Starting phenix.real_space_refine on Wed Feb 14 00:35:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oz3_13119/02_2024/7oz3_13119_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oz3_13119/02_2024/7oz3_13119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oz3_13119/02_2024/7oz3_13119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oz3_13119/02_2024/7oz3_13119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oz3_13119/02_2024/7oz3_13119_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oz3_13119/02_2024/7oz3_13119_updated.pdb" } resolution = 4.46 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 92 5.49 5 S 8 5.16 5 C 4932 2.51 5 N 1411 2.21 5 O 1766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8209 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1584 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "B" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "C" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1580 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "D" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1558 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 5, 'TRANS': 192} Chain: "F" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 900 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "G" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 904 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Classifications: {'RNA': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Classifications: {'RNA': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ARG C 210 " occ=0.75 ... (9 atoms not shown) pdb=" NH2 ARG C 210 " occ=0.75 Time building chain proxies: 4.87, per 1000 atoms: 0.59 Number of scatterers: 8209 At special positions: 0 Unit cell: (77.404, 93.094, 161.084, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 P 92 15.00 O 1766 8.00 N 1411 7.00 C 4932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 1.4 seconds 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 6 sheets defined 51.4% alpha, 9.1% beta 44 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 49 through 61 Processing helix chain 'A' and resid 79 through 131 removed outlier: 5.168A pdb=" N SER A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LYS A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 156 No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 197 through 206 Processing helix chain 'B' and resid 12 through 26 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 49 through 61 Processing helix chain 'B' and resid 79 through 131 removed outlier: 3.603A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER B 130 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYS B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 156 No H-bonds generated for 'chain 'B' and resid 153 through 156' Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'C' and resid 12 through 26 removed outlier: 4.157A pdb=" N ILE C 16 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ALA C 17 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 45 Processing helix chain 'C' and resid 49 through 61 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 95 through 126 Processing helix chain 'C' and resid 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 197 through 207 Processing helix chain 'D' and resid 14 through 26 Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 49 through 61 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 95 through 125 Processing helix chain 'D' and resid 133 through 135 No H-bonds generated for 'chain 'D' and resid 133 through 135' Processing helix chain 'D' and resid 153 through 156 No H-bonds generated for 'chain 'D' and resid 153 through 156' Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 197 through 207 Processing sheet with id= A, first strand: chain 'A' and resid 65 through 68 removed outlier: 3.637A pdb=" N GLY A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 138 through 141 removed outlier: 3.500A pdb=" N PHE A 193 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 194 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE A 166 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 169 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 65 through 68 Processing sheet with id= D, first strand: chain 'B' and resid 174 through 177 removed outlier: 3.503A pdb=" N ILE B 169 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE B 192 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 169 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS B 190 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 138 through 141 removed outlier: 3.656A pdb=" N HIS C 190 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C 194 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE C 166 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 138 through 141 removed outlier: 6.462A pdb=" N VAL D 194 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE D 166 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS D 171 " --> pdb=" O LYS D 174 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1578 1.33 - 1.45: 2406 1.45 - 1.57: 4362 1.57 - 1.69: 185 1.69 - 1.81: 16 Bond restraints: 8547 Sorted by residual: bond pdb=" C1' 2BA A 301 " pdb=" C2' 2BA A 301 " ideal model delta sigma weight residual 1.541 1.347 0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" C1' 2BA B 301 " pdb=" C2' 2BA B 301 " ideal model delta sigma weight residual 1.541 1.347 0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb="C1'1 2BA A 301 " pdb="C2'1 2BA A 301 " ideal model delta sigma weight residual 1.532 1.349 0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb="C1'1 2BA B 301 " pdb="C2'1 2BA B 301 " ideal model delta sigma weight residual 1.532 1.349 0.183 2.00e-02 2.50e+03 8.38e+01 bond pdb="C1'1 2BA B 301 " pdb="O4'1 2BA B 301 " ideal model delta sigma weight residual 1.408 1.573 -0.165 2.00e-02 2.50e+03 6.84e+01 ... (remaining 8542 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.81: 643 105.81 - 112.91: 4498 112.91 - 120.02: 3338 120.02 - 127.12: 3219 127.12 - 134.23: 257 Bond angle restraints: 11955 Sorted by residual: angle pdb=" O3' DA F 22 " pdb=" C3' DA F 22 " pdb=" C2' DA F 22 " ideal model delta sigma weight residual 111.50 122.86 -11.36 1.50e+00 4.44e-01 5.74e+01 angle pdb=" N SER C 143 " pdb=" CA SER C 143 " pdb=" C SER C 143 " ideal model delta sigma weight residual 111.69 103.91 7.78 1.23e+00 6.61e-01 4.00e+01 angle pdb=" N GLU D 147 " pdb=" CA GLU D 147 " pdb=" C GLU D 147 " ideal model delta sigma weight residual 112.54 105.73 6.81 1.22e+00 6.72e-01 3.11e+01 angle pdb=" N GLU C 147 " pdb=" CA GLU C 147 " pdb=" C GLU C 147 " ideal model delta sigma weight residual 112.54 105.75 6.79 1.22e+00 6.72e-01 3.09e+01 angle pdb=" N ILE B 41 " pdb=" CA ILE B 41 " pdb=" C ILE B 41 " ideal model delta sigma weight residual 111.44 104.21 7.23 1.34e+00 5.57e-01 2.91e+01 ... (remaining 11950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.97: 3890 19.97 - 39.94: 707 39.94 - 59.91: 384 59.91 - 79.88: 8 79.88 - 99.85: 4 Dihedral angle restraints: 4993 sinusoidal: 2661 harmonic: 2332 Sorted by residual: dihedral pdb=" C PHE A 207 " pdb=" N PHE A 207 " pdb=" CA PHE A 207 " pdb=" CB PHE A 207 " ideal model delta harmonic sigma weight residual -122.60 -133.85 11.25 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" C PHE B 207 " pdb=" N PHE B 207 " pdb=" CA PHE B 207 " pdb=" CB PHE B 207 " ideal model delta harmonic sigma weight residual -122.60 -133.83 11.23 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" CA ASN A 157 " pdb=" C ASN A 157 " pdb=" N VAL A 158 " pdb=" CA VAL A 158 " ideal model delta harmonic sigma weight residual 180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 4990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1006 0.082 - 0.165: 288 0.165 - 0.247: 63 0.247 - 0.329: 9 0.329 - 0.411: 5 Chirality restraints: 1371 Sorted by residual: chirality pdb=" C2' 2BA A 301 " pdb=" C1' 2BA A 301 " pdb=" C3' 2BA A 301 " pdb=" O2' 2BA A 301 " both_signs ideal model delta sigma weight residual False -2.80 -2.39 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C2' 2BA B 301 " pdb=" C1' 2BA B 301 " pdb=" C3' 2BA B 301 " pdb=" O2' 2BA B 301 " both_signs ideal model delta sigma weight residual False -2.80 -2.40 -0.41 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA PHE A 207 " pdb=" N PHE A 207 " pdb=" C PHE A 207 " pdb=" CB PHE A 207 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 1368 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 64 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ILE B 64 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE B 64 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 65 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 70 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.91e+00 pdb=" C GLY A 70 " -0.052 2.00e-02 2.50e+03 pdb=" O GLY A 70 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 71 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT F 19 " 0.001 2.00e-02 2.50e+03 1.84e-02 8.49e+00 pdb=" N1 DT F 19 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DT F 19 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT F 19 " -0.030 2.00e-02 2.50e+03 pdb=" N3 DT F 19 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DT F 19 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT F 19 " 0.015 2.00e-02 2.50e+03 pdb=" C5 DT F 19 " 0.006 2.00e-02 2.50e+03 pdb=" C7 DT F 19 " -0.037 2.00e-02 2.50e+03 pdb=" C6 DT F 19 " 0.016 2.00e-02 2.50e+03 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 2691 2.85 - 3.36: 7794 3.36 - 3.87: 14992 3.87 - 4.39: 16894 4.39 - 4.90: 25967 Nonbonded interactions: 68338 Sorted by model distance: nonbonded pdb=" NZ LYS A 98 " pdb=" OD1 ASP B 120 " model vdw 2.334 2.520 nonbonded pdb=" OD1 ASP B 28 " pdb=" N TYR B 29 " model vdw 2.334 2.520 nonbonded pdb=" O ALA D 107 " pdb=" OE1 GLU D 111 " model vdw 2.381 3.040 nonbonded pdb=" O LEU A 85 " pdb=" OE1 GLU A 89 " model vdw 2.407 3.040 nonbonded pdb=" O LEU C 123 " pdb=" OG1 THR C 126 " model vdw 2.432 2.440 ... (remaining 68333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 13 through 209) selection = (chain 'B' and resid 13 through 209) selection = (chain 'C' and resid 13 through 209) selection = (chain 'D' and resid 13 through 209) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.830 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.450 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.011 0.194 8547 Z= 0.626 Angle : 1.273 11.360 11955 Z= 0.870 Chirality : 0.079 0.411 1371 Planarity : 0.005 0.038 1203 Dihedral : 23.029 99.849 3489 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.29 % Allowed : 3.80 % Favored : 95.91 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.30), residues: 796 helix: 1.86 (0.24), residues: 431 sheet: -1.60 (0.54), residues: 72 loop : -1.23 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP B 159 HIS 0.004 0.001 HIS C 148 PHE 0.019 0.002 PHE A 122 TYR 0.025 0.002 TYR A 206 ARG 0.008 0.001 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8328 (tp30) cc_final: 0.7813 (tp30) REVERT: A 189 ASP cc_start: 0.8403 (m-30) cc_final: 0.7805 (m-30) REVERT: A 207 PHE cc_start: 0.8466 (m-80) cc_final: 0.7293 (m-10) REVERT: B 110 GLN cc_start: 0.8990 (mt0) cc_final: 0.8499 (mp10) REVERT: B 121 ASP cc_start: 0.9039 (t70) cc_final: 0.8564 (t70) REVERT: B 133 TYR cc_start: 0.8332 (p90) cc_final: 0.7764 (p90) REVERT: B 189 ASP cc_start: 0.7421 (m-30) cc_final: 0.7178 (m-30) REVERT: B 191 ILE cc_start: 0.9263 (mt) cc_final: 0.8893 (mt) REVERT: C 190 HIS cc_start: 0.8223 (m-70) cc_final: 0.7519 (m170) REVERT: D 26 ASN cc_start: 0.9392 (t0) cc_final: 0.8860 (t0) REVERT: D 28 ASP cc_start: 0.8251 (m-30) cc_final: 0.7360 (m-30) REVERT: D 142 VAL cc_start: 0.8832 (m) cc_final: 0.8517 (p) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.2402 time to fit residues: 58.4457 Evaluate side-chains 83 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 GLN B 161 GLN B 171 HIS C 26 ASN C 57 ASN C 69 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8547 Z= 0.218 Angle : 0.602 6.320 11955 Z= 0.357 Chirality : 0.040 0.320 1371 Planarity : 0.004 0.049 1203 Dihedral : 24.800 98.659 1969 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.15 % Allowed : 4.97 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.30), residues: 796 helix: 2.22 (0.24), residues: 429 sheet: -1.07 (0.55), residues: 68 loop : -1.07 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 159 HIS 0.017 0.001 HIS A 171 PHE 0.021 0.002 PHE C 207 TYR 0.017 0.002 TYR D 200 ARG 0.007 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 PHE cc_start: 0.8532 (m-80) cc_final: 0.8069 (m-10) REVERT: B 110 GLN cc_start: 0.8967 (mt0) cc_final: 0.8467 (mp10) REVERT: B 121 ASP cc_start: 0.9102 (t70) cc_final: 0.8364 (t0) REVERT: B 133 TYR cc_start: 0.8273 (p90) cc_final: 0.7838 (p90) REVERT: C 112 MET cc_start: 0.8138 (tpp) cc_final: 0.7916 (tpp) REVERT: C 162 THR cc_start: 0.8703 (p) cc_final: 0.8262 (t) REVERT: C 190 HIS cc_start: 0.7905 (m-70) cc_final: 0.7445 (m170) REVERT: C 192 PHE cc_start: 0.9006 (m-80) cc_final: 0.8725 (m-80) REVERT: D 26 ASN cc_start: 0.9462 (t0) cc_final: 0.9181 (t0) REVERT: D 28 ASP cc_start: 0.8283 (m-30) cc_final: 0.7971 (m-30) REVERT: D 142 VAL cc_start: 0.8828 (m) cc_final: 0.8519 (p) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.2003 time to fit residues: 32.5693 Evaluate side-chains 73 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 148 HIS B 171 HIS ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN D 57 ASN D 92 HIS D 108 GLN ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8547 Z= 0.236 Angle : 0.574 5.419 11955 Z= 0.337 Chirality : 0.038 0.147 1371 Planarity : 0.004 0.048 1203 Dihedral : 24.563 86.889 1969 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.44 % Allowed : 3.95 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.30), residues: 796 helix: 2.38 (0.24), residues: 427 sheet: -0.64 (0.59), residues: 70 loop : -0.96 (0.37), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 159 HIS 0.009 0.001 HIS A 171 PHE 0.018 0.002 PHE A 122 TYR 0.021 0.002 TYR C 206 ARG 0.007 0.001 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 THR cc_start: 0.8814 (p) cc_final: 0.8213 (p) REVERT: A 167 VAL cc_start: 0.9428 (t) cc_final: 0.9202 (m) REVERT: A 203 MET cc_start: 0.8991 (tpp) cc_final: 0.8309 (tpp) REVERT: A 207 PHE cc_start: 0.8515 (m-80) cc_final: 0.8057 (m-10) REVERT: B 133 TYR cc_start: 0.8388 (p90) cc_final: 0.8055 (p90) REVERT: B 189 ASP cc_start: 0.7893 (m-30) cc_final: 0.7675 (m-30) REVERT: C 193 PHE cc_start: 0.8717 (p90) cc_final: 0.8055 (p90) REVERT: D 26 ASN cc_start: 0.9382 (t0) cc_final: 0.9052 (t0) REVERT: D 28 ASP cc_start: 0.8299 (m-30) cc_final: 0.7846 (m-30) outliers start: 3 outliers final: 0 residues processed: 97 average time/residue: 0.2054 time to fit residues: 28.2707 Evaluate side-chains 71 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN B 171 HIS ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN D 92 HIS ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 8547 Z= 0.291 Angle : 0.595 5.708 11955 Z= 0.346 Chirality : 0.040 0.153 1371 Planarity : 0.004 0.045 1203 Dihedral : 23.964 72.533 1969 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.15 % Allowed : 4.68 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.30), residues: 796 helix: 2.10 (0.24), residues: 426 sheet: -0.27 (0.64), residues: 69 loop : -0.91 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 159 HIS 0.012 0.001 HIS A 171 PHE 0.019 0.002 PHE A 122 TYR 0.018 0.002 TYR A 13 ARG 0.005 0.001 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.9091 (tpp) cc_final: 0.8433 (tpp) REVERT: A 207 PHE cc_start: 0.8452 (m-80) cc_final: 0.8080 (m-10) REVERT: B 171 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.7307 (t-90) REVERT: D 26 ASN cc_start: 0.9311 (t0) cc_final: 0.8918 (t0) REVERT: D 28 ASP cc_start: 0.8282 (m-30) cc_final: 0.7726 (m-30) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.2062 time to fit residues: 23.9476 Evaluate side-chains 54 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 0.0050 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8547 Z= 0.171 Angle : 0.524 7.270 11955 Z= 0.306 Chirality : 0.038 0.162 1371 Planarity : 0.003 0.044 1203 Dihedral : 23.584 67.644 1969 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.31), residues: 796 helix: 2.39 (0.24), residues: 427 sheet: -0.19 (0.66), residues: 68 loop : -0.78 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 159 HIS 0.008 0.001 HIS A 171 PHE 0.014 0.001 PHE A 122 TYR 0.017 0.001 TYR C 206 ARG 0.005 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.9014 (tpp) cc_final: 0.8370 (tpp) REVERT: A 207 PHE cc_start: 0.8346 (m-80) cc_final: 0.7981 (m-10) REVERT: B 121 ASP cc_start: 0.8934 (t70) cc_final: 0.8509 (t70) REVERT: C 57 ASN cc_start: 0.8667 (m110) cc_final: 0.8406 (m-40) REVERT: D 26 ASN cc_start: 0.9307 (t0) cc_final: 0.8913 (t0) REVERT: D 28 ASP cc_start: 0.8298 (m-30) cc_final: 0.7686 (m-30) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2122 time to fit residues: 27.0222 Evaluate side-chains 62 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8547 Z= 0.283 Angle : 0.574 6.776 11955 Z= 0.334 Chirality : 0.040 0.153 1371 Planarity : 0.003 0.043 1203 Dihedral : 23.198 62.422 1969 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.31), residues: 796 helix: 2.21 (0.24), residues: 427 sheet: -0.03 (0.67), residues: 68 loop : -0.80 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 159 HIS 0.010 0.001 HIS A 171 PHE 0.018 0.002 PHE D 207 TYR 0.017 0.002 TYR A 13 ARG 0.008 0.001 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.9066 (tpp) cc_final: 0.8587 (tpp) REVERT: A 207 PHE cc_start: 0.8400 (m-80) cc_final: 0.8017 (m-10) REVERT: C 57 ASN cc_start: 0.8681 (m110) cc_final: 0.8429 (m-40) REVERT: C 190 HIS cc_start: 0.7967 (m-70) cc_final: 0.7760 (m170) REVERT: C 193 PHE cc_start: 0.8971 (p90) cc_final: 0.8560 (p90) REVERT: C 200 TYR cc_start: 0.8699 (t80) cc_final: 0.8215 (t80) REVERT: D 26 ASN cc_start: 0.9303 (t0) cc_final: 0.8875 (t0) REVERT: D 28 ASP cc_start: 0.8387 (m-30) cc_final: 0.7708 (m-30) REVERT: D 58 ILE cc_start: 0.8106 (mt) cc_final: 0.7896 (mt) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2015 time to fit residues: 24.1014 Evaluate side-chains 60 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 52 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8547 Z= 0.177 Angle : 0.517 7.670 11955 Z= 0.303 Chirality : 0.038 0.158 1371 Planarity : 0.003 0.043 1203 Dihedral : 23.104 59.897 1969 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.31), residues: 796 helix: 2.33 (0.24), residues: 427 sheet: 0.07 (0.67), residues: 68 loop : -0.74 (0.38), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 159 HIS 0.008 0.001 HIS B 171 PHE 0.017 0.001 PHE C 175 TYR 0.018 0.001 TYR C 206 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.9032 (tpp) cc_final: 0.8579 (tpp) REVERT: A 207 PHE cc_start: 0.8350 (m-80) cc_final: 0.7928 (m-10) REVERT: C 57 ASN cc_start: 0.8628 (m110) cc_final: 0.8351 (m-40) REVERT: C 112 MET cc_start: 0.8117 (tpp) cc_final: 0.7740 (tpp) REVERT: C 190 HIS cc_start: 0.8011 (m-70) cc_final: 0.7807 (m170) REVERT: D 26 ASN cc_start: 0.9276 (t0) cc_final: 0.8861 (t0) REVERT: D 28 ASP cc_start: 0.8371 (m-30) cc_final: 0.7658 (m-30) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2221 time to fit residues: 26.0352 Evaluate side-chains 63 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8547 Z= 0.217 Angle : 0.535 6.774 11955 Z= 0.312 Chirality : 0.038 0.148 1371 Planarity : 0.003 0.042 1203 Dihedral : 22.913 59.990 1969 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.31), residues: 796 helix: 2.30 (0.24), residues: 433 sheet: 0.05 (0.67), residues: 68 loop : -0.76 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 159 HIS 0.008 0.001 HIS B 171 PHE 0.013 0.002 PHE D 207 TYR 0.013 0.001 TYR A 13 ARG 0.002 0.000 ARG C 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 199 VAL cc_start: 0.9104 (t) cc_final: 0.8900 (t) REVERT: A 203 MET cc_start: 0.9050 (tpp) cc_final: 0.8583 (tpp) REVERT: A 207 PHE cc_start: 0.8362 (m-80) cc_final: 0.7924 (m-10) REVERT: C 57 ASN cc_start: 0.8655 (m110) cc_final: 0.8398 (m-40) REVERT: C 86 ASN cc_start: 0.8618 (m110) cc_final: 0.8186 (m110) REVERT: C 112 MET cc_start: 0.8236 (tpp) cc_final: 0.7730 (tpp) REVERT: D 26 ASN cc_start: 0.9288 (t0) cc_final: 0.8855 (t0) REVERT: D 28 ASP cc_start: 0.8417 (m-30) cc_final: 0.7673 (m-30) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2197 time to fit residues: 25.7132 Evaluate side-chains 61 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 0.2980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN D 46 ASN ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8547 Z= 0.199 Angle : 0.524 6.112 11955 Z= 0.307 Chirality : 0.038 0.146 1371 Planarity : 0.003 0.043 1203 Dihedral : 22.801 59.866 1969 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.15 % Allowed : 1.17 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.31), residues: 796 helix: 2.24 (0.24), residues: 434 sheet: -0.06 (0.67), residues: 68 loop : -0.70 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 159 HIS 0.007 0.001 HIS B 171 PHE 0.018 0.001 PHE C 175 TYR 0.012 0.001 TYR B 13 ARG 0.003 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.9052 (tpp) cc_final: 0.8682 (tpp) REVERT: A 207 PHE cc_start: 0.8336 (m-80) cc_final: 0.7962 (m-10) REVERT: C 57 ASN cc_start: 0.8629 (m110) cc_final: 0.8360 (m-40) REVERT: C 86 ASN cc_start: 0.8599 (m110) cc_final: 0.8260 (m110) REVERT: C 112 MET cc_start: 0.8227 (tpp) cc_final: 0.7808 (tpp) REVERT: D 26 ASN cc_start: 0.9287 (t0) cc_final: 0.8813 (t0) REVERT: D 28 ASP cc_start: 0.8408 (m-30) cc_final: 0.7641 (m-30) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1901 time to fit residues: 22.0131 Evaluate side-chains 60 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 73 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.0870 chunk 10 optimal weight: 0.0670 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN D 92 HIS ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8547 Z= 0.155 Angle : 0.506 6.791 11955 Z= 0.295 Chirality : 0.037 0.142 1371 Planarity : 0.003 0.043 1203 Dihedral : 22.695 59.828 1969 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.31), residues: 796 helix: 2.35 (0.25), residues: 434 sheet: -0.07 (0.68), residues: 67 loop : -0.69 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 159 HIS 0.006 0.001 HIS B 171 PHE 0.008 0.001 PHE D 192 TYR 0.018 0.001 TYR C 206 ARG 0.002 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1592 Ramachandran restraints generated. 796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.9046 (tpp) cc_final: 0.8659 (tpp) REVERT: A 207 PHE cc_start: 0.8289 (m-80) cc_final: 0.7887 (m-10) REVERT: A 208 ASN cc_start: 0.8473 (t0) cc_final: 0.8257 (t0) REVERT: B 124 LEU cc_start: 0.8838 (mm) cc_final: 0.8401 (tp) REVERT: C 86 ASN cc_start: 0.8447 (m110) cc_final: 0.8206 (m110) REVERT: C 112 MET cc_start: 0.8190 (tpp) cc_final: 0.7814 (tpp) REVERT: C 200 TYR cc_start: 0.8832 (t80) cc_final: 0.8579 (t80) REVERT: C 202 ARG cc_start: 0.8649 (mmm-85) cc_final: 0.8290 (mmm160) REVERT: D 26 ASN cc_start: 0.9296 (t0) cc_final: 0.8828 (t0) REVERT: D 28 ASP cc_start: 0.8425 (m-30) cc_final: 0.7628 (m-30) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2110 time to fit residues: 26.9009 Evaluate side-chains 70 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN D 46 ASN ** D 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.058790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.046558 restraints weight = 36647.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.048085 restraints weight = 20759.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.049122 restraints weight = 13904.652| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8547 Z= 0.178 Angle : 0.504 5.550 11955 Z= 0.295 Chirality : 0.037 0.146 1371 Planarity : 0.003 0.043 1203 Dihedral : 22.588 59.551 1969 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.31), residues: 796 helix: 2.41 (0.25), residues: 428 sheet: -0.27 (0.67), residues: 70 loop : -0.66 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 159 HIS 0.007 0.001 HIS A 171 PHE 0.018 0.001 PHE C 175 TYR 0.013 0.001 TYR B 13 ARG 0.003 0.000 ARG A 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1610.44 seconds wall clock time: 30 minutes 29.06 seconds (1829.06 seconds total)