Starting phenix.real_space_refine on Fri Aug 2 16:47:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b34_44125/08_2024/9b34_44125.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b34_44125/08_2024/9b34_44125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b34_44125/08_2024/9b34_44125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b34_44125/08_2024/9b34_44125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b34_44125/08_2024/9b34_44125.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b34_44125/08_2024/9b34_44125.cif" } resolution = 3.58 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= 0.015 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 S 4 5.16 5 C 2281 2.51 5 N 604 2.21 5 O 726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 158": "NH1" <-> "NH2" Residue "E PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "F PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3619 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1806 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1809 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.75, per 1000 atoms: 0.76 Number of scatterers: 3619 At special positions: 0 Unit cell: (63.3889, 57.9941, 93.0603, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 4 16.00 O 726 8.00 N 604 7.00 C 2281 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: 1.43 Conformation dependent library (CDL) restraints added in 672.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 24 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 24 " 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 884 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 10 sheets defined 1.1% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'E' and resid 14 through 18 removed outlier: 3.809A pdb=" N GLY E 18 " --> pdb=" O THR E 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.601A pdb=" N SER E 94 " --> pdb=" O ALA E 211 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY E 92 " --> pdb=" O PHE E 213 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER E 215 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG E 90 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.601A pdb=" N SER E 94 " --> pdb=" O ALA E 211 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY E 92 " --> pdb=" O PHE E 213 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER E 215 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG E 90 " --> pdb=" O SER E 215 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL E 179 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 9 through 10 Processing sheet with id=AA4, first strand: chain 'E' and resid 49 through 54 Processing sheet with id=AA5, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AA6, first strand: chain 'E' and resid 128 through 130 removed outlier: 3.844A pdb=" N THR E 194 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 36 through 39 removed outlier: 4.256A pdb=" N LYS F 36 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 212 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY F 92 " --> pdb=" O PHE F 213 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL F 91 " --> pdb=" O PHE F 175 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU F 174 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 36 through 39 removed outlier: 4.256A pdb=" N LYS F 36 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE F 212 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY F 92 " --> pdb=" O PHE F 213 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL F 179 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 77 through 78 removed outlier: 3.511A pdb=" N TYR F 77 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA F 50 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE F 52 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR F 194 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER F 108 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU F 198 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE F 106 " --> pdb=" O LEU F 198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 77 through 78 removed outlier: 3.511A pdb=" N TYR F 77 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA F 50 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE F 52 " --> pdb=" O ALA F 193 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR F 194 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER F 108 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU F 198 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE F 106 " --> pdb=" O LEU F 198 " (cutoff:3.500A) 110 hydrogen bonds defined for protein. 264 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: 0.97 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1103 1.34 - 1.45: 640 1.45 - 1.57: 1948 1.57 - 1.69: 0 1.69 - 1.81: 8 Bond restraints: 3699 Sorted by residual: bond pdb=" CA ASP F 208 " pdb=" C ASP F 208 " ideal model delta sigma weight residual 1.521 1.559 -0.037 1.14e-02 7.69e+03 1.08e+01 bond pdb=" C SER F 21 " pdb=" N TYR F 22 " ideal model delta sigma weight residual 1.327 1.296 0.031 1.39e-02 5.18e+03 4.88e+00 bond pdb=" N SER E 119 " pdb=" CA SER E 119 " ideal model delta sigma weight residual 1.457 1.484 -0.026 1.29e-02 6.01e+03 4.19e+00 bond pdb=" CB ASN E 69 " pdb=" CG ASN E 69 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.85e+00 bond pdb=" CA ALA F 186 " pdb=" C ALA F 186 " ideal model delta sigma weight residual 1.523 1.549 -0.025 1.34e-02 5.57e+03 3.60e+00 ... (remaining 3694 not shown) Histogram of bond angle deviations from ideal: 100.42 - 108.04: 250 108.04 - 115.65: 2186 115.65 - 123.27: 2297 123.27 - 130.88: 287 130.88 - 138.50: 24 Bond angle restraints: 5044 Sorted by residual: angle pdb=" N GLY F 48 " pdb=" CA GLY F 48 " pdb=" C GLY F 48 " ideal model delta sigma weight residual 113.18 133.23 -20.05 2.37e+00 1.78e-01 7.16e+01 angle pdb=" N GLY E 48 " pdb=" CA GLY E 48 " pdb=" C GLY E 48 " ideal model delta sigma weight residual 115.33 138.50 -23.17 2.74e+00 1.33e-01 7.15e+01 angle pdb=" N ALA E 207 " pdb=" CA ALA E 207 " pdb=" C ALA E 207 " ideal model delta sigma weight residual 107.20 118.76 -11.56 1.70e+00 3.46e-01 4.62e+01 angle pdb=" N ALA E 186 " pdb=" CA ALA E 186 " pdb=" C ALA E 186 " ideal model delta sigma weight residual 110.80 122.94 -12.14 2.13e+00 2.20e-01 3.25e+01 angle pdb=" N ALA F 186 " pdb=" CA ALA F 186 " pdb=" C ALA F 186 " ideal model delta sigma weight residual 110.80 122.84 -12.04 2.13e+00 2.20e-01 3.20e+01 ... (remaining 5039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 1978 14.84 - 29.69: 146 29.69 - 44.53: 44 44.53 - 59.38: 10 59.38 - 74.22: 4 Dihedral angle restraints: 2182 sinusoidal: 812 harmonic: 1370 Sorted by residual: dihedral pdb=" CA ALA E 207 " pdb=" C ALA E 207 " pdb=" N ASP E 208 " pdb=" CA ASP E 208 " ideal model delta harmonic sigma weight residual 180.00 109.71 70.29 0 5.00e+00 4.00e-02 1.98e+02 dihedral pdb=" CA VAL F 47 " pdb=" C VAL F 47 " pdb=" N GLY F 48 " pdb=" CA GLY F 48 " ideal model delta harmonic sigma weight residual 180.00 117.97 62.03 0 5.00e+00 4.00e-02 1.54e+02 dihedral pdb=" CA VAL E 47 " pdb=" C VAL E 47 " pdb=" N GLY E 48 " pdb=" CA GLY E 48 " ideal model delta harmonic sigma weight residual 180.00 121.49 58.51 0 5.00e+00 4.00e-02 1.37e+02 ... (remaining 2179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 420 0.067 - 0.133: 109 0.133 - 0.200: 34 0.200 - 0.266: 11 0.266 - 0.333: 6 Chirality restraints: 580 Sorted by residual: chirality pdb=" CB VAL F 187 " pdb=" CA VAL F 187 " pdb=" CG1 VAL F 187 " pdb=" CG2 VAL F 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CB VAL E 187 " pdb=" CA VAL E 187 " pdb=" CG1 VAL E 187 " pdb=" CG2 VAL E 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB VAL F 75 " pdb=" CA VAL F 75 " pdb=" CG1 VAL F 75 " pdb=" CG2 VAL F 75 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 577 not shown) Planarity restraints: 651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 141 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.35e+00 pdb=" C ILE F 141 " -0.050 2.00e-02 2.50e+03 pdb=" O ILE F 141 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU F 142 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 208 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" CG ASP E 208 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASP E 208 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP E 208 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 118 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.96e+00 pdb=" C ASN F 118 " 0.049 2.00e-02 2.50e+03 pdb=" O ASN F 118 " -0.018 2.00e-02 2.50e+03 pdb=" N SER F 119 " -0.017 2.00e-02 2.50e+03 ... (remaining 648 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 139 2.68 - 3.23: 3433 3.23 - 3.79: 5728 3.79 - 4.34: 7350 4.34 - 4.90: 12555 Nonbonded interactions: 29205 Sorted by model distance: nonbonded pdb=" OD2 ASP E 10 " pdb="ZN ZN E1001 " model vdw 2.121 2.230 nonbonded pdb=" OD1 ASP E 19 " pdb="ZN ZN E1001 " model vdw 2.133 2.230 nonbonded pdb=" OD2 ASP F 10 " pdb="ZN ZN F1001 " model vdw 2.151 2.230 nonbonded pdb=" OD1 ASP F 19 " pdb="ZN ZN F1001 " model vdw 2.181 2.230 nonbonded pdb=" OG SER E 108 " pdb=" OG1 THR E 196 " model vdw 2.261 3.040 ... (remaining 29200 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 1 through 144 or (resid 145 through 146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 147 through 237 or resid 1001 th \ rough 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.820 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 3699 Z= 0.407 Angle : 1.466 23.170 5044 Z= 0.788 Chirality : 0.077 0.333 580 Planarity : 0.009 0.060 651 Dihedral : 12.857 74.220 1298 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 1.91 % Allowed : 23.62 % Favored : 74.47 % Rotamer: Outliers : 0.49 % Allowed : 5.68 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.95 (0.31), residues: 470 helix: None (None), residues: 0 sheet: -4.50 (0.34), residues: 126 loop : -4.04 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP E 182 HIS 0.004 0.001 HIS E 51 PHE 0.036 0.005 PHE E 130 TYR 0.016 0.003 TYR E 176 ARG 0.009 0.002 ARG F 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 ILE cc_start: 0.9158 (tt) cc_final: 0.8886 (mt) REVERT: E 39 LYS cc_start: 0.8538 (tttt) cc_final: 0.8171 (tppp) REVERT: E 53 ILE cc_start: 0.7856 (pp) cc_final: 0.7608 (mt) REVERT: E 55 ASN cc_start: 0.8361 (p0) cc_final: 0.8143 (p0) REVERT: E 126 LEU cc_start: 0.9085 (tp) cc_final: 0.8771 (tp) REVERT: E 158 ARG cc_start: 0.6605 (mtp-110) cc_final: 0.5844 (ptm160) REVERT: E 195 PHE cc_start: 0.7046 (t80) cc_final: 0.6783 (t80) REVERT: E 228 ARG cc_start: 0.7664 (ptp-110) cc_final: 0.5364 (mmt180) REVERT: E 229 LEU cc_start: 0.8479 (mt) cc_final: 0.8220 (mt) REVERT: F 126 LEU cc_start: 0.8408 (tp) cc_final: 0.8126 (tp) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.1743 time to fit residues: 29.1467 Evaluate side-chains 79 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.0470 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 ASN E 162 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN F 162 ASN F 180 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3699 Z= 0.222 Angle : 1.024 19.053 5044 Z= 0.520 Chirality : 0.054 0.194 580 Planarity : 0.007 0.052 651 Dihedral : 10.769 51.545 500 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 1.28 % Allowed : 21.49 % Favored : 77.23 % Rotamer: Outliers : 2.72 % Allowed : 16.30 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.47 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -4.06 (0.36), residues: 156 loop : -3.59 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 182 HIS 0.006 0.001 HIS E 121 PHE 0.018 0.002 PHE F 128 TYR 0.016 0.002 TYR E 12 ARG 0.004 0.001 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 ILE cc_start: 0.8818 (tt) cc_final: 0.8605 (mt) REVERT: E 39 LYS cc_start: 0.8447 (tttt) cc_final: 0.8078 (tppt) REVERT: E 53 ILE cc_start: 0.7938 (pp) cc_final: 0.7657 (mt) REVERT: E 129 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6757 (ttp) REVERT: E 158 ARG cc_start: 0.6610 (mtp-110) cc_final: 0.5945 (mmm-85) REVERT: E 228 ARG cc_start: 0.7325 (ptp-110) cc_final: 0.5053 (mpt180) REVERT: E 229 LEU cc_start: 0.8325 (mt) cc_final: 0.7975 (mt) REVERT: F 54 TYR cc_start: 0.7222 (t80) cc_final: 0.6699 (t80) REVERT: F 126 LEU cc_start: 0.8575 (tp) cc_final: 0.8246 (tp) outliers start: 11 outliers final: 4 residues processed: 97 average time/residue: 0.1498 time to fit residues: 17.9659 Evaluate side-chains 80 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 180 HIS Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 51 HIS E 162 ASN F 14 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3699 Z= 0.272 Angle : 0.967 17.454 5044 Z= 0.494 Chirality : 0.053 0.196 580 Planarity : 0.006 0.044 651 Dihedral : 10.478 54.201 500 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 1.28 % Allowed : 21.70 % Favored : 77.02 % Rotamer: Outliers : 4.69 % Allowed : 17.04 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -3.65 (0.39), residues: 150 loop : -3.45 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 182 HIS 0.016 0.002 HIS F 180 PHE 0.020 0.002 PHE E 191 TYR 0.014 0.002 TYR F 12 ARG 0.004 0.001 ARG F 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 39 LYS cc_start: 0.8495 (tttt) cc_final: 0.8282 (ttmt) REVERT: E 129 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.7161 (ttp) REVERT: E 158 ARG cc_start: 0.6461 (mtp-110) cc_final: 0.6000 (mmm-85) REVERT: E 182 TRP cc_start: 0.7315 (t60) cc_final: 0.7044 (t60) REVERT: E 228 ARG cc_start: 0.7580 (ptp-110) cc_final: 0.5261 (mpt180) REVERT: F 54 TYR cc_start: 0.7520 (t80) cc_final: 0.7313 (t80) REVERT: F 145 ASP cc_start: 0.7243 (m-30) cc_final: 0.6862 (t0) REVERT: F 159 VAL cc_start: 0.6678 (p) cc_final: 0.6022 (m) outliers start: 19 outliers final: 10 residues processed: 93 average time/residue: 0.1459 time to fit residues: 16.8357 Evaluate side-chains 85 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 ASN E 180 HIS F 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 3699 Z= 0.343 Angle : 1.015 16.980 5044 Z= 0.519 Chirality : 0.055 0.210 580 Planarity : 0.006 0.040 651 Dihedral : 10.705 56.622 500 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 1.70 % Allowed : 24.26 % Favored : 74.04 % Rotamer: Outliers : 6.67 % Allowed : 15.80 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.02 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -3.23 (0.41), residues: 142 loop : -3.63 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 109 HIS 0.005 0.001 HIS E 121 PHE 0.017 0.002 PHE E 130 TYR 0.020 0.002 TYR F 12 ARG 0.004 0.001 ARG E 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 136 ASP cc_start: 0.8273 (t70) cc_final: 0.7952 (t0) REVERT: E 158 ARG cc_start: 0.6204 (mtp-110) cc_final: 0.5573 (mmm-85) REVERT: E 182 TRP cc_start: 0.7329 (t60) cc_final: 0.7016 (t60) REVERT: E 232 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7821 (pp) REVERT: F 94 SER cc_start: 0.8489 (t) cc_final: 0.7715 (p) REVERT: F 145 ASP cc_start: 0.7554 (m-30) cc_final: 0.6987 (t0) outliers start: 27 outliers final: 15 residues processed: 102 average time/residue: 0.1222 time to fit residues: 16.2108 Evaluate side-chains 91 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 232 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.0040 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.6138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3699 Z= 0.223 Angle : 0.951 17.632 5044 Z= 0.479 Chirality : 0.053 0.180 580 Planarity : 0.006 0.042 651 Dihedral : 10.135 50.609 500 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 1.28 % Allowed : 20.85 % Favored : 77.87 % Rotamer: Outliers : 6.67 % Allowed : 19.01 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.11 % 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: -4.79 (0.35), residues: 470 helix: None (None), residues: 0 sheet: -2.93 (0.44), residues: 140 loop : -3.54 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 182 HIS 0.006 0.001 HIS E 121 PHE 0.024 0.002 PHE E 191 TYR 0.020 0.002 TYR F 54 ARG 0.004 0.001 ARG F 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 80 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 136 ASP cc_start: 0.8077 (t70) cc_final: 0.7697 (t0) REVERT: E 162 ASN cc_start: 0.6667 (OUTLIER) cc_final: 0.6349 (p0) REVERT: E 166 GLN cc_start: 0.7522 (tp-100) cc_final: 0.7321 (tt0) REVERT: E 232 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7645 (pp) REVERT: F 8 GLU cc_start: 0.8341 (pt0) cc_final: 0.8083 (pt0) REVERT: F 94 SER cc_start: 0.8468 (t) cc_final: 0.7896 (p) REVERT: F 145 ASP cc_start: 0.7448 (m-30) cc_final: 0.6927 (t0) REVERT: F 208 ASP cc_start: 0.5432 (OUTLIER) cc_final: 0.4513 (m-30) REVERT: F 221 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8530 (pt) REVERT: F 223 SER cc_start: 0.7349 (OUTLIER) cc_final: 0.7065 (t) outliers start: 27 outliers final: 17 residues processed: 97 average time/residue: 0.1487 time to fit residues: 18.3347 Evaluate side-chains 100 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 232 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 131 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3699 Z= 0.232 Angle : 0.927 16.131 5044 Z= 0.469 Chirality : 0.052 0.173 580 Planarity : 0.006 0.043 651 Dihedral : 9.969 46.873 500 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 1.06 % Allowed : 23.19 % Favored : 75.74 % Rotamer: Outliers : 7.65 % Allowed : 17.78 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.11 % 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: -4.67 (0.35), residues: 470 helix: None (None), residues: 0 sheet: -2.74 (0.44), residues: 144 loop : -3.52 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 182 HIS 0.006 0.001 HIS E 121 PHE 0.014 0.002 PHE F 195 TYR 0.011 0.001 TYR F 12 ARG 0.006 0.001 ARG E 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 78 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: E 51 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.5866 (t70) REVERT: E 136 ASP cc_start: 0.8121 (t70) cc_final: 0.7741 (t0) REVERT: E 232 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7677 (pp) REVERT: F 8 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8192 (pt0) REVERT: F 60 ARG cc_start: 0.7605 (mmm160) cc_final: 0.7223 (ttt-90) REVERT: F 94 SER cc_start: 0.8431 (t) cc_final: 0.7895 (p) REVERT: F 145 ASP cc_start: 0.7249 (m-30) cc_final: 0.6750 (t0) REVERT: F 208 ASP cc_start: 0.5980 (OUTLIER) cc_final: 0.5493 (m-30) REVERT: F 217 ILE cc_start: 0.8863 (pt) cc_final: 0.8649 (mm) REVERT: F 221 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8592 (pt) REVERT: F 223 SER cc_start: 0.7406 (OUTLIER) cc_final: 0.7106 (t) outliers start: 31 outliers final: 20 residues processed: 95 average time/residue: 0.1329 time to fit residues: 16.0734 Evaluate side-chains 97 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 71 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 176 TYR Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 232 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.0770 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3699 Z= 0.199 Angle : 0.913 14.549 5044 Z= 0.456 Chirality : 0.052 0.219 580 Planarity : 0.006 0.041 651 Dihedral : 9.563 45.898 500 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 1.06 % Allowed : 21.70 % Favored : 77.23 % Rotamer: Outliers : 7.16 % Allowed : 19.75 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.11 % 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: -4.48 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.51 (0.46), residues: 144 loop : -3.43 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP E 182 HIS 0.007 0.001 HIS F 121 PHE 0.026 0.002 PHE E 191 TYR 0.007 0.001 TYR F 12 ARG 0.006 0.001 ARG E 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 76 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: E 51 HIS cc_start: 0.6975 (OUTLIER) cc_final: 0.5842 (t70) REVERT: E 136 ASP cc_start: 0.8012 (t70) cc_final: 0.7642 (t0) REVERT: E 158 ARG cc_start: 0.7300 (mmm-85) cc_final: 0.6971 (mmm-85) REVERT: E 162 ASN cc_start: 0.6786 (OUTLIER) cc_final: 0.6339 (p0) REVERT: E 232 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7809 (pp) REVERT: F 8 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8206 (pt0) REVERT: F 59 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7840 (tppt) REVERT: F 94 SER cc_start: 0.8380 (t) cc_final: 0.7940 (p) REVERT: F 145 ASP cc_start: 0.7048 (m-30) cc_final: 0.6656 (t0) REVERT: F 217 ILE cc_start: 0.8811 (pt) cc_final: 0.8597 (mm) REVERT: F 221 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8466 (pt) REVERT: F 223 SER cc_start: 0.7376 (OUTLIER) cc_final: 0.6955 (t) outliers start: 29 outliers final: 17 residues processed: 94 average time/residue: 0.1358 time to fit residues: 16.2351 Evaluate side-chains 92 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 68 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 232 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.7103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3699 Z= 0.287 Angle : 0.954 13.750 5044 Z= 0.483 Chirality : 0.054 0.218 580 Planarity : 0.006 0.044 651 Dihedral : 9.791 45.625 500 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 1.06 % Allowed : 22.77 % Favored : 76.17 % Rotamer: Outliers : 5.68 % Allowed : 22.72 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.11 % 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: -4.38 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.50 (0.46), residues: 144 loop : -3.33 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP E 182 HIS 0.005 0.001 HIS E 121 PHE 0.022 0.002 PHE F 195 TYR 0.014 0.002 TYR F 12 ARG 0.009 0.001 ARG E 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 51 HIS cc_start: 0.7008 (OUTLIER) cc_final: 0.5889 (t70) REVERT: E 129 MET cc_start: 0.7440 (ttp) cc_final: 0.6204 (tmm) REVERT: E 130 PHE cc_start: 0.7665 (m-80) cc_final: 0.7228 (m-80) REVERT: E 136 ASP cc_start: 0.8161 (t70) cc_final: 0.7752 (t0) REVERT: E 158 ARG cc_start: 0.7150 (mmm-85) cc_final: 0.6857 (mmm-85) REVERT: E 162 ASN cc_start: 0.6474 (OUTLIER) cc_final: 0.6225 (p0) REVERT: E 213 PHE cc_start: 0.8851 (p90) cc_final: 0.7948 (p90) REVERT: E 232 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7826 (pp) REVERT: E 235 ASP cc_start: 0.7786 (t70) cc_final: 0.7379 (t70) REVERT: F 8 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: F 59 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7907 (tppt) REVERT: F 94 SER cc_start: 0.8438 (t) cc_final: 0.7864 (p) REVERT: F 145 ASP cc_start: 0.7098 (m-30) cc_final: 0.6676 (t0) REVERT: F 223 SER cc_start: 0.7508 (OUTLIER) cc_final: 0.7121 (t) outliers start: 23 outliers final: 15 residues processed: 93 average time/residue: 0.1386 time to fit residues: 16.2850 Evaluate side-chains 95 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 218 ASP Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 232 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 27 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 30 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.7197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3699 Z= 0.214 Angle : 0.930 14.148 5044 Z= 0.466 Chirality : 0.052 0.243 580 Planarity : 0.006 0.042 651 Dihedral : 9.448 45.564 500 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.85 % Allowed : 22.13 % Favored : 77.02 % Rotamer: Outliers : 5.19 % Allowed : 23.70 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % 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: -4.26 (0.37), residues: 470 helix: None (None), residues: 0 sheet: -2.39 (0.47), residues: 140 loop : -3.26 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP E 182 HIS 0.005 0.001 HIS E 121 PHE 0.034 0.003 PHE F 195 TYR 0.009 0.001 TYR F 176 ARG 0.008 0.001 ARG E 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: E 51 HIS cc_start: 0.6957 (OUTLIER) cc_final: 0.5809 (t70) REVERT: E 129 MET cc_start: 0.7293 (ttp) cc_final: 0.6026 (tmm) REVERT: E 130 PHE cc_start: 0.7585 (m-80) cc_final: 0.7158 (m-80) REVERT: E 136 ASP cc_start: 0.8081 (t70) cc_final: 0.7677 (t0) REVERT: E 213 PHE cc_start: 0.8780 (p90) cc_final: 0.7993 (p90) REVERT: E 232 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7825 (pp) REVERT: E 235 ASP cc_start: 0.7784 (t70) cc_final: 0.7429 (t70) REVERT: F 8 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8213 (pt0) REVERT: F 59 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7772 (tppt) REVERT: F 94 SER cc_start: 0.8569 (t) cc_final: 0.7994 (p) REVERT: F 145 ASP cc_start: 0.6815 (m-30) cc_final: 0.6588 (t0) REVERT: F 223 SER cc_start: 0.7246 (OUTLIER) cc_final: 0.6868 (t) outliers start: 21 outliers final: 15 residues processed: 89 average time/residue: 0.1552 time to fit residues: 17.4962 Evaluate side-chains 91 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.7445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3699 Z= 0.247 Angle : 0.939 13.795 5044 Z= 0.470 Chirality : 0.053 0.232 580 Planarity : 0.006 0.039 651 Dihedral : 9.476 45.697 500 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.85 % Allowed : 22.77 % Favored : 76.38 % Rotamer: Outliers : 5.43 % Allowed : 23.95 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % 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: -4.30 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.39 (0.47), residues: 140 loop : -3.30 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP E 182 HIS 0.005 0.001 HIS E 121 PHE 0.043 0.003 PHE F 195 TYR 0.012 0.002 TYR F 12 ARG 0.005 0.001 ARG E 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: E 51 HIS cc_start: 0.6968 (OUTLIER) cc_final: 0.5868 (t70) REVERT: E 130 PHE cc_start: 0.7711 (m-80) cc_final: 0.7289 (m-80) REVERT: E 136 ASP cc_start: 0.8122 (t70) cc_final: 0.7704 (t0) REVERT: E 162 ASN cc_start: 0.6278 (OUTLIER) cc_final: 0.5981 (p0) REVERT: E 213 PHE cc_start: 0.8840 (p90) cc_final: 0.7972 (p90) REVERT: E 232 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7853 (pp) REVERT: E 235 ASP cc_start: 0.7699 (t70) cc_final: 0.7387 (t70) REVERT: F 8 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8069 (pt0) REVERT: F 59 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7792 (tppt) REVERT: F 94 SER cc_start: 0.8424 (t) cc_final: 0.7911 (p) REVERT: F 145 ASP cc_start: 0.6854 (m-30) cc_final: 0.6604 (t0) REVERT: F 223 SER cc_start: 0.7456 (OUTLIER) cc_final: 0.7029 (t) outliers start: 22 outliers final: 15 residues processed: 84 average time/residue: 0.1302 time to fit residues: 14.0986 Evaluate side-chains 90 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 51 HIS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain F residue 8 GLU Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.0670 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 0.0000 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 overall best weight: 0.4522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.140500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.122569 restraints weight = 6241.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.126101 restraints weight = 3858.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.128390 restraints weight = 2709.708| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.7425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 3699 Z= 0.353 Angle : 1.425 58.883 5044 Z= 0.825 Chirality : 0.060 0.680 580 Planarity : 0.006 0.055 651 Dihedral : 9.479 45.543 500 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 1.06 % Allowed : 22.77 % Favored : 76.17 % Rotamer: Outliers : 5.68 % Allowed : 23.95 % Favored : 70.37 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % 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: -4.29 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.40 (0.47), residues: 140 loop : -3.29 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP E 182 HIS 0.005 0.001 HIS E 121 PHE 0.036 0.003 PHE F 195 TYR 0.011 0.001 TYR F 12 ARG 0.004 0.001 ARG F 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1275.01 seconds wall clock time: 23 minutes 13.21 seconds (1393.21 seconds total)