Starting phenix.real_space_refine on Mon Jun 24 17:13:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b34_44125/06_2024/9b34_44125.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b34_44125/06_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_44125/06_2024/9b34_44125.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b34_44125/06_2024/9b34_44125.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b34_44125/06_2024/9b34_44125.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b34_44125/06_2024/9b34_44125.pdb" } 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-5370/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: 2.64, per 1000 atoms: 0.73 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: 1.41 Conformation dependent library (CDL) restraints added in 722.6 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: 0.50 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: 0.99 Time building geometry restraints manager: 1.49 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 2.440 ... (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 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.500 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 15.390 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.250 ------------------------------------------------------------------------------- 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 : 0.459 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: 0.1754 time to fit residues: 29.4594 Evaluate side-chains 79 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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: 0.2980 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.6961 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3699 Z= 0.228 Angle : 1.006 19.413 5044 Z= 0.508 Chirality : 0.054 0.205 580 Planarity : 0.007 0.049 651 Dihedral : 10.821 53.749 500 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 1.28 % Allowed : 22.13 % Favored : 76.60 % Rotamer: Outliers : 3.70 % Allowed : 14.81 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.78 % 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: -5.53 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -4.18 (0.35), residues: 152 loop : -3.60 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 182 HIS 0.006 0.002 HIS E 121 PHE 0.019 0.002 PHE F 128 TYR 0.015 0.002 TYR E 12 ARG 0.003 0.001 ARG F 33 *********************** 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 105 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 ILE cc_start: 0.8882 (tt) cc_final: 0.8624 (mt) REVERT: E 39 LYS cc_start: 0.8512 (tttt) cc_final: 0.8144 (tppt) REVERT: E 53 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7838 (mt) REVERT: E 93 LEU cc_start: 0.8561 (mt) cc_final: 0.7879 (mt) REVERT: E 126 LEU cc_start: 0.9125 (tp) cc_final: 0.8794 (tp) REVERT: E 129 MET cc_start: 0.6961 (ttm) cc_final: 0.6705 (ttp) REVERT: E 158 ARG cc_start: 0.6654 (mtp-110) cc_final: 0.5933 (mmm-85) REVERT: E 228 ARG cc_start: 0.7449 (ptp-110) cc_final: 0.5140 (mpt180) REVERT: E 229 LEU cc_start: 0.8392 (mt) cc_final: 0.8041 (mt) REVERT: F 54 TYR cc_start: 0.7098 (t80) cc_final: 0.6730 (t80) REVERT: F 126 LEU cc_start: 0.8687 (tp) cc_final: 0.8372 (tp) REVERT: F 208 ASP cc_start: 0.4065 (t0) cc_final: 0.3818 (t0) outliers start: 15 outliers final: 6 residues processed: 99 average time/residue: 0.1567 time to fit residues: 19.1074 Evaluate side-chains 80 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 53 ILE 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 220 SER 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: 3.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.0000 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 0.0870 overall best weight: 0.9566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 ASN ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3699 Z= 0.251 Angle : 0.947 17.990 5044 Z= 0.484 Chirality : 0.052 0.194 580 Planarity : 0.006 0.042 651 Dihedral : 10.357 52.845 500 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 1.49 % Allowed : 23.40 % Favored : 75.11 % Rotamer: Outliers : 4.94 % Allowed : 16.79 % Favored : 78.27 % 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: -5.18 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -3.73 (0.39), residues: 142 loop : -3.53 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 182 HIS 0.015 0.002 HIS F 180 PHE 0.015 0.002 PHE E 128 TYR 0.014 0.002 TYR F 12 ARG 0.006 0.001 ARG F 33 *********************** 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 101 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 41 ASN cc_start: 0.8434 (t0) cc_final: 0.7916 (t0) REVERT: E 53 ILE cc_start: 0.8009 (pp) cc_final: 0.7772 (mt) REVERT: E 126 LEU cc_start: 0.9114 (tp) cc_final: 0.8858 (tp) REVERT: E 129 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.7033 (ttp) REVERT: E 158 ARG cc_start: 0.6573 (mtp-110) cc_final: 0.6045 (mmm-85) REVERT: E 228 ARG cc_start: 0.7606 (ptp-110) cc_final: 0.5321 (mpt180) REVERT: F 126 LEU cc_start: 0.8636 (tp) cc_final: 0.8399 (tp) outliers start: 20 outliers final: 12 residues processed: 93 average time/residue: 0.1405 time to fit residues: 16.5031 Evaluate side-chains 91 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ASP 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 91 VAL Chi-restraints excluded: chain F residue 110 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7189 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3699 Z= 0.270 Angle : 0.938 17.417 5044 Z= 0.478 Chirality : 0.053 0.183 580 Planarity : 0.006 0.040 651 Dihedral : 10.313 54.362 500 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 1.91 % Allowed : 24.04 % Favored : 74.04 % Rotamer: Outliers : 5.19 % Allowed : 17.28 % Favored : 77.53 % 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: -5.11 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -3.25 (0.44), residues: 134 loop : -3.72 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 40 HIS 0.006 0.002 HIS E 121 PHE 0.016 0.002 PHE E 128 TYR 0.018 0.002 TYR F 12 ARG 0.003 0.001 ARG E 90 *********************** 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 100 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 53 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7902 (mt) REVERT: E 126 LEU cc_start: 0.9082 (tp) cc_final: 0.8840 (tp) REVERT: E 158 ARG cc_start: 0.6347 (mtp-110) cc_final: 0.5729 (mmm-85) REVERT: F 93 LEU cc_start: 0.8711 (mp) cc_final: 0.8483 (mp) REVERT: F 94 SER cc_start: 0.8481 (t) cc_final: 0.7701 (p) REVERT: F 126 LEU cc_start: 0.8789 (tp) cc_final: 0.8547 (tp) REVERT: F 145 ASP cc_start: 0.7559 (m-30) cc_final: 0.6980 (t0) outliers start: 21 outliers final: 11 residues processed: 93 average time/residue: 0.1365 time to fit residues: 16.1610 Evaluate side-chains 85 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 210 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 220 SER Chi-restraints excluded: chain F residue 223 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 0.0870 chunk 39 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 51 HIS E 180 HIS F 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.6215 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= 0.281 Angle : 0.938 18.588 5044 Z= 0.479 Chirality : 0.052 0.174 580 Planarity : 0.006 0.049 651 Dihedral : 10.102 54.734 500 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 1.91 % Allowed : 23.62 % Favored : 74.47 % Rotamer: Outliers : 6.91 % Allowed : 18.27 % Favored : 74.81 % 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: -4.97 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -3.07 (0.47), residues: 124 loop : -3.69 (0.28), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 182 HIS 0.006 0.002 HIS E 121 PHE 0.014 0.002 PHE E 128 TYR 0.019 0.002 TYR F 12 ARG 0.005 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 106 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 78 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 40 TRP cc_start: 0.8143 (t60) cc_final: 0.7281 (t60) REVERT: E 53 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7916 (mt) REVERT: E 126 LEU cc_start: 0.9040 (tp) cc_final: 0.8824 (tp) REVERT: E 136 ASP cc_start: 0.8233 (t70) cc_final: 0.7937 (t0) REVERT: E 158 ARG cc_start: 0.6690 (mtp-110) cc_final: 0.6170 (mmm-85) REVERT: F 10 ASP cc_start: 0.5876 (t0) cc_final: 0.5646 (t0) REVERT: F 94 SER cc_start: 0.8327 (t) cc_final: 0.7668 (p) REVERT: F 145 ASP cc_start: 0.7600 (m-30) cc_final: 0.6976 (t0) REVERT: F 208 ASP cc_start: 0.6619 (OUTLIER) cc_final: 0.6074 (m-30) outliers start: 28 outliers final: 19 residues processed: 96 average time/residue: 0.1452 time to fit residues: 17.3937 Evaluate side-chains 95 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 210 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 106 ILE Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 208 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3699 Z= 0.204 Angle : 0.917 18.363 5044 Z= 0.456 Chirality : 0.051 0.172 580 Planarity : 0.005 0.036 651 Dihedral : 9.710 52.124 500 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 1.70 % Allowed : 21.91 % Favored : 76.38 % Rotamer: Outliers : 5.68 % Allowed : 19.51 % Favored : 74.81 % 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: -4.76 (0.35), residues: 470 helix: None (None), residues: 0 sheet: -2.82 (0.48), residues: 124 loop : -3.59 (0.28), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 182 HIS 0.006 0.001 HIS E 121 PHE 0.025 0.002 PHE E 191 TYR 0.011 0.001 TYR F 12 ARG 0.005 0.001 ARG F 33 *********************** 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 100 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 40 TRP cc_start: 0.8137 (t60) cc_final: 0.7756 (t60) REVERT: E 41 ASN cc_start: 0.8297 (t0) cc_final: 0.7954 (t0) REVERT: E 53 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7855 (mt) REVERT: E 126 LEU cc_start: 0.8942 (tp) cc_final: 0.8708 (tp) REVERT: E 136 ASP cc_start: 0.8212 (t70) cc_final: 0.7842 (t0) REVERT: E 208 ASP cc_start: 0.6706 (t0) cc_final: 0.6037 (t70) REVERT: F 11 THR cc_start: 0.8417 (m) cc_final: 0.8172 (m) REVERT: F 60 ARG cc_start: 0.6835 (mtt90) cc_final: 0.6404 (ttp-170) REVERT: F 94 SER cc_start: 0.8479 (t) cc_final: 0.7920 (p) REVERT: F 145 ASP cc_start: 0.7484 (m-30) cc_final: 0.6913 (t0) REVERT: F 208 ASP cc_start: 0.6749 (OUTLIER) cc_final: 0.6374 (m-30) REVERT: F 223 SER cc_start: 0.7316 (OUTLIER) cc_final: 0.7030 (t) outliers start: 23 outliers final: 17 residues processed: 92 average time/residue: 0.1414 time to fit residues: 16.4356 Evaluate side-chains 93 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 96 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 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 74 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 208 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 0.3980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.0040 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.6783 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= 0.209 Angle : 0.898 18.162 5044 Z= 0.450 Chirality : 0.051 0.216 580 Planarity : 0.005 0.034 651 Dihedral : 9.492 50.461 500 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 1.49 % Allowed : 22.55 % Favored : 75.96 % Rotamer: Outliers : 6.42 % Allowed : 19.26 % Favored : 74.32 % 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: -4.57 (0.35), residues: 470 helix: None (None), residues: 0 sheet: -2.62 (0.48), residues: 130 loop : -3.47 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 182 HIS 0.007 0.001 HIS E 121 PHE 0.019 0.002 PHE E 128 TYR 0.009 0.001 TYR F 12 ARG 0.011 0.001 ARG E 33 *********************** 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: 26 poor density : 79 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: E 40 TRP cc_start: 0.8104 (t60) cc_final: 0.7216 (t60) REVERT: E 41 ASN cc_start: 0.8414 (t0) cc_final: 0.8150 (t0) REVERT: E 53 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7850 (mt) REVERT: E 126 LEU cc_start: 0.8940 (tp) cc_final: 0.8739 (tp) REVERT: E 129 MET cc_start: 0.7660 (mmm) cc_final: 0.7228 (mmm) REVERT: E 136 ASP cc_start: 0.8231 (t70) cc_final: 0.7882 (t0) REVERT: E 158 ARG cc_start: 0.7202 (mmm-85) cc_final: 0.6945 (mmm-85) REVERT: E 208 ASP cc_start: 0.6632 (t0) cc_final: 0.5988 (t70) REVERT: E 232 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7968 (pp) REVERT: E 235 ASP cc_start: 0.7785 (t70) cc_final: 0.7428 (t70) REVERT: F 60 ARG cc_start: 0.6908 (mtt90) cc_final: 0.6458 (ttp-170) REVERT: F 94 SER cc_start: 0.8469 (t) cc_final: 0.7961 (p) REVERT: F 107 LEU cc_start: 0.7954 (tp) cc_final: 0.7677 (pp) REVERT: F 145 ASP cc_start: 0.7491 (m-30) cc_final: 0.6924 (t0) REVERT: F 208 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6740 (m-30) REVERT: F 223 SER cc_start: 0.7326 (OUTLIER) cc_final: 0.7021 (t) outliers start: 26 outliers final: 17 residues processed: 93 average time/residue: 0.1479 time to fit residues: 17.4978 Evaluate side-chains 93 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 132 GLN 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 25 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 208 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 41 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.7023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3699 Z= 0.197 Angle : 0.895 17.810 5044 Z= 0.443 Chirality : 0.050 0.222 580 Planarity : 0.005 0.033 651 Dihedral : 9.352 49.500 500 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 1.28 % Allowed : 22.13 % Favored : 76.60 % Rotamer: Outliers : 4.44 % Allowed : 21.98 % Favored : 73.58 % 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: -4.51 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.53 (0.48), residues: 136 loop : -3.45 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 182 HIS 0.006 0.001 HIS E 121 PHE 0.025 0.002 PHE E 191 TYR 0.008 0.001 TYR F 12 ARG 0.007 0.001 ARG E 158 *********************** 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 98 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: E 33 ARG cc_start: 0.7807 (mtt-85) cc_final: 0.7189 (mtt-85) REVERT: E 40 TRP cc_start: 0.8134 (t60) cc_final: 0.7880 (t60) REVERT: E 53 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7827 (mt) REVERT: E 126 LEU cc_start: 0.8903 (tp) cc_final: 0.8686 (tp) REVERT: E 129 MET cc_start: 0.7649 (mmm) cc_final: 0.7308 (mmm) REVERT: E 136 ASP cc_start: 0.7983 (t70) cc_final: 0.7723 (t0) REVERT: E 208 ASP cc_start: 0.6603 (t0) cc_final: 0.6000 (t70) REVERT: E 232 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7929 (pp) REVERT: E 235 ASP cc_start: 0.7705 (t70) cc_final: 0.7322 (t70) REVERT: F 60 ARG cc_start: 0.6996 (mtt90) cc_final: 0.6558 (ttp-170) REVERT: F 94 SER cc_start: 0.8506 (t) cc_final: 0.7984 (p) REVERT: F 145 ASP cc_start: 0.7266 (m-30) cc_final: 0.6797 (t0) REVERT: F 208 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6591 (m-30) REVERT: F 223 SER cc_start: 0.7273 (OUTLIER) cc_final: 0.6892 (t) outliers start: 18 outliers final: 13 residues processed: 90 average time/residue: 0.1474 time to fit residues: 16.6039 Evaluate side-chains 89 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 99 LEU 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 25 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 208 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: 0.9980 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 153 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.7256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3699 Z= 0.221 Angle : 0.919 17.495 5044 Z= 0.456 Chirality : 0.051 0.234 580 Planarity : 0.005 0.033 651 Dihedral : 9.324 50.139 500 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 1.28 % Allowed : 22.77 % Favored : 75.96 % Rotamer: Outliers : 4.44 % Allowed : 23.70 % Favored : 71.85 % 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: -4.46 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.53 (0.47), residues: 140 loop : -3.41 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP E 182 HIS 0.006 0.001 HIS E 121 PHE 0.017 0.002 PHE E 128 TYR 0.013 0.001 TYR F 12 ARG 0.005 0.001 ARG F 33 *********************** 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 90 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 40 TRP cc_start: 0.8009 (t60) cc_final: 0.7720 (t60) REVERT: E 53 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7837 (mt) REVERT: E 112 THR cc_start: 0.7601 (m) cc_final: 0.7344 (m) REVERT: E 126 LEU cc_start: 0.8934 (tp) cc_final: 0.8726 (tp) REVERT: E 129 MET cc_start: 0.7582 (mmm) cc_final: 0.7357 (mmm) REVERT: E 136 ASP cc_start: 0.8077 (t70) cc_final: 0.7752 (t0) REVERT: E 208 ASP cc_start: 0.6653 (t0) cc_final: 0.6035 (t70) REVERT: E 232 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7963 (pp) REVERT: E 235 ASP cc_start: 0.7596 (t70) cc_final: 0.7257 (t70) REVERT: F 60 ARG cc_start: 0.6997 (mtt90) cc_final: 0.6525 (ttp-170) REVERT: F 94 SER cc_start: 0.8532 (t) cc_final: 0.7991 (p) REVERT: F 145 ASP cc_start: 0.7319 (m-30) cc_final: 0.6830 (t0) REVERT: F 208 ASP cc_start: 0.7127 (m-30) cc_final: 0.6670 (m-30) REVERT: F 223 SER cc_start: 0.7394 (OUTLIER) cc_final: 0.6984 (t) outliers start: 18 outliers final: 13 residues processed: 83 average time/residue: 0.1495 time to fit residues: 15.5686 Evaluate side-chains 86 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 53 ILE 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 25 ILE Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 179 VAL 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: 0.0020 chunk 42 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.0060 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 overall best weight: 0.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.7430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3699 Z= 0.185 Angle : 0.902 17.654 5044 Z= 0.442 Chirality : 0.050 0.244 580 Planarity : 0.005 0.035 651 Dihedral : 8.977 45.030 500 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 1.06 % Allowed : 21.91 % Favored : 77.02 % Rotamer: Outliers : 3.70 % Allowed : 24.69 % Favored : 71.60 % 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: -4.44 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.46 (0.47), residues: 138 loop : -3.42 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 40 HIS 0.006 0.001 HIS E 121 PHE 0.024 0.002 PHE E 191 TYR 0.015 0.001 TYR F 12 ARG 0.004 0.001 ARG F 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: 15 poor density : 77 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: E 40 TRP cc_start: 0.7942 (t60) cc_final: 0.7688 (t60) REVERT: E 53 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7830 (mt) REVERT: E 126 LEU cc_start: 0.8667 (tp) cc_final: 0.8457 (tp) REVERT: E 129 MET cc_start: 0.7513 (mmm) cc_final: 0.7186 (mmm) REVERT: E 136 ASP cc_start: 0.7954 (t70) cc_final: 0.7545 (t0) REVERT: E 208 ASP cc_start: 0.6729 (t0) cc_final: 0.6121 (t70) REVERT: E 232 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7895 (pp) REVERT: E 235 ASP cc_start: 0.7699 (t70) cc_final: 0.7482 (t70) REVERT: F 60 ARG cc_start: 0.6807 (mtt90) cc_final: 0.6361 (ttp-170) REVERT: F 94 SER cc_start: 0.8503 (t) cc_final: 0.8147 (p) REVERT: F 145 ASP cc_start: 0.6997 (m-30) cc_final: 0.6553 (t0) outliers start: 15 outliers final: 10 residues processed: 85 average time/residue: 0.1564 time to fit residues: 16.6543 Evaluate side-chains 85 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 91 VAL 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 25 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 179 VAL 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: 3.9990 chunk 37 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 0.0570 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 162 ASN ** 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 = 0.3983 r_free = 0.3983 target = 0.144928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.126715 restraints weight = 6245.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.130490 restraints weight = 3751.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.133096 restraints weight = 2587.461| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.7648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3699 Z= 0.212 Angle : 0.908 17.055 5044 Z= 0.446 Chirality : 0.050 0.198 580 Planarity : 0.005 0.032 651 Dihedral : 9.038 47.476 500 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.64 % Allowed : 24.04 % Favored : 75.32 % Rotamer: Outliers : 2.72 % Allowed : 25.43 % Favored : 71.85 % 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: -4.39 (0.36), residues: 470 helix: None (None), residues: 0 sheet: -2.48 (0.47), residues: 140 loop : -3.35 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP E 182 HIS 0.006 0.001 HIS E 121 PHE 0.016 0.002 PHE E 128 TYR 0.013 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: 1349.92 seconds wall clock time: 24 minutes 56.53 seconds (1496.53 seconds total)