Starting phenix.real_space_refine on Sat Mar 16 09:15:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnf_7971/03_2024/6dnf_7971_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnf_7971/03_2024/6dnf_7971.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/6dnf_7971/03_2024/6dnf_7971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnf_7971/03_2024/6dnf_7971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnf_7971/03_2024/6dnf_7971_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dnf_7971/03_2024/6dnf_7971_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.456 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 4 5.49 5 S 20 5.16 5 C 4692 2.51 5 N 1224 2.21 5 O 1308 1.98 5 H 6868 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 14119 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3487 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3487 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3487 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3487 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' CA': 2, 'DGG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'DGG:plan-1': 1, 'DGG:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' CA': 1, 'DGG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'DGG:plan-1': 1, 'DGG:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'DGG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'DGG:plan-1': 1, 'DGG:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'DGG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'DGG:plan-1': 1, 'DGG:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 6.40, per 1000 atoms: 0.45 Number of scatterers: 14119 At special positions: 0 Unit cell: (80.073, 83.517, 139.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 20 16.00 P 4 15.00 O 1308 8.00 N 1224 7.00 C 4692 6.00 H 6868 1.00 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: 10.47 Conformation dependent library (CDL) restraints added in 1.5 seconds 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 8 sheets defined 56.2% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 167 through 218 removed outlier: 3.984A pdb=" N LYS A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 250 Proline residue: A 229 - end of helix Processing helix chain 'A' and resid 278 through 302 removed outlier: 3.512A pdb=" N ALA A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 128 through 136 removed outlier: 4.937A pdb=" N ARG B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 168 through 218 removed outlier: 3.840A pdb=" N GLY B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 250 Proline residue: B 229 - end of helix Processing helix chain 'B' and resid 278 through 302 Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 132 through 138 Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 167 through 218 removed outlier: 3.984A pdb=" N LYS C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C 180 " --> pdb=" O LYS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 250 Proline residue: C 229 - end of helix Processing helix chain 'C' and resid 278 through 302 removed outlier: 3.512A pdb=" N ALA C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 128 through 136 removed outlier: 4.937A pdb=" N ARG D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 168 through 218 removed outlier: 3.840A pdb=" N GLY D 205 " --> pdb=" O ALA D 201 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 206 " --> pdb=" O GLY D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 250 Proline residue: D 229 - end of helix Processing helix chain 'D' and resid 278 through 302 Processing sheet with id= A, first strand: chain 'A' and resid 11 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 112 through 115 Processing sheet with id= C, first strand: chain 'B' and resid 11 through 13 Processing sheet with id= D, first strand: chain 'B' and resid 113 through 115 Processing sheet with id= E, first strand: chain 'C' and resid 11 through 13 Processing sheet with id= F, first strand: chain 'C' and resid 112 through 115 Processing sheet with id= G, first strand: chain 'D' and resid 11 through 13 Processing sheet with id= H, first strand: chain 'D' and resid 113 through 115 448 hydrogen bonds defined for protein. 1278 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: 4.46 Time building geometry restraints manager: 10.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 6860 1.02 - 1.22: 12 1.22 - 1.41: 3104 1.41 - 1.61: 4264 1.61 - 1.81: 36 Bond restraints: 14276 Sorted by residual: bond pdb=" C1 DGG C 502 " pdb=" O17 DGG C 502 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C1 DGG A 401 " pdb=" O17 DGG A 401 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C21 DGG A 401 " pdb=" O19 DGG A 401 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C21 DGG C 502 " pdb=" O19 DGG C 502 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C21 DGG B 403 " pdb=" O19 DGG B 403 " ideal model delta sigma weight residual 1.331 1.406 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 14271 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.25: 234 106.25 - 113.19: 16259 113.19 - 120.13: 4375 120.13 - 127.08: 4605 127.08 - 134.02: 123 Bond angle restraints: 25596 Sorted by residual: angle pdb=" OP1 DGG D 502 " pdb=" P DGG D 502 " pdb=" OP3 DGG D 502 " ideal model delta sigma weight residual 123.21 100.67 22.54 3.00e+00 1.11e-01 5.64e+01 angle pdb=" OP1 DGG B 403 " pdb=" P DGG B 403 " pdb=" OP3 DGG B 403 " ideal model delta sigma weight residual 123.21 100.67 22.54 3.00e+00 1.11e-01 5.64e+01 angle pdb=" N ASP A 221 " pdb=" CA ASP A 221 " pdb=" C ASP A 221 " ideal model delta sigma weight residual 113.17 107.71 5.46 1.26e+00 6.30e-01 1.88e+01 angle pdb=" N ASP C 221 " pdb=" CA ASP C 221 " pdb=" C ASP C 221 " ideal model delta sigma weight residual 113.17 107.73 5.44 1.26e+00 6.30e-01 1.87e+01 angle pdb=" N LEU C 166 " pdb=" CA LEU C 166 " pdb=" C LEU C 166 " ideal model delta sigma weight residual 112.72 108.01 4.71 1.28e+00 6.10e-01 1.35e+01 ... (remaining 25591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.30: 6119 15.30 - 30.60: 444 30.60 - 45.90: 92 45.90 - 61.20: 115 61.20 - 76.50: 6 Dihedral angle restraints: 6776 sinusoidal: 3652 harmonic: 3124 Sorted by residual: dihedral pdb=" CA GLY C 117 " pdb=" C GLY C 117 " pdb=" N GLU C 118 " pdb=" CA GLU C 118 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLY A 117 " pdb=" C GLY A 117 " pdb=" N GLU A 118 " pdb=" CA GLU A 118 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA GLU D 118 " pdb=" C GLU D 118 " pdb=" N PHE D 119 " pdb=" CA PHE D 119 " ideal model delta harmonic sigma weight residual -180.00 -153.87 -26.13 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 6773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 668 0.032 - 0.063: 249 0.063 - 0.095: 111 0.095 - 0.127: 45 0.127 - 0.158: 11 Chirality restraints: 1084 Sorted by residual: chirality pdb=" CA ASP B 305 " pdb=" N ASP B 305 " pdb=" C ASP B 305 " pdb=" CB ASP B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA ASP D 305 " pdb=" N ASP D 305 " pdb=" C ASP D 305 " pdb=" CB ASP D 305 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA ASP A 305 " pdb=" N ASP A 305 " pdb=" C ASP A 305 " pdb=" CB ASP A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 1081 not shown) Planarity restraints: 2096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 249 " -0.012 2.00e-02 2.50e+03 2.29e-02 5.27e+00 pdb=" N ASN B 250 " 0.039 2.00e-02 2.50e+03 pdb=" CA ASN B 250 " -0.010 2.00e-02 2.50e+03 pdb=" H ASN B 250 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 156 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO C 157 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 157 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 157 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 156 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO A 157 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " -0.030 5.00e-02 4.00e+02 ... (remaining 2093 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 1342 2.26 - 2.84: 30694 2.84 - 3.43: 31942 3.43 - 4.01: 41042 4.01 - 4.60: 65171 Nonbonded interactions: 170191 Sorted by model distance: nonbonded pdb=" O ALA C 299 " pdb=" H ASP C 303 " model vdw 1.669 1.850 nonbonded pdb=" O ALA A 299 " pdb=" H ASP A 303 " model vdw 1.669 1.850 nonbonded pdb=" O ALA D 299 " pdb=" H ASP D 303 " model vdw 1.707 1.850 nonbonded pdb=" O ALA B 299 " pdb=" H ASP B 303 " model vdw 1.707 1.850 nonbonded pdb=" O ILE A 128 " pdb=" H PHE A 131 " model vdw 1.735 1.850 ... (remaining 170186 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 8 through 309) selection = (chain 'B' and resid 8 through 309) selection = (chain 'C' and resid 8 through 309) selection = (chain 'D' and resid 8 through 309) } 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: 3.740 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: 0.210 Extract box with map and model: 12.980 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 45.060 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 0.124 7408 Z= 0.561 Angle : 1.057 22.538 10016 Z= 0.532 Chirality : 0.044 0.158 1084 Planarity : 0.007 0.054 1252 Dihedral : 9.994 76.501 2732 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.26), residues: 868 helix: 0.56 (0.20), residues: 528 sheet: -1.83 (0.41), residues: 114 loop : -3.44 (0.36), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 122 HIS 0.004 0.001 HIS A 40 PHE 0.024 0.003 PHE A 141 TYR 0.019 0.002 TYR C 165 ARG 0.006 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 CYS cc_start: 0.8861 (m) cc_final: 0.8481 (m) REVERT: A 279 GLN cc_start: 0.8181 (mt0) cc_final: 0.7640 (tm-30) REVERT: B 15 LYS cc_start: 0.6910 (tttp) cc_final: 0.6312 (mttp) REVERT: B 210 TRP cc_start: 0.8849 (t60) cc_final: 0.8372 (t60) REVERT: B 221 ASP cc_start: 0.8231 (m-30) cc_final: 0.7638 (t0) REVERT: B 287 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8094 (tm-30) REVERT: C 187 CYS cc_start: 0.8857 (m) cc_final: 0.8478 (m) REVERT: C 248 TRP cc_start: 0.8240 (t-100) cc_final: 0.7901 (t-100) REVERT: C 279 GLN cc_start: 0.8174 (mt0) cc_final: 0.7637 (tm-30) REVERT: D 15 LYS cc_start: 0.6902 (tttp) cc_final: 0.6306 (mttp) REVERT: D 210 TRP cc_start: 0.8847 (t60) cc_final: 0.8376 (t60) REVERT: D 221 ASP cc_start: 0.8214 (m-30) cc_final: 0.7627 (t0) REVERT: D 287 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8095 (tm-30) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.4361 time to fit residues: 138.9429 Evaluate side-chains 133 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS B 289 ASN C 192 HIS D 289 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7408 Z= 0.206 Angle : 0.566 4.571 10016 Z= 0.304 Chirality : 0.036 0.146 1084 Planarity : 0.005 0.043 1252 Dihedral : 7.644 66.629 1136 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.84 % Allowed : 5.23 % Favored : 92.94 % 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: 1.00 (0.30), residues: 868 helix: 2.47 (0.22), residues: 532 sheet: -1.40 (0.44), residues: 114 loop : -2.90 (0.37), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 281 HIS 0.003 0.001 HIS A 40 PHE 0.014 0.001 PHE A 141 TYR 0.013 0.001 TYR D 284 ARG 0.005 0.001 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 CYS cc_start: 0.8898 (m) cc_final: 0.8504 (m) REVERT: A 279 GLN cc_start: 0.8194 (mt0) cc_final: 0.7690 (tm-30) REVERT: B 15 LYS cc_start: 0.7436 (tttp) cc_final: 0.6761 (mttp) REVERT: B 189 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7600 (mptt) REVERT: B 210 TRP cc_start: 0.8844 (t60) cc_final: 0.8154 (t60) REVERT: B 221 ASP cc_start: 0.8242 (m-30) cc_final: 0.7660 (t0) REVERT: C 187 CYS cc_start: 0.8893 (m) cc_final: 0.8498 (m) REVERT: C 248 TRP cc_start: 0.8311 (t-100) cc_final: 0.7948 (t-100) REVERT: C 279 GLN cc_start: 0.8189 (mt0) cc_final: 0.7687 (tm-30) REVERT: D 15 LYS cc_start: 0.7436 (tttp) cc_final: 0.6760 (mttp) REVERT: D 189 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7600 (mptt) REVERT: D 210 TRP cc_start: 0.8845 (t60) cc_final: 0.8196 (t60) REVERT: D 221 ASP cc_start: 0.8200 (m-30) cc_final: 0.7604 (t0) outliers start: 13 outliers final: 9 residues processed: 161 average time/residue: 0.3482 time to fit residues: 76.7660 Evaluate side-chains 144 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN D 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7408 Z= 0.337 Angle : 0.617 5.129 10016 Z= 0.341 Chirality : 0.037 0.152 1084 Planarity : 0.004 0.040 1252 Dihedral : 7.600 64.029 1136 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.54 % Allowed : 9.75 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.30), residues: 868 helix: 2.71 (0.22), residues: 532 sheet: -0.98 (0.48), residues: 114 loop : -2.44 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 248 HIS 0.005 0.001 HIS A 40 PHE 0.022 0.002 PHE C 141 TYR 0.011 0.001 TYR A 284 ARG 0.004 0.001 ARG C 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 CYS cc_start: 0.9038 (m) cc_final: 0.8664 (m) REVERT: A 279 GLN cc_start: 0.8255 (mt0) cc_final: 0.7793 (tm-30) REVERT: A 286 GLU cc_start: 0.8772 (tp30) cc_final: 0.8436 (tp30) REVERT: B 15 LYS cc_start: 0.7665 (tttp) cc_final: 0.7168 (mptt) REVERT: B 141 PHE cc_start: 0.7710 (t80) cc_final: 0.7394 (t80) REVERT: B 210 TRP cc_start: 0.8884 (t60) cc_final: 0.8296 (t60) REVERT: B 221 ASP cc_start: 0.8360 (m-30) cc_final: 0.7803 (t0) REVERT: B 227 MET cc_start: 0.9224 (mmm) cc_final: 0.8915 (mmm) REVERT: C 187 CYS cc_start: 0.9034 (m) cc_final: 0.8658 (m) REVERT: C 248 TRP cc_start: 0.8338 (t-100) cc_final: 0.8005 (t-100) REVERT: C 279 GLN cc_start: 0.8251 (mt0) cc_final: 0.7791 (tm-30) REVERT: C 286 GLU cc_start: 0.8785 (tp30) cc_final: 0.8449 (tp30) REVERT: D 15 LYS cc_start: 0.7664 (tttp) cc_final: 0.7167 (mptt) REVERT: D 141 PHE cc_start: 0.7720 (t80) cc_final: 0.7405 (t80) REVERT: D 210 TRP cc_start: 0.8881 (t60) cc_final: 0.8118 (t60) REVERT: D 221 ASP cc_start: 0.8344 (m-30) cc_final: 0.7774 (t0) REVERT: D 227 MET cc_start: 0.9226 (mmm) cc_final: 0.8877 (mmm) outliers start: 18 outliers final: 16 residues processed: 161 average time/residue: 0.4446 time to fit residues: 92.4063 Evaluate side-chains 139 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 245 TRP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7408 Z= 0.249 Angle : 0.542 4.621 10016 Z= 0.295 Chirality : 0.036 0.141 1084 Planarity : 0.005 0.078 1252 Dihedral : 7.268 54.890 1136 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.82 % Allowed : 10.88 % Favored : 86.30 % 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: 2.03 (0.31), residues: 868 helix: 3.04 (0.22), residues: 534 sheet: -0.67 (0.49), residues: 114 loop : -2.05 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 281 HIS 0.002 0.001 HIS B 25 PHE 0.018 0.002 PHE C 141 TYR 0.008 0.001 TYR B 284 ARG 0.007 0.001 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 CYS cc_start: 0.9019 (m) cc_final: 0.8627 (m) REVERT: A 279 GLN cc_start: 0.8184 (mt0) cc_final: 0.7703 (tm-30) REVERT: A 286 GLU cc_start: 0.8763 (tp30) cc_final: 0.8508 (tp30) REVERT: B 15 LYS cc_start: 0.7683 (tttp) cc_final: 0.7073 (mmtm) REVERT: B 210 TRP cc_start: 0.8893 (t60) cc_final: 0.8169 (t60) REVERT: B 221 ASP cc_start: 0.8467 (m-30) cc_final: 0.7864 (t70) REVERT: B 227 MET cc_start: 0.9212 (mmm) cc_final: 0.8837 (mmm) REVERT: C 187 CYS cc_start: 0.9015 (m) cc_final: 0.8621 (m) REVERT: C 279 GLN cc_start: 0.8178 (mt0) cc_final: 0.7700 (tm-30) REVERT: C 286 GLU cc_start: 0.8776 (tp30) cc_final: 0.8521 (tp30) REVERT: D 15 LYS cc_start: 0.7680 (tttp) cc_final: 0.7070 (mmtm) REVERT: D 134 ASP cc_start: 0.8612 (m-30) cc_final: 0.8241 (m-30) REVERT: D 210 TRP cc_start: 0.8872 (t60) cc_final: 0.8167 (t60) REVERT: D 221 ASP cc_start: 0.8439 (m-30) cc_final: 0.7832 (t0) REVERT: D 227 MET cc_start: 0.9214 (mmm) cc_final: 0.8824 (mmm) outliers start: 20 outliers final: 14 residues processed: 144 average time/residue: 0.3065 time to fit residues: 62.6770 Evaluate side-chains 140 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 245 TRP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7408 Z= 0.233 Angle : 0.515 4.515 10016 Z= 0.280 Chirality : 0.036 0.134 1084 Planarity : 0.004 0.039 1252 Dihedral : 7.116 51.070 1136 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.97 % Allowed : 12.29 % Favored : 84.75 % 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: 2.26 (0.30), residues: 868 helix: 3.19 (0.22), residues: 532 sheet: -0.44 (0.49), residues: 114 loop : -1.87 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 281 HIS 0.002 0.001 HIS C 40 PHE 0.016 0.001 PHE C 141 TYR 0.007 0.001 TYR C 165 ARG 0.002 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 CYS cc_start: 0.9002 (m) cc_final: 0.8582 (m) REVERT: A 279 GLN cc_start: 0.8183 (mt0) cc_final: 0.7680 (tm-30) REVERT: A 286 GLU cc_start: 0.8717 (tp30) cc_final: 0.8475 (tp30) REVERT: B 15 LYS cc_start: 0.7684 (tttp) cc_final: 0.7086 (mmtm) REVERT: B 134 ASP cc_start: 0.8927 (m-30) cc_final: 0.8721 (m-30) REVERT: B 141 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7402 (t80) REVERT: B 210 TRP cc_start: 0.8874 (t60) cc_final: 0.8106 (t60) REVERT: B 221 ASP cc_start: 0.8468 (m-30) cc_final: 0.7923 (t70) REVERT: B 227 MET cc_start: 0.9220 (mmm) cc_final: 0.8821 (mmm) REVERT: C 187 CYS cc_start: 0.8999 (m) cc_final: 0.8580 (m) REVERT: C 279 GLN cc_start: 0.8176 (mt0) cc_final: 0.7677 (tm-30) REVERT: C 286 GLU cc_start: 0.8731 (tp30) cc_final: 0.8487 (tp30) REVERT: D 15 LYS cc_start: 0.7681 (tttp) cc_final: 0.7083 (mmtm) REVERT: D 141 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7412 (t80) REVERT: D 210 TRP cc_start: 0.8877 (t60) cc_final: 0.8108 (t60) REVERT: D 221 ASP cc_start: 0.8444 (m-30) cc_final: 0.7874 (t70) outliers start: 21 outliers final: 15 residues processed: 140 average time/residue: 0.2787 time to fit residues: 57.7261 Evaluate side-chains 139 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 TRP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 245 TRP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7408 Z= 0.227 Angle : 0.504 4.696 10016 Z= 0.274 Chirality : 0.035 0.134 1084 Planarity : 0.004 0.039 1252 Dihedral : 6.957 49.674 1136 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.97 % Allowed : 13.28 % Favored : 83.76 % 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: 2.42 (0.30), residues: 868 helix: 3.35 (0.22), residues: 530 sheet: -0.31 (0.49), residues: 114 loop : -1.91 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 281 HIS 0.002 0.001 HIS A 40 PHE 0.015 0.001 PHE C 141 TYR 0.007 0.001 TYR C 284 ARG 0.003 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 CYS cc_start: 0.8992 (m) cc_final: 0.8571 (m) REVERT: A 279 GLN cc_start: 0.8197 (mt0) cc_final: 0.7701 (tm-30) REVERT: A 286 GLU cc_start: 0.8688 (tp30) cc_final: 0.8447 (tp30) REVERT: B 15 LYS cc_start: 0.7648 (tttp) cc_final: 0.7085 (mmtm) REVERT: B 141 PHE cc_start: 0.7681 (OUTLIER) cc_final: 0.7387 (t80) REVERT: B 221 ASP cc_start: 0.8498 (m-30) cc_final: 0.7979 (t70) REVERT: C 187 CYS cc_start: 0.8987 (m) cc_final: 0.8565 (m) REVERT: C 279 GLN cc_start: 0.8191 (mt0) cc_final: 0.7699 (tm-30) REVERT: C 286 GLU cc_start: 0.8698 (tp30) cc_final: 0.8457 (tp30) REVERT: D 15 LYS cc_start: 0.7649 (tttp) cc_final: 0.7084 (mmtm) REVERT: D 141 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7393 (t80) REVERT: D 221 ASP cc_start: 0.8484 (m-30) cc_final: 0.7941 (t70) outliers start: 21 outliers final: 13 residues processed: 137 average time/residue: 0.2999 time to fit residues: 58.8605 Evaluate side-chains 133 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7408 Z= 0.174 Angle : 0.476 4.155 10016 Z= 0.256 Chirality : 0.035 0.144 1084 Planarity : 0.004 0.036 1252 Dihedral : 6.716 48.820 1136 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.69 % Allowed : 15.25 % Favored : 83.05 % 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: 2.68 (0.30), residues: 868 helix: 3.56 (0.22), residues: 530 sheet: -0.33 (0.49), residues: 114 loop : -1.73 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 245 HIS 0.001 0.000 HIS C 249 PHE 0.012 0.001 PHE C 141 TYR 0.006 0.001 TYR D 302 ARG 0.004 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 CYS cc_start: 0.8970 (m) cc_final: 0.8547 (m) REVERT: A 279 GLN cc_start: 0.8152 (mt0) cc_final: 0.7675 (tm-30) REVERT: A 286 GLU cc_start: 0.8635 (tp30) cc_final: 0.8382 (tp30) REVERT: B 15 LYS cc_start: 0.7588 (tttp) cc_final: 0.6991 (mmtm) REVERT: B 141 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7284 (t80) REVERT: B 221 ASP cc_start: 0.8493 (m-30) cc_final: 0.8046 (t70) REVERT: C 187 CYS cc_start: 0.8966 (m) cc_final: 0.8541 (m) REVERT: C 279 GLN cc_start: 0.8146 (mt0) cc_final: 0.7673 (tm-30) REVERT: C 286 GLU cc_start: 0.8663 (tp30) cc_final: 0.8415 (tp30) REVERT: D 15 LYS cc_start: 0.7584 (tttp) cc_final: 0.6988 (mmtm) REVERT: D 141 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7289 (t80) REVERT: D 221 ASP cc_start: 0.8470 (m-30) cc_final: 0.7994 (t70) outliers start: 12 outliers final: 10 residues processed: 136 average time/residue: 0.2727 time to fit residues: 55.2351 Evaluate side-chains 132 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7408 Z= 0.188 Angle : 0.479 4.165 10016 Z= 0.258 Chirality : 0.035 0.139 1084 Planarity : 0.004 0.036 1252 Dihedral : 6.577 49.592 1136 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.98 % Allowed : 15.25 % Favored : 82.77 % 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: 2.87 (0.30), residues: 868 helix: 3.68 (0.22), residues: 530 sheet: -0.29 (0.48), residues: 114 loop : -1.58 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 245 HIS 0.003 0.001 HIS C 249 PHE 0.012 0.001 PHE C 141 TYR 0.006 0.001 TYR C 209 ARG 0.003 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 CYS cc_start: 0.8957 (m) cc_final: 0.8540 (m) REVERT: A 279 GLN cc_start: 0.8156 (mt0) cc_final: 0.7703 (tm-30) REVERT: A 286 GLU cc_start: 0.8633 (tp30) cc_final: 0.8382 (tp30) REVERT: B 15 LYS cc_start: 0.7616 (tttp) cc_final: 0.7032 (mmtm) REVERT: B 141 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7239 (t80) REVERT: B 221 ASP cc_start: 0.8570 (m-30) cc_final: 0.8064 (t70) REVERT: C 187 CYS cc_start: 0.8954 (m) cc_final: 0.8535 (m) REVERT: C 279 GLN cc_start: 0.8150 (mt0) cc_final: 0.7700 (tm-30) REVERT: C 286 GLU cc_start: 0.8644 (tp30) cc_final: 0.8394 (tp30) REVERT: D 15 LYS cc_start: 0.7613 (tttp) cc_final: 0.7029 (mmtm) REVERT: D 141 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7235 (t80) REVERT: D 221 ASP cc_start: 0.8555 (m-30) cc_final: 0.8015 (t70) outliers start: 14 outliers final: 9 residues processed: 137 average time/residue: 0.2723 time to fit residues: 55.2646 Evaluate side-chains 132 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 34 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7408 Z= 0.181 Angle : 0.473 4.103 10016 Z= 0.254 Chirality : 0.035 0.132 1084 Planarity : 0.004 0.036 1252 Dihedral : 6.460 49.604 1136 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.84 % Allowed : 15.11 % Favored : 83.05 % 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: 3.00 (0.30), residues: 868 helix: 3.77 (0.22), residues: 530 sheet: -0.17 (0.48), residues: 114 loop : -1.51 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 245 HIS 0.003 0.000 HIS C 249 PHE 0.011 0.001 PHE C 141 TYR 0.006 0.001 TYR A 209 ARG 0.002 0.000 ARG D 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 CYS cc_start: 0.8949 (m) cc_final: 0.8541 (m) REVERT: A 249 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7806 (t-90) REVERT: A 279 GLN cc_start: 0.8104 (mt0) cc_final: 0.7681 (tm-30) REVERT: A 286 GLU cc_start: 0.8629 (tp30) cc_final: 0.8374 (tp30) REVERT: B 15 LYS cc_start: 0.7602 (tttp) cc_final: 0.6990 (mmtm) REVERT: B 221 ASP cc_start: 0.8602 (m-30) cc_final: 0.8079 (t70) REVERT: C 187 CYS cc_start: 0.8946 (m) cc_final: 0.8538 (m) REVERT: C 279 GLN cc_start: 0.8099 (mt0) cc_final: 0.7680 (tm-30) REVERT: C 286 GLU cc_start: 0.8639 (tp30) cc_final: 0.8386 (tp30) REVERT: D 15 LYS cc_start: 0.7599 (tttp) cc_final: 0.6988 (mmtm) REVERT: D 141 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7193 (t80) REVERT: D 221 ASP cc_start: 0.8578 (m-30) cc_final: 0.8061 (t70) outliers start: 13 outliers final: 11 residues processed: 133 average time/residue: 0.2950 time to fit residues: 58.2786 Evaluate side-chains 135 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7408 Z= 0.260 Angle : 0.519 5.974 10016 Z= 0.280 Chirality : 0.036 0.133 1084 Planarity : 0.004 0.038 1252 Dihedral : 6.725 53.250 1136 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.40 % Allowed : 15.11 % Favored : 82.49 % 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: 2.85 (0.30), residues: 868 helix: 3.66 (0.22), residues: 528 sheet: -0.16 (0.48), residues: 114 loop : -1.62 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 248 HIS 0.003 0.001 HIS A 40 PHE 0.015 0.002 PHE C 141 TYR 0.007 0.001 TYR C 284 ARG 0.002 0.000 ARG A 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LYS 139 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 CYS cc_start: 0.8951 (m) cc_final: 0.8544 (m) REVERT: A 249 HIS cc_start: 0.8077 (OUTLIER) cc_final: 0.7783 (t-90) REVERT: A 279 GLN cc_start: 0.8131 (mt0) cc_final: 0.7714 (tm-30) REVERT: B 15 LYS cc_start: 0.7743 (tttp) cc_final: 0.7171 (mmtm) REVERT: B 141 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7432 (t80) REVERT: B 221 ASP cc_start: 0.8637 (m-30) cc_final: 0.8111 (t70) REVERT: C 187 CYS cc_start: 0.8949 (m) cc_final: 0.8540 (m) REVERT: C 279 GLN cc_start: 0.8128 (mt0) cc_final: 0.7714 (tm-30) REVERT: D 15 LYS cc_start: 0.7742 (tttp) cc_final: 0.7169 (mmtm) REVERT: D 141 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.7444 (t80) REVERT: D 221 ASP cc_start: 0.8624 (m-30) cc_final: 0.8102 (t70) outliers start: 17 outliers final: 13 residues processed: 137 average time/residue: 0.2727 time to fit residues: 54.8002 Evaluate side-chains 136 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 300 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4291 > 50: distance: 160 - 170: 28.441 distance: 170 - 171: 11.117 distance: 170 - 175: 58.373 distance: 171 - 172: 55.234 distance: 171 - 174: 3.821 distance: 171 - 176: 53.196 distance: 172 - 173: 39.521 distance: 172 - 177: 39.402 distance: 177 - 178: 56.355 distance: 177 - 181: 42.627 distance: 178 - 179: 56.171 distance: 178 - 182: 40.393 distance: 178 - 183: 39.475 distance: 179 - 184: 59.350 distance: 184 - 185: 24.119 distance: 184 - 193: 14.111 distance: 185 - 186: 41.216 distance: 185 - 188: 13.687 distance: 185 - 194: 56.338 distance: 186 - 199: 40.201 distance: 188 - 189: 48.113 distance: 188 - 195: 36.754 distance: 188 - 196: 32.111 distance: 189 - 190: 46.505 distance: 189 - 197: 44.867 distance: 189 - 198: 46.146 distance: 190 - 191: 31.866 distance: 199 - 200: 39.817 distance: 199 - 210: 56.568 distance: 200 - 201: 40.661 distance: 200 - 203: 68.431 distance: 200 - 211: 47.168 distance: 201 - 202: 43.231 distance: 201 - 219: 57.207 distance: 203 - 204: 23.015 distance: 203 - 212: 40.118 distance: 203 - 213: 23.854 distance: 204 - 205: 56.344 distance: 204 - 206: 44.375 distance: 205 - 207: 45.045 distance: 205 - 214: 62.206 distance: 206 - 208: 36.418 distance: 206 - 215: 29.268 distance: 207 - 209: 13.923 distance: 207 - 216: 10.118 distance: 208 - 217: 23.830 distance: 209 - 218: 15.833 distance: 219 - 220: 39.350 distance: 219 - 226: 57.153 distance: 220 - 221: 35.656 distance: 220 - 223: 31.370 distance: 220 - 227: 54.243 distance: 221 - 222: 17.991 distance: 221 - 235: 48.248 distance: 223 - 224: 35.550 distance: 223 - 225: 57.586 distance: 223 - 228: 40.192 distance: 224 - 229: 24.932 distance: 224 - 230: 51.395 distance: 224 - 231: 34.166 distance: 225 - 232: 20.158 distance: 225 - 233: 15.676 distance: 225 - 234: 26.034 distance: 235 - 236: 10.933 distance: 235 - 246: 35.023 distance: 236 - 237: 50.694 distance: 236 - 239: 20.047 distance: 236 - 247: 39.594 distance: 237 - 238: 49.550 distance: 237 - 259: 56.610 distance: 239 - 240: 39.056 distance: 239 - 248: 5.601 distance: 239 - 249: 19.917 distance: 240 - 241: 24.826 distance: 240 - 250: 43.105 distance: 240 - 251: 41.452 distance: 241 - 242: 26.922 distance: 241 - 252: 27.419 distance: 241 - 253: 25.394 distance: 242 - 243: 30.408 distance: 242 - 254: 11.368 distance: 243 - 244: 20.938 distance: 243 - 245: 23.291 distance: 244 - 255: 6.966 distance: 244 - 256: 8.446 distance: 245 - 257: 23.929 distance: 245 - 258: 25.307 distance: 259 - 260: 22.545 distance: 259 - 273: 62.483 distance: 260 - 261: 33.150 distance: 260 - 263: 24.372 distance: 260 - 274: 37.002 distance: 261 - 283: 41.139 distance: 263 - 264: 14.453 distance: 263 - 275: 41.779 distance: 263 - 276: 30.212 distance: 264 - 265: 17.839 distance: 264 - 266: 16.618 distance: 265 - 267: 52.396 distance: 265 - 277: 51.737 distance: 266 - 268: 32.377 distance: 266 - 269: 29.221 distance: 267 - 268: 16.037 distance: 267 - 278: 39.864 distance: 268 - 270: 25.007 distance: 269 - 271: 13.069 distance: 269 - 279: 46.559 distance: 270 - 272: 31.154 distance: 270 - 280: 11.281 distance: 271 - 272: 46.203 distance: 271 - 281: 12.307 distance: 272 - 282: 18.684 distance: 283 - 284: 48.503 distance: 283 - 289: 39.623 distance: 284 - 285: 42.501 distance: 284 - 287: 30.171 distance: 284 - 290: 47.882 distance: 285 - 286: 46.258 distance: 285 - 294: 43.972 distance: 287 - 288: 20.209 distance: 287 - 291: 18.553 distance: 287 - 292: 44.342 distance: 288 - 293: 8.790 distance: 294 - 295: 61.035 distance: 294 - 300: 19.224 distance: 295 - 296: 51.544 distance: 295 - 298: 50.558 distance: 295 - 301: 27.115 distance: 296 - 297: 34.438 distance: 296 - 308: 42.718 distance: 298 - 299: 38.374 distance: 298 - 302: 46.796 distance: 298 - 303: 52.177 distance: 299 - 300: 20.200 distance: 299 - 304: 60.812 distance: 299 - 305: 52.681 distance: 300 - 306: 39.510 distance: 300 - 307: 53.269 distance: 308 - 309: 24.628 distance: 308 - 314: 43.596 distance: 309 - 310: 39.807 distance: 309 - 315: 39.647 distance: 310 - 319: 34.432 distance: 312 - 313: 57.876 distance: 312 - 316: 56.357 distance: 312 - 317: 57.072 distance: 313 - 318: 45.219