT: D 25 MET cc_start: 0.7264 (mtt) cc_final: 0.6949 (mtt) outliers start: 25 outliers final: 18 residues processed: 112 average time/residue: 0.1807 time to fit residues: 27.7120 Evaluate side-chains 105 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.0470 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 69 optimal weight: 0.0000 chunk 73 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.4484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6718 Z= 0.152 Angle : 0.489 5.835 9100 Z= 0.247 Chirality : 0.046 0.141 1068 Planarity : 0.003 0.027 1186 Dihedral : 4.141 22.436 886 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.91 % Allowed : 11.51 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.29), residues: 832 helix: -0.06 (0.36), residues: 218 sheet: -2.62 (0.30), residues: 248 loop : -1.41 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 168 HIS 0.001 0.000 HIS A 273 PHE 0.010 0.001 PHE B 103 TYR 0.031 0.001 TYR D 47 ARG 0.001 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4687 (ttm) cc_final: 0.4429 (ttm) REVERT: A 44 ILE cc_start: 0.7277 (pt) cc_final: 0.7037 (pt) REVERT: A 106 LEU cc_start: 0.7310 (mp) cc_final: 0.6972 (mm) REVERT: A 158 GLU cc_start: 0.7737 (mp0) cc_final: 0.7327 (tm-30) REVERT: A 171 GLN cc_start: 0.8474 (pt0) cc_final: 0.8092 (mt0) REVERT: A 206 LYS cc_start: 0.8204 (ptpp) cc_final: 0.7883 (mtmm) REVERT: A 230 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8333 (mm-40) REVERT: A 243 ARG cc_start: 0.7060 (ttp80) cc_final: 0.6486 (ttm110) REVERT: A 246 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7820 (mm-30) REVERT: A 263 LYS cc_start: 0.8282 (ttmt) cc_final: 0.7801 (ttmm) REVERT: A 313 GLU cc_start: 0.8105 (mp0) cc_final: 0.7613 (mp0) REVERT: C 25 MET cc_start: 0.7292 (mtt) cc_final: 0.6986 (mtt) REVERT: B 1 MET cc_start: 0.4774 (ttm) cc_final: 0.4542 (ttm) REVERT: B 44 ILE cc_start: 0.7279 (pt) cc_final: 0.7037 (pt) REVERT: B 106 LEU cc_start: 0.7316 (mp) cc_final: 0.6974 (mm) REVERT: B 158 GLU cc_start: 0.7736 (mp0) cc_final: 0.7329 (tm-30) REVERT: B 171 GLN cc_start: 0.8475 (pt0) cc_final: 0.8095 (mt0) REVERT: B 206 LYS cc_start: 0.8205 (ptpp) cc_final: 0.7883 (mtmm) REVERT: B 230 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8336 (mm-40) REVERT: B 243 ARG cc_start: 0.7061 (ttp80) cc_final: 0.6490 (ttm110) REVERT: B 246 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7819 (mm-30) REVERT: B 263 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7772 (ttmm) REVERT: B 313 GLU cc_start: 0.8086 (mp0) cc_final: 0.7599 (mp0) REVERT: D 25 MET cc_start: 0.7242 (mtt) cc_final: 0.6985 (mtt) outliers start: 22 outliers final: 20 residues processed: 104 average time/residue: 0.1987 time to fit residues: 27.6114 Evaluate side-chains 105 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6718 Z= 0.189 Angle : 0.505 6.731 9100 Z= 0.252 Chirality : 0.046 0.144 1068 Planarity : 0.003 0.026 1186 Dihedral : 4.253 23.130 886 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.91 % Allowed : 12.43 % Favored : 84.66 % 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: -2.19 (0.29), residues: 832 helix: 0.18 (0.36), residues: 214 sheet: -2.61 (0.30), residues: 248 loop : -1.44 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 168 HIS 0.001 0.000 HIS A 273 PHE 0.009 0.001 PHE B 103 TYR 0.030 0.001 TYR C 47 ARG 0.004 0.000 ARG B 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4666 (ttm) cc_final: 0.4402 (ttm) REVERT: A 44 ILE cc_start: 0.7243 (pt) cc_final: 0.7022 (pt) REVERT: A 106 LEU cc_start: 0.7328 (mp) cc_final: 0.6979 (mm) REVERT: A 149 GLN cc_start: 0.7552 (mt0) cc_final: 0.7239 (mt0) REVERT: A 158 GLU cc_start: 0.7710 (mp0) cc_final: 0.7301 (tm-30) REVERT: A 171 GLN cc_start: 0.8457 (pt0) cc_final: 0.8051 (mt0) REVERT: A 206 LYS cc_start: 0.8173 (ptpp) cc_final: 0.7857 (mtmm) REVERT: A 230 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8339 (mm-40) REVERT: A 243 ARG cc_start: 0.7035 (ttp80) cc_final: 0.6470 (ttm110) REVERT: A 246 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7809 (mm-30) REVERT: A 263 LYS cc_start: 0.8287 (ttmt) cc_final: 0.7799 (ttmm) REVERT: A 313 GLU cc_start: 0.8110 (mp0) cc_final: 0.7615 (mp0) REVERT: A 326 LYS cc_start: 0.8468 (mttm) cc_final: 0.7946 (mmtt) REVERT: C 25 MET cc_start: 0.7344 (mtt) cc_final: 0.7033 (mtt) REVERT: B 1 MET cc_start: 0.4782 (ttm) cc_final: 0.4554 (ttm) REVERT: B 44 ILE cc_start: 0.7245 (pt) cc_final: 0.7018 (pt) REVERT: B 106 LEU cc_start: 0.7290 (mp) cc_final: 0.6938 (mm) REVERT: B 149 GLN cc_start: 0.7564 (mt0) cc_final: 0.7243 (mt0) REVERT: B 158 GLU cc_start: 0.7710 (mp0) cc_final: 0.7301 (tm-30) REVERT: B 171 GLN cc_start: 0.8458 (pt0) cc_final: 0.8057 (mt0) REVERT: B 206 LYS cc_start: 0.8181 (ptpp) cc_final: 0.7865 (mtmm) REVERT: B 230 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8342 (mm-40) REVERT: B 243 ARG cc_start: 0.7038 (ttp80) cc_final: 0.6477 (ttm110) REVERT: B 246 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7808 (mm-30) REVERT: B 263 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7753 (ttmm) REVERT: B 313 GLU cc_start: 0.8111 (mp0) cc_final: 0.7618 (mp0) REVERT: D 25 MET cc_start: 0.7317 (mtt) cc_final: 0.7033 (mtt) outliers start: 22 outliers final: 20 residues processed: 104 average time/residue: 0.1746 time to fit residues: 24.7192 Evaluate side-chains 105 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 370 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 0.0270 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.150151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.118386 restraints weight = 7698.933| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.25 r_work: 0.3478 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6718 Z= 0.150 Angle : 0.489 6.687 9100 Z= 0.243 Chirality : 0.046 0.140 1068 Planarity : 0.003 0.025 1186 Dihedral : 4.121 21.629 886 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.78 % Allowed : 13.23 % Favored : 83.99 % 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: -2.03 (0.29), residues: 832 helix: 0.46 (0.37), residues: 214 sheet: -2.54 (0.30), residues: 248 loop : -1.42 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 168 HIS 0.000 0.000 HIS B 183 PHE 0.008 0.001 PHE B 103 TYR 0.029 0.001 TYR C 47 ARG 0.004 0.000 ARG A 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1689.82 seconds wall clock time: 31 minutes 20.07 seconds (1880.07 seconds total)