Starting phenix.real_space_refine on Mon Mar 11 10:04:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqz_13035/03_2024/7oqz_13035_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqz_13035/03_2024/7oqz_13035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqz_13035/03_2024/7oqz_13035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqz_13035/03_2024/7oqz_13035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqz_13035/03_2024/7oqz_13035_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqz_13035/03_2024/7oqz_13035_updated.pdb" } resolution = 3.27 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= 0.002 sd= 0.037 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 8 5.49 5 S 52 5.16 5 C 5468 2.51 5 N 1196 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7996 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 4.82, per 1000 atoms: 0.60 Number of scatterers: 7996 At special positions: 0 Unit cell: (92.65, 92.65, 76.3, 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 52 16.00 P 8 15.00 O 1272 8.00 N 1196 7.00 C 5468 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: 3.12 Conformation dependent library (CDL) restraints added in 1.4 seconds 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 0 sheets defined 79.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 4 through 33 Proline residue: A 10 - end of helix Processing helix chain 'A' and resid 43 through 68 Processing helix chain 'A' and resid 90 through 114 Processing helix chain 'A' and resid 121 through 140 removed outlier: 3.574A pdb=" N ASN A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 172 Processing helix chain 'A' and resid 177 through 201 Processing helix chain 'A' and resid 215 through 250 Processing helix chain 'B' and resid 4 through 33 Proline residue: B 10 - end of helix Processing helix chain 'B' and resid 43 through 68 Processing helix chain 'B' and resid 90 through 114 Processing helix chain 'B' and resid 121 through 140 removed outlier: 3.574A pdb=" N ASN B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 172 Processing helix chain 'B' and resid 177 through 201 Processing helix chain 'B' and resid 215 through 250 Processing helix chain 'C' and resid 4 through 33 Proline residue: C 10 - end of helix Processing helix chain 'C' and resid 43 through 68 Processing helix chain 'C' and resid 90 through 114 Processing helix chain 'C' and resid 121 through 140 removed outlier: 3.573A pdb=" N ASN C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 172 Processing helix chain 'C' and resid 177 through 201 Processing helix chain 'C' and resid 215 through 250 Processing helix chain 'D' and resid 4 through 33 Proline residue: D 10 - end of helix Processing helix chain 'D' and resid 43 through 68 Processing helix chain 'D' and resid 90 through 114 Processing helix chain 'D' and resid 121 through 140 removed outlier: 3.574A pdb=" N ASN D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 172 Processing helix chain 'D' and resid 177 through 201 Processing helix chain 'D' and resid 215 through 250 628 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1104 1.31 - 1.43: 2440 1.43 - 1.56: 4461 1.56 - 1.68: 130 1.68 - 1.81: 81 Bond restraints: 8216 Sorted by residual: bond pdb=" C31 PC1 C 302 " pdb=" O31 PC1 C 302 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C31 PC1 A 301 " pdb=" O31 PC1 A 301 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C31 PC1 B 302 " pdb=" O31 PC1 B 302 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C31 PC1 C 303 " pdb=" O31 PC1 C 303 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C31 PC1 D 303 " pdb=" O31 PC1 D 303 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.94e+01 ... (remaining 8211 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.38: 261 107.38 - 114.03: 4882 114.03 - 120.68: 3435 120.68 - 127.33: 2374 127.33 - 133.98: 116 Bond angle restraints: 11068 Sorted by residual: angle pdb=" O12 PC1 D 303 " pdb=" P PC1 D 303 " pdb=" O14 PC1 D 303 " ideal model delta sigma weight residual 123.67 109.34 14.33 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 C 302 " pdb=" P PC1 C 302 " pdb=" O14 PC1 C 302 " ideal model delta sigma weight residual 123.67 109.35 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 A 302 " pdb=" P PC1 A 302 " pdb=" O14 PC1 A 302 " ideal model delta sigma weight residual 123.67 109.35 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 B 302 " pdb=" P PC1 B 302 " pdb=" O14 PC1 B 302 " ideal model delta sigma weight residual 123.67 109.36 14.31 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 A 301 " pdb=" P PC1 A 301 " pdb=" O14 PC1 A 301 " ideal model delta sigma weight residual 123.67 109.36 14.31 3.00e+00 1.11e-01 2.28e+01 ... (remaining 11063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 4169 14.33 - 28.65: 331 28.65 - 42.98: 96 42.98 - 57.31: 76 57.31 - 71.63: 32 Dihedral angle restraints: 4704 sinusoidal: 1996 harmonic: 2708 Sorted by residual: dihedral pdb=" N PHE A 194 " pdb=" CA PHE A 194 " pdb=" CB PHE A 194 " pdb=" CG PHE A 194 " ideal model delta sinusoidal sigma weight residual -60.00 -118.53 58.53 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N PHE B 194 " pdb=" CA PHE B 194 " pdb=" CB PHE B 194 " pdb=" CG PHE B 194 " ideal model delta sinusoidal sigma weight residual -60.00 -118.52 58.52 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N PHE D 194 " pdb=" CA PHE D 194 " pdb=" CB PHE D 194 " pdb=" CG PHE D 194 " ideal model delta sinusoidal sigma weight residual -60.00 -118.51 58.51 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 811 0.024 - 0.049: 253 0.049 - 0.073: 128 0.073 - 0.098: 20 0.098 - 0.122: 8 Chirality restraints: 1220 Sorted by residual: chirality pdb=" CA ILE A 71 " pdb=" N ILE A 71 " pdb=" C ILE A 71 " pdb=" CB ILE A 71 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE D 71 " pdb=" N ILE D 71 " pdb=" C ILE D 71 " pdb=" CB ILE D 71 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 1217 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 130 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.44e+00 pdb=" C ALA A 130 " 0.021 2.00e-02 2.50e+03 pdb=" O ALA A 130 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU A 131 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 130 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.44e+00 pdb=" C ALA B 130 " 0.021 2.00e-02 2.50e+03 pdb=" O ALA B 130 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU B 131 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 130 " 0.006 2.00e-02 2.50e+03 1.20e-02 1.43e+00 pdb=" C ALA D 130 " -0.021 2.00e-02 2.50e+03 pdb=" O ALA D 130 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU D 131 " 0.007 2.00e-02 2.50e+03 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1712 2.79 - 3.31: 8129 3.31 - 3.84: 12951 3.84 - 4.37: 13568 4.37 - 4.90: 25055 Nonbonded interactions: 61415 Sorted by model distance: nonbonded pdb=" O LEU D 125 " pdb=" OG SER D 128 " model vdw 2.257 2.440 nonbonded pdb=" O LEU B 125 " pdb=" OG SER B 128 " model vdw 2.257 2.440 nonbonded pdb=" O LEU C 125 " pdb=" OG SER C 128 " model vdw 2.257 2.440 nonbonded pdb=" O LEU A 125 " pdb=" OG SER A 128 " model vdw 2.257 2.440 nonbonded pdb=" NE1 TRP B 21 " pdb=" OE2 GLU B 53 " model vdw 2.342 2.520 ... (remaining 61410 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' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'B' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'C' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'D' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.750 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.420 Find NCS groups from input model: 0.500 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.009 0.109 8216 Z= 0.577 Angle : 0.981 14.327 11068 Z= 0.384 Chirality : 0.030 0.122 1220 Planarity : 0.003 0.019 1288 Dihedral : 14.990 71.632 2960 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.51 % Allowed : 3.06 % Favored : 96.43 % 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: 4.83 (0.27), residues: 932 helix: 3.85 (0.17), residues: 780 sheet: None (None), residues: 0 loop : -0.84 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 193 HIS 0.003 0.001 HIS A 153 PHE 0.007 0.001 PHE A 96 TYR 0.005 0.001 TYR A 229 ARG 0.001 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 377 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 PHE cc_start: 0.8707 (m-10) cc_final: 0.8269 (m-80) REVERT: A 146 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7623 (mp0) REVERT: A 147 MET cc_start: 0.8447 (ptp) cc_final: 0.8195 (ptt) REVERT: A 211 ASP cc_start: 0.8161 (t0) cc_final: 0.7945 (t0) REVERT: A 215 HIS cc_start: 0.8117 (m-70) cc_final: 0.7588 (m90) REVERT: A 217 ASN cc_start: 0.9221 (m-40) cc_final: 0.8955 (m110) REVERT: B 13 PHE cc_start: 0.8648 (m-10) cc_final: 0.8179 (m-80) REVERT: B 146 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7652 (mp0) REVERT: B 211 ASP cc_start: 0.8173 (t0) cc_final: 0.7937 (t0) REVERT: B 217 ASN cc_start: 0.9219 (m-40) cc_final: 0.8888 (m-40) REVERT: B 227 TRP cc_start: 0.8554 (m100) cc_final: 0.8313 (m100) REVERT: B 235 ILE cc_start: 0.9282 (mt) cc_final: 0.9052 (mt) REVERT: C 13 PHE cc_start: 0.8630 (m-10) cc_final: 0.8138 (m-80) REVERT: C 143 HIS cc_start: 0.7095 (t70) cc_final: 0.6689 (t-90) REVERT: C 146 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7613 (mp0) REVERT: C 211 ASP cc_start: 0.8080 (t0) cc_final: 0.7872 (t0) REVERT: C 217 ASN cc_start: 0.9158 (m-40) cc_final: 0.8836 (m-40) REVERT: C 227 TRP cc_start: 0.8446 (m100) cc_final: 0.8241 (m-10) REVERT: C 235 ILE cc_start: 0.9292 (mt) cc_final: 0.9010 (mt) REVERT: C 242 PHE cc_start: 0.8377 (t80) cc_final: 0.7865 (m-80) REVERT: D 13 PHE cc_start: 0.8523 (m-10) cc_final: 0.8010 (m-80) REVERT: D 146 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7523 (mp0) REVERT: D 149 ASP cc_start: 0.7346 (t70) cc_final: 0.7142 (t0) REVERT: D 217 ASN cc_start: 0.9131 (m-40) cc_final: 0.8868 (m-40) REVERT: D 229 TYR cc_start: 0.9124 (t80) cc_final: 0.8709 (t80) REVERT: D 235 ILE cc_start: 0.9312 (mt) cc_final: 0.9037 (mt) REVERT: D 238 MET cc_start: 0.8067 (mtp) cc_final: 0.7832 (mtp) REVERT: D 242 PHE cc_start: 0.8396 (t80) cc_final: 0.7896 (m-80) outliers start: 4 outliers final: 4 residues processed: 381 average time/residue: 0.1933 time to fit residues: 98.7544 Evaluate side-chains 224 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 220 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain D residue 194 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 HIS C 3 ASN C 34 GLN C 129 ASN D 34 GLN D 215 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8216 Z= 0.169 Angle : 0.523 12.008 11068 Z= 0.270 Chirality : 0.034 0.120 1220 Planarity : 0.005 0.025 1288 Dihedral : 16.600 87.352 1388 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.70 % Allowed : 15.56 % Favored : 80.74 % 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: 4.55 (0.26), residues: 932 helix: 3.65 (0.16), residues: 780 sheet: None (None), residues: 0 loop : -0.92 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 193 HIS 0.007 0.001 HIS B 215 PHE 0.022 0.001 PHE B 4 TYR 0.006 0.000 TYR D 229 ARG 0.006 0.001 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 233 time to evaluate : 0.871 Fit side-chains REVERT: A 50 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8413 (mm-30) REVERT: A 124 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7898 (mmmt) REVERT: A 146 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7357 (mp0) REVERT: A 147 MET cc_start: 0.8453 (ptp) cc_final: 0.8110 (ptt) REVERT: A 170 GLU cc_start: 0.8850 (tt0) cc_final: 0.8464 (tt0) REVERT: A 211 ASP cc_start: 0.8225 (t0) cc_final: 0.7879 (t0) REVERT: A 227 TRP cc_start: 0.8751 (m100) cc_final: 0.8453 (m100) REVERT: A 229 TYR cc_start: 0.9165 (t80) cc_final: 0.8955 (t80) REVERT: B 50 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8499 (mm-30) REVERT: B 124 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7735 (mmmt) REVERT: B 146 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7331 (mp0) REVERT: B 170 GLU cc_start: 0.8798 (tt0) cc_final: 0.8420 (tt0) REVERT: B 211 ASP cc_start: 0.8291 (t0) cc_final: 0.7848 (t0) REVERT: B 214 ASP cc_start: 0.7251 (t0) cc_final: 0.6449 (t0) REVERT: B 217 ASN cc_start: 0.9181 (m-40) cc_final: 0.8794 (m-40) REVERT: B 227 TRP cc_start: 0.8604 (m100) cc_final: 0.8363 (m100) REVERT: C 5 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8067 (ttm170) REVERT: C 53 GLU cc_start: 0.9077 (pt0) cc_final: 0.8651 (pt0) REVERT: C 124 LYS cc_start: 0.8344 (mmmt) cc_final: 0.7946 (mmmt) REVERT: C 146 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7339 (mp0) REVERT: C 170 GLU cc_start: 0.8851 (tt0) cc_final: 0.8400 (tt0) REVERT: C 211 ASP cc_start: 0.8235 (t0) cc_final: 0.7750 (t0) REVERT: C 217 ASN cc_start: 0.9182 (m-40) cc_final: 0.8804 (m-40) REVERT: C 227 TRP cc_start: 0.8519 (m100) cc_final: 0.8191 (m-10) REVERT: C 235 ILE cc_start: 0.9224 (mt) cc_final: 0.8954 (mt) REVERT: D 124 LYS cc_start: 0.8357 (mmmt) cc_final: 0.7987 (mmmt) REVERT: D 129 ASN cc_start: 0.9016 (t0) cc_final: 0.8800 (t0) REVERT: D 146 GLU cc_start: 0.7930 (mm-30) cc_final: 0.6959 (mp0) REVERT: D 170 GLU cc_start: 0.8854 (tt0) cc_final: 0.8422 (tt0) REVERT: D 217 ASN cc_start: 0.9080 (m-40) cc_final: 0.8793 (m-40) REVERT: D 227 TRP cc_start: 0.8786 (m100) cc_final: 0.8581 (m100) REVERT: D 235 ILE cc_start: 0.9315 (mt) cc_final: 0.9103 (mt) REVERT: D 242 PHE cc_start: 0.8304 (t80) cc_final: 0.7822 (m-80) outliers start: 29 outliers final: 20 residues processed: 251 average time/residue: 0.2115 time to fit residues: 69.6538 Evaluate side-chains 228 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 56 optimal weight: 0.1980 chunk 23 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8216 Z= 0.179 Angle : 0.495 7.571 11068 Z= 0.264 Chirality : 0.035 0.138 1220 Planarity : 0.004 0.029 1288 Dihedral : 16.066 89.619 1388 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.70 % Allowed : 18.24 % Favored : 78.06 % 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: 4.04 (0.27), residues: 932 helix: 3.43 (0.17), residues: 764 sheet: None (None), residues: 0 loop : -1.30 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 193 HIS 0.003 0.001 HIS A 215 PHE 0.015 0.001 PHE A 13 TYR 0.005 0.001 TYR C 229 ARG 0.005 0.001 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 220 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8560 (mm-30) REVERT: A 147 MET cc_start: 0.8370 (ptp) cc_final: 0.8127 (ptt) REVERT: A 170 GLU cc_start: 0.8857 (tt0) cc_final: 0.8617 (tt0) REVERT: A 227 TRP cc_start: 0.8706 (m100) cc_final: 0.8448 (m100) REVERT: A 229 TYR cc_start: 0.9143 (t80) cc_final: 0.8926 (t80) REVERT: B 48 ARG cc_start: 0.8800 (mmm-85) cc_final: 0.8383 (mtm110) REVERT: B 49 LEU cc_start: 0.9446 (mt) cc_final: 0.9211 (mt) REVERT: B 50 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8554 (mm-30) REVERT: B 170 GLU cc_start: 0.8806 (tt0) cc_final: 0.8584 (tt0) REVERT: B 213 MET cc_start: 0.7166 (mmm) cc_final: 0.6918 (mmm) REVERT: B 217 ASN cc_start: 0.9235 (m-40) cc_final: 0.8792 (m-40) REVERT: B 227 TRP cc_start: 0.8595 (m100) cc_final: 0.8338 (m-10) REVERT: C 50 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8501 (mm-30) REVERT: C 170 GLU cc_start: 0.8877 (tt0) cc_final: 0.8671 (tt0) REVERT: C 211 ASP cc_start: 0.8211 (t0) cc_final: 0.7718 (t0) REVERT: C 217 ASN cc_start: 0.9204 (m-40) cc_final: 0.8913 (m-40) REVERT: C 235 ILE cc_start: 0.9188 (mt) cc_final: 0.8922 (mt) REVERT: D 49 LEU cc_start: 0.9524 (mt) cc_final: 0.9233 (mt) REVERT: D 50 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8426 (mm-30) REVERT: D 124 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8134 (mmmt) REVERT: D 129 ASN cc_start: 0.8988 (t0) cc_final: 0.8748 (t0) REVERT: D 170 GLU cc_start: 0.8867 (tt0) cc_final: 0.8345 (tt0) REVERT: D 217 ASN cc_start: 0.9124 (m-40) cc_final: 0.8801 (m-40) REVERT: D 220 PHE cc_start: 0.8954 (t80) cc_final: 0.8589 (t80) REVERT: D 242 PHE cc_start: 0.8293 (t80) cc_final: 0.7749 (m-80) outliers start: 29 outliers final: 18 residues processed: 237 average time/residue: 0.2001 time to fit residues: 63.5036 Evaluate side-chains 222 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8216 Z= 0.250 Angle : 0.530 6.241 11068 Z= 0.284 Chirality : 0.035 0.140 1220 Planarity : 0.004 0.027 1288 Dihedral : 16.074 82.052 1388 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.85 % Allowed : 18.49 % Favored : 76.66 % 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: 3.81 (0.27), residues: 932 helix: 3.26 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -1.16 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 245 HIS 0.006 0.001 HIS A 215 PHE 0.023 0.001 PHE A 242 TYR 0.005 0.001 TYR D 29 ARG 0.007 0.001 ARG C 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9545 (mt) cc_final: 0.9333 (mt) REVERT: A 50 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8622 (mm-30) REVERT: A 124 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8329 (mmmt) REVERT: A 147 MET cc_start: 0.8284 (ptp) cc_final: 0.7725 (ptt) REVERT: A 170 GLU cc_start: 0.8934 (tt0) cc_final: 0.8696 (tt0) REVERT: A 213 MET cc_start: 0.8170 (mmm) cc_final: 0.7587 (mmm) REVERT: B 50 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8696 (mm-30) REVERT: B 96 PHE cc_start: 0.9351 (t80) cc_final: 0.9038 (t80) REVERT: B 124 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8235 (mmmt) REVERT: B 170 GLU cc_start: 0.8860 (tt0) cc_final: 0.8658 (tt0) REVERT: B 174 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8329 (mmt90) REVERT: B 215 HIS cc_start: 0.8551 (m-70) cc_final: 0.8093 (m-70) REVERT: B 217 ASN cc_start: 0.9251 (m-40) cc_final: 0.8834 (m-40) REVERT: B 227 TRP cc_start: 0.8734 (m100) cc_final: 0.8442 (m-10) REVERT: C 49 LEU cc_start: 0.9532 (mt) cc_final: 0.9324 (mt) REVERT: C 50 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8619 (mm-30) REVERT: C 96 PHE cc_start: 0.9279 (t80) cc_final: 0.8972 (t80) REVERT: C 124 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8291 (mmmt) REVERT: C 170 GLU cc_start: 0.8893 (tt0) cc_final: 0.8652 (tt0) REVERT: C 174 ARG cc_start: 0.8605 (mmm-85) cc_final: 0.8310 (mmt90) REVERT: C 217 ASN cc_start: 0.9241 (m-40) cc_final: 0.8892 (m-40) REVERT: C 235 ILE cc_start: 0.9203 (mt) cc_final: 0.8937 (mt) REVERT: D 49 LEU cc_start: 0.9593 (mt) cc_final: 0.9347 (mt) REVERT: D 50 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8549 (mm-30) REVERT: D 96 PHE cc_start: 0.9308 (t80) cc_final: 0.9009 (t80) REVERT: D 124 LYS cc_start: 0.8753 (mmmt) cc_final: 0.8161 (mmmt) REVERT: D 170 GLU cc_start: 0.8907 (tt0) cc_final: 0.8425 (tt0) REVERT: D 174 ARG cc_start: 0.8645 (mmm-85) cc_final: 0.8291 (mmt90) REVERT: D 217 ASN cc_start: 0.9199 (m-40) cc_final: 0.8904 (m-40) REVERT: D 242 PHE cc_start: 0.8317 (t80) cc_final: 0.7759 (m-80) outliers start: 38 outliers final: 21 residues processed: 221 average time/residue: 0.2026 time to fit residues: 59.5184 Evaluate side-chains 217 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 143 HIS Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS B 143 HIS C 3 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS D 215 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8216 Z= 0.218 Angle : 0.518 6.578 11068 Z= 0.275 Chirality : 0.035 0.127 1220 Planarity : 0.004 0.026 1288 Dihedral : 15.516 76.438 1388 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.21 % Allowed : 18.88 % Favored : 76.91 % 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: 3.69 (0.27), residues: 932 helix: 3.20 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -1.28 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 193 HIS 0.008 0.001 HIS B 143 PHE 0.032 0.001 PHE D 13 TYR 0.005 0.001 TYR C 229 ARG 0.005 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 203 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8722 (mm-30) REVERT: A 124 LYS cc_start: 0.8666 (mmmt) cc_final: 0.8274 (mmmt) REVERT: A 147 MET cc_start: 0.8262 (ptp) cc_final: 0.7865 (ptt) REVERT: A 170 GLU cc_start: 0.8892 (tt0) cc_final: 0.8589 (tt0) REVERT: A 213 MET cc_start: 0.8333 (mmm) cc_final: 0.8116 (mmm) REVERT: A 229 TYR cc_start: 0.9152 (t80) cc_final: 0.8850 (t80) REVERT: B 50 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8724 (mm-30) REVERT: B 96 PHE cc_start: 0.9303 (t80) cc_final: 0.9042 (t80) REVERT: B 124 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8231 (mmmt) REVERT: B 170 GLU cc_start: 0.8882 (tt0) cc_final: 0.8579 (tt0) REVERT: B 174 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8330 (mmt90) REVERT: B 215 HIS cc_start: 0.8397 (m-70) cc_final: 0.7968 (m-70) REVERT: C 50 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8613 (mm-30) REVERT: C 96 PHE cc_start: 0.9289 (t80) cc_final: 0.9042 (t80) REVERT: C 124 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8215 (mmmt) REVERT: C 170 GLU cc_start: 0.8886 (tt0) cc_final: 0.8557 (tt0) REVERT: C 174 ARG cc_start: 0.8616 (mmm-85) cc_final: 0.8302 (mmt90) REVERT: C 215 HIS cc_start: 0.8478 (m-70) cc_final: 0.8223 (m-70) REVERT: C 216 GLU cc_start: 0.8626 (mp0) cc_final: 0.8351 (pm20) REVERT: C 217 ASN cc_start: 0.9232 (m-40) cc_final: 0.8812 (m-40) REVERT: C 235 ILE cc_start: 0.9196 (mt) cc_final: 0.8924 (mt) REVERT: D 49 LEU cc_start: 0.9597 (mt) cc_final: 0.9361 (mt) REVERT: D 50 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8669 (mm-30) REVERT: D 96 PHE cc_start: 0.9312 (t80) cc_final: 0.9070 (t80) REVERT: D 146 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8057 (mp0) REVERT: D 174 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8301 (mmt90) REVERT: D 216 GLU cc_start: 0.8484 (mp0) cc_final: 0.8219 (pm20) REVERT: D 217 ASN cc_start: 0.9194 (m-40) cc_final: 0.8809 (m-40) REVERT: D 242 PHE cc_start: 0.8345 (t80) cc_final: 0.7791 (m-80) outliers start: 33 outliers final: 22 residues processed: 222 average time/residue: 0.1955 time to fit residues: 58.4238 Evaluate side-chains 220 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 198 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 0.0770 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN D 3 ASN D 129 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8216 Z= 0.169 Angle : 0.510 9.229 11068 Z= 0.269 Chirality : 0.035 0.148 1220 Planarity : 0.004 0.037 1288 Dihedral : 14.735 73.067 1388 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.70 % Allowed : 19.64 % Favored : 76.66 % 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: 3.73 (0.27), residues: 932 helix: 3.24 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -1.36 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 193 HIS 0.009 0.001 HIS D 143 PHE 0.036 0.001 PHE D 13 TYR 0.005 0.000 TYR D 229 ARG 0.004 0.001 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 207 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.9528 (mt) cc_final: 0.9266 (mp) REVERT: A 50 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8620 (mm-30) REVERT: A 124 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8256 (mmmt) REVERT: A 147 MET cc_start: 0.8224 (ptp) cc_final: 0.7465 (ptt) REVERT: A 170 GLU cc_start: 0.8833 (tt0) cc_final: 0.8538 (tt0) REVERT: A 213 MET cc_start: 0.8329 (mmm) cc_final: 0.7720 (mmm) REVERT: B 50 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8675 (mm-30) REVERT: B 124 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8176 (mmmt) REVERT: B 170 GLU cc_start: 0.8811 (tt0) cc_final: 0.8511 (tt0) REVERT: B 174 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8248 (mmt90) REVERT: B 215 HIS cc_start: 0.8471 (m-70) cc_final: 0.8144 (m-70) REVERT: B 216 GLU cc_start: 0.8575 (mp0) cc_final: 0.8302 (pm20) REVERT: B 227 TRP cc_start: 0.8750 (m100) cc_final: 0.8460 (m-10) REVERT: C 50 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8558 (mm-30) REVERT: C 124 LYS cc_start: 0.8624 (mmmt) cc_final: 0.8198 (mmmt) REVERT: C 170 GLU cc_start: 0.8809 (tt0) cc_final: 0.8477 (tt0) REVERT: C 174 ARG cc_start: 0.8577 (mmm-85) cc_final: 0.8255 (mmt90) REVERT: C 215 HIS cc_start: 0.8480 (m-70) cc_final: 0.8132 (m-70) REVERT: C 216 GLU cc_start: 0.8496 (mp0) cc_final: 0.8215 (pm20) REVERT: C 217 ASN cc_start: 0.9191 (m-40) cc_final: 0.8843 (m-40) REVERT: C 229 TYR cc_start: 0.9073 (t80) cc_final: 0.8779 (t80) REVERT: C 235 ILE cc_start: 0.9151 (mt) cc_final: 0.8872 (mt) REVERT: D 49 LEU cc_start: 0.9586 (mt) cc_final: 0.9359 (mt) REVERT: D 50 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8628 (mm-30) REVERT: D 96 PHE cc_start: 0.9304 (t80) cc_final: 0.9078 (t80) REVERT: D 124 LYS cc_start: 0.8585 (mmmt) cc_final: 0.8327 (mmmt) REVERT: D 146 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8184 (mp0) REVERT: D 174 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8244 (mmt90) REVERT: D 216 GLU cc_start: 0.8486 (mp0) cc_final: 0.8211 (pm20) REVERT: D 217 ASN cc_start: 0.9156 (m-40) cc_final: 0.8816 (m-40) REVERT: D 242 PHE cc_start: 0.8306 (t80) cc_final: 0.7737 (m-80) outliers start: 29 outliers final: 21 residues processed: 224 average time/residue: 0.2015 time to fit residues: 60.6439 Evaluate side-chains 218 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 197 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 88 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 ASN D 129 ASN D 215 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8216 Z= 0.361 Angle : 0.602 7.127 11068 Z= 0.322 Chirality : 0.038 0.149 1220 Planarity : 0.004 0.022 1288 Dihedral : 15.580 80.263 1388 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.46 % Allowed : 22.58 % Favored : 72.96 % 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: 3.29 (0.27), residues: 932 helix: 2.90 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -1.33 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 227 HIS 0.008 0.001 HIS D 143 PHE 0.032 0.002 PHE D 13 TYR 0.006 0.001 TYR D 29 ARG 0.005 0.001 ARG C 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 186 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8770 (mm-30) REVERT: A 124 LYS cc_start: 0.8772 (mmmt) cc_final: 0.8461 (mmmt) REVERT: A 147 MET cc_start: 0.8391 (ptp) cc_final: 0.8163 (ptt) REVERT: B 50 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8775 (mm-30) REVERT: B 174 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.8267 (mmt90) REVERT: B 215 HIS cc_start: 0.8273 (m-70) cc_final: 0.7913 (m-70) REVERT: C 50 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8648 (mm-30) REVERT: C 124 LYS cc_start: 0.8806 (mmmt) cc_final: 0.8474 (mmmt) REVERT: C 174 ARG cc_start: 0.8608 (mmm-85) cc_final: 0.8285 (mmt90) REVERT: C 216 GLU cc_start: 0.8580 (mp0) cc_final: 0.8268 (pm20) REVERT: C 217 ASN cc_start: 0.9247 (m-40) cc_final: 0.8839 (m-40) REVERT: C 235 ILE cc_start: 0.9234 (mt) cc_final: 0.8976 (mt) REVERT: D 49 LEU cc_start: 0.9650 (mt) cc_final: 0.9444 (mt) REVERT: D 50 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8790 (mm-30) REVERT: D 146 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8078 (mp0) REVERT: D 174 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8272 (mmt90) REVERT: D 217 ASN cc_start: 0.9201 (m-40) cc_final: 0.8876 (m-40) REVERT: D 242 PHE cc_start: 0.8299 (t80) cc_final: 0.7813 (m-80) outliers start: 35 outliers final: 26 residues processed: 207 average time/residue: 0.2118 time to fit residues: 58.2945 Evaluate side-chains 210 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 184 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 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 215 HIS B 215 HIS C 3 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 ASN D 215 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8216 Z= 0.184 Angle : 0.563 7.935 11068 Z= 0.290 Chirality : 0.037 0.152 1220 Planarity : 0.004 0.023 1288 Dihedral : 13.932 72.660 1388 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.95 % Allowed : 23.34 % Favored : 72.70 % 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: 3.57 (0.27), residues: 932 helix: 3.19 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -1.24 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 227 HIS 0.008 0.001 HIS D 143 PHE 0.022 0.001 PHE B 13 TYR 0.005 0.000 TYR D 229 ARG 0.004 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8702 (mm-30) REVERT: A 124 LYS cc_start: 0.8478 (mmmt) cc_final: 0.8147 (mmmt) REVERT: A 147 MET cc_start: 0.8218 (ptp) cc_final: 0.7668 (ptt) REVERT: A 213 MET cc_start: 0.8368 (mmm) cc_final: 0.8110 (mmm) REVERT: B 50 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8602 (mm-30) REVERT: B 124 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8329 (mmmt) REVERT: B 129 ASN cc_start: 0.9014 (t0) cc_final: 0.8723 (t0) REVERT: B 217 ASN cc_start: 0.9166 (m-40) cc_final: 0.8632 (m-40) REVERT: C 50 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8570 (mm-30) REVERT: C 124 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8301 (mmmt) REVERT: C 174 ARG cc_start: 0.8590 (mmm-85) cc_final: 0.8211 (mmt90) REVERT: C 216 GLU cc_start: 0.8446 (mp0) cc_final: 0.8157 (pm20) REVERT: C 217 ASN cc_start: 0.9159 (m-40) cc_final: 0.8760 (m-40) REVERT: C 224 CYS cc_start: 0.8203 (t) cc_final: 0.7883 (t) REVERT: C 229 TYR cc_start: 0.9185 (t80) cc_final: 0.8800 (t80) REVERT: C 235 ILE cc_start: 0.9169 (mt) cc_final: 0.8891 (mt) REVERT: D 49 LEU cc_start: 0.9617 (mt) cc_final: 0.9413 (mt) REVERT: D 50 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8723 (mm-30) REVERT: D 174 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8288 (mmt90) REVERT: D 216 GLU cc_start: 0.8483 (mp0) cc_final: 0.8078 (pm20) REVERT: D 217 ASN cc_start: 0.9154 (m-40) cc_final: 0.8827 (m-40) REVERT: D 242 PHE cc_start: 0.8300 (t80) cc_final: 0.7740 (m-80) outliers start: 31 outliers final: 21 residues processed: 218 average time/residue: 0.1927 time to fit residues: 56.4592 Evaluate side-chains 211 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 190 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8216 Z= 0.385 Angle : 0.675 7.518 11068 Z= 0.354 Chirality : 0.039 0.146 1220 Planarity : 0.004 0.023 1288 Dihedral : 14.563 72.213 1388 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.08 % Allowed : 23.98 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.27), residues: 932 helix: 2.71 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -1.31 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 227 HIS 0.008 0.001 HIS D 143 PHE 0.032 0.002 PHE D 96 TYR 0.006 0.001 TYR A 29 ARG 0.004 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8776 (mm-30) REVERT: A 124 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8380 (mmmt) REVERT: A 147 MET cc_start: 0.8429 (ptp) cc_final: 0.7880 (ptt) REVERT: A 213 MET cc_start: 0.8304 (mmm) cc_final: 0.8074 (mmm) REVERT: B 50 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8778 (mm-30) REVERT: B 124 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8370 (mmmt) REVERT: B 217 ASN cc_start: 0.9211 (m-40) cc_final: 0.8934 (m-40) REVERT: C 50 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8790 (mm-30) REVERT: C 124 LYS cc_start: 0.8806 (mmmt) cc_final: 0.8590 (mmmt) REVERT: C 217 ASN cc_start: 0.9213 (m-40) cc_final: 0.8943 (m110) REVERT: C 235 ILE cc_start: 0.9243 (mt) cc_final: 0.8986 (mt) REVERT: D 50 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8779 (mm-30) REVERT: D 65 MET cc_start: 0.8248 (tpt) cc_final: 0.8041 (tpp) REVERT: D 174 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8263 (mmt90) REVERT: D 216 GLU cc_start: 0.8605 (mp0) cc_final: 0.8200 (pm20) REVERT: D 217 ASN cc_start: 0.9224 (m-40) cc_final: 0.8860 (m-40) REVERT: D 242 PHE cc_start: 0.8298 (t80) cc_final: 0.7802 (m-80) outliers start: 32 outliers final: 23 residues processed: 197 average time/residue: 0.2125 time to fit residues: 56.1139 Evaluate side-chains 200 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 56 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 HIS C 3 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8216 Z= 0.190 Angle : 0.619 10.999 11068 Z= 0.318 Chirality : 0.037 0.157 1220 Planarity : 0.004 0.024 1288 Dihedral : 13.578 65.846 1388 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.04 % Allowed : 26.28 % Favored : 71.68 % 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 (0.28), residues: 932 helix: 3.12 (0.18), residues: 740 sheet: None (None), residues: 0 loop : -1.18 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.010 0.001 HIS C 143 PHE 0.023 0.001 PHE D 96 TYR 0.004 0.000 TYR C 139 ARG 0.005 0.001 ARG A 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 PHE cc_start: 0.8117 (m-80) cc_final: 0.7915 (m-80) REVERT: A 50 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8740 (mm-30) REVERT: A 124 LYS cc_start: 0.8554 (mmmt) cc_final: 0.8220 (mmmt) REVERT: A 147 MET cc_start: 0.8278 (ptp) cc_final: 0.7758 (ptt) REVERT: A 213 MET cc_start: 0.8448 (mmm) cc_final: 0.8196 (mmm) REVERT: B 50 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8721 (mm-30) REVERT: B 129 ASN cc_start: 0.9049 (t0) cc_final: 0.8757 (t0) REVERT: C 50 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8688 (mm-30) REVERT: C 124 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8366 (mmmt) REVERT: C 217 ASN cc_start: 0.9154 (m-40) cc_final: 0.8902 (m110) REVERT: C 229 TYR cc_start: 0.9208 (t80) cc_final: 0.8833 (t80) REVERT: C 235 ILE cc_start: 0.9170 (mt) cc_final: 0.8886 (mt) REVERT: D 50 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8721 (mm-30) REVERT: D 174 ARG cc_start: 0.8636 (mmm-85) cc_final: 0.8299 (mmt90) REVERT: D 216 GLU cc_start: 0.8478 (mp0) cc_final: 0.8090 (pm20) REVERT: D 217 ASN cc_start: 0.9154 (m-40) cc_final: 0.8845 (m-40) REVERT: D 242 PHE cc_start: 0.8303 (t80) cc_final: 0.7737 (m-80) outliers start: 16 outliers final: 16 residues processed: 205 average time/residue: 0.2048 time to fit residues: 55.9438 Evaluate side-chains 204 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 HIS ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 HIS D 3 ASN ** D 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.114518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.083639 restraints weight = 17070.121| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.61 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8216 Z= 0.246 Angle : 0.627 8.369 11068 Z= 0.324 Chirality : 0.037 0.155 1220 Planarity : 0.004 0.025 1288 Dihedral : 13.681 65.475 1388 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.93 % Allowed : 25.77 % Favored : 71.30 % 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: 3.31 (0.27), residues: 932 helix: 2.90 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -1.23 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 227 HIS 0.009 0.001 HIS D 143 PHE 0.043 0.001 PHE D 96 TYR 0.005 0.001 TYR D 99 ARG 0.004 0.001 ARG B 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1847.94 seconds wall clock time: 34 minutes 29.24 seconds (2069.24 seconds total)