Starting phenix.real_space_refine on Sat Mar 16 00:13:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/03_2024/7uml_26603.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/03_2024/7uml_26603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/03_2024/7uml_26603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/03_2024/7uml_26603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/03_2024/7uml_26603.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uml_26603/03_2024/7uml_26603.pdb" } resolution = 3.5 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= 0.053 sd= 1.358 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 P 13 5.49 5 S 37 5.16 5 C 4272 2.51 5 N 1126 2.21 5 O 1302 1.98 5 H 6477 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13227 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 5980 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 361} Chain breaks: 1 Chain: "B" Number of atoms: 2741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2741 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "C" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2770 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 551 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 4, 'TRANS': 29} Chain: "E" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 531 Classifications: {'peptide': 39} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 34} Chain: "F" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 263 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "R" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 391 Classifications: {'RNA': 13} Modifications used: {'3*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 11} Time building chain proxies: 6.75, per 1000 atoms: 0.51 Number of scatterers: 13227 At special positions: 0 Unit cell: (143.65, 100.3, 114.75, 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) S 37 16.00 P 13 15.00 O 1302 8.00 N 1126 7.00 C 4272 6.00 H 6477 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1516 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 38.2% alpha, 13.5% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 28 through 33 removed outlier: 3.732A pdb=" N PHE A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 62 removed outlier: 3.636A pdb=" N LYS A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.539A pdb=" N VAL A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 149 through 169 removed outlier: 4.075A pdb=" N THR A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 189 through 205 Processing helix chain 'A' and resid 210 through 221 removed outlier: 4.623A pdb=" N ILE A 218 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 220 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 221 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 323 through 341 removed outlier: 4.412A pdb=" N LEU A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 390 through 401 Processing helix chain 'A' and resid 411 through 420 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 101 through 115 removed outlier: 3.718A pdb=" N ASN B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 removed outlier: 3.755A pdb=" N LEU B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 201 through 208 removed outlier: 3.571A pdb=" N PHE B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.733A pdb=" N VAL C 84 " --> pdb=" O THR C 80 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 119 through 125 removed outlier: 3.593A pdb=" N LEU C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 removed outlier: 3.550A pdb=" N HIS C 192 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE C 193 " --> pdb=" O TRP C 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 193' Processing helix chain 'C' and resid 200 through 209 Processing helix chain 'D' and resid 27 through 35 removed outlier: 4.510A pdb=" N TYR D 31 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42 removed outlier: 6.420A pdb=" N LEU A 40 " --> pdb=" O LYS A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 90 Processing sheet with id=AA3, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'B' and resid 211 through 213 removed outlier: 6.959A pdb=" N ILE B 211 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 130 through 143 Processing sheet with id=AA6, first strand: chain 'D' and resid 13 through 14 removed outlier: 3.578A pdb=" N ILE D 14 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL D 5 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS E 349 " --> pdb=" O LYS D 6 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 4.12 Time building geometry restraints manager: 9.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6470 1.03 - 1.23: 22 1.23 - 1.42: 3001 1.42 - 1.62: 3863 1.62 - 1.81: 67 Bond restraints: 13423 Sorted by residual: bond pdb=" CA PHE B 198 " pdb=" CB PHE B 198 " ideal model delta sigma weight residual 1.530 1.551 -0.020 1.69e-02 3.50e+03 1.46e+00 bond pdb=" N GLY C 146 " pdb=" CA GLY C 146 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.88e-01 bond pdb=" CA PHE A 182 " pdb=" CB PHE A 182 " ideal model delta sigma weight residual 1.533 1.547 -0.014 1.66e-02 3.63e+03 6.66e-01 bond pdb=" C ASN B 75 " pdb=" N ARG B 76 " ideal model delta sigma weight residual 1.331 1.348 -0.017 2.07e-02 2.33e+03 6.56e-01 bond pdb=" CB PHE B 78 " pdb=" CG PHE B 78 " ideal model delta sigma weight residual 1.502 1.484 0.018 2.30e-02 1.89e+03 6.44e-01 ... (remaining 13418 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.69: 322 106.69 - 113.51: 15450 113.51 - 120.33: 4505 120.33 - 127.15: 3839 127.15 - 133.97: 89 Bond angle restraints: 24205 Sorted by residual: angle pdb=" C SER C 224 " pdb=" N ILE C 225 " pdb=" CA ILE C 225 " ideal model delta sigma weight residual 121.97 129.52 -7.55 1.80e+00 3.09e-01 1.76e+01 angle pdb=" N ILE C 225 " pdb=" CA ILE C 225 " pdb=" C ILE C 225 " ideal model delta sigma weight residual 109.34 102.84 6.50 2.08e+00 2.31e-01 9.78e+00 angle pdb=" C ASP A 85 " pdb=" N LYS A 86 " pdb=" CA LYS A 86 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.91e+00 angle pdb=" C LYS B 197 " pdb=" N PHE B 198 " pdb=" CA PHE B 198 " ideal model delta sigma weight residual 121.54 127.06 -5.52 1.91e+00 2.74e-01 8.37e+00 angle pdb=" N PHE B 198 " pdb=" CA PHE B 198 " pdb=" CB PHE B 198 " ideal model delta sigma weight residual 110.49 115.35 -4.86 1.69e+00 3.50e-01 8.27e+00 ... (remaining 24200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 6170 34.69 - 69.38: 237 69.38 - 104.07: 6 104.07 - 138.76: 1 138.76 - 173.45: 1 Dihedral angle restraints: 6415 sinusoidal: 3523 harmonic: 2892 Sorted by residual: dihedral pdb=" CA ILE C 225 " pdb=" C ILE C 225 " pdb=" N SER C 226 " pdb=" CA SER C 226 " ideal model delta harmonic sigma weight residual -180.00 -133.49 -46.51 0 5.00e+00 4.00e-02 8.65e+01 dihedral pdb=" O4' U R 36 " pdb=" C1' U R 36 " pdb=" N1 U R 36 " pdb=" C2 U R 36 " ideal model delta sinusoidal sigma weight residual -160.00 13.45 -173.45 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U R 27 " pdb=" C1' U R 27 " pdb=" N1 U R 27 " pdb=" C2 U R 27 " ideal model delta sinusoidal sigma weight residual -160.00 -26.98 -133.02 1 1.50e+01 4.44e-03 7.18e+01 ... (remaining 6412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 703 0.034 - 0.068: 223 0.068 - 0.102: 57 0.102 - 0.135: 26 0.135 - 0.169: 6 Chirality restraints: 1015 Sorted by residual: chirality pdb=" C1' U R 36 " pdb=" O4' U R 36 " pdb=" C2' U R 36 " pdb=" N1 U R 36 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA ILE C 225 " pdb=" N ILE C 225 " pdb=" C ILE C 225 " pdb=" CB ILE C 225 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA VAL B 68 " pdb=" N VAL B 68 " pdb=" C VAL B 68 " pdb=" CB VAL B 68 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 1012 not shown) Planarity restraints: 1933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 197 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C LYS B 197 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS B 197 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE B 198 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 128 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO C 129 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 160 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO B 161 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 161 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 161 " -0.026 5.00e-02 4.00e+02 ... (remaining 1930 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1020 2.21 - 2.81: 26688 2.81 - 3.41: 33005 3.41 - 4.00: 42734 4.00 - 4.60: 65211 Nonbonded interactions: 168658 Sorted by model distance: nonbonded pdb=" HE1 TRP B 190 " pdb=" O TRP B 220 " model vdw 1.616 1.850 nonbonded pdb=" HH TYR A 152 " pdb=" OP2 U R 35 " model vdw 1.618 1.850 nonbonded pdb=" H SER A 291 " pdb=" OP2 U R 31 " model vdw 1.644 1.850 nonbonded pdb=" O ARG D 7 " pdb=" H ASN D 11 " model vdw 1.659 1.850 nonbonded pdb=" OE1 GLN E 346 " pdb=" H TYR E 355 " model vdw 1.682 1.850 ... (remaining 168653 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 'B' and ((resid 58 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 59 through 227)) selection = (chain 'C' and resid 58 through 227) } 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=0.50 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: 0.890 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: 0.200 Extract box with map and model: 4.090 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 45.040 Find NCS groups from input model: 0.270 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 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 : 0.003 0.024 6946 Z= 0.166 Angle : 0.579 7.548 9448 Z= 0.314 Chirality : 0.040 0.169 1015 Planarity : 0.005 0.051 1173 Dihedral : 16.391 173.453 2661 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.63 % Allowed : 2.01 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 2.22 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.27), residues: 798 helix: -0.80 (0.30), residues: 273 sheet: -0.74 (0.49), residues: 99 loop : -2.91 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 88 HIS 0.003 0.001 HIS A 298 PHE 0.013 0.001 PHE C 208 TYR 0.014 0.001 TYR B 178 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 TYR cc_start: 0.7194 (m-10) cc_final: 0.6984 (m-10) REVERT: C 188 MET cc_start: 0.6581 (mmp) cc_final: 0.6269 (mmt) REVERT: D 4 THR cc_start: 0.8169 (p) cc_final: 0.7964 (t) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.4306 time to fit residues: 98.9440 Evaluate side-chains 132 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7099 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6946 Z= 0.297 Angle : 0.611 4.970 9448 Z= 0.328 Chirality : 0.041 0.164 1015 Planarity : 0.005 0.042 1173 Dihedral : 14.878 171.310 1096 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.77 % Favored : 90.60 % Rotamer: Outliers : 2.30 % Allowed : 8.78 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.28), residues: 798 helix: -0.37 (0.30), residues: 284 sheet: -0.72 (0.45), residues: 119 loop : -2.97 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 248 HIS 0.004 0.001 HIS B 192 PHE 0.012 0.002 PHE B 110 TYR 0.012 0.002 TYR C 178 ARG 0.003 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ASP cc_start: 0.6033 (p0) cc_final: 0.5504 (p0) REVERT: B 92 ASP cc_start: 0.7681 (p0) cc_final: 0.7353 (p0) REVERT: C 188 MET cc_start: 0.6633 (mmp) cc_final: 0.6263 (mmt) REVERT: D 4 THR cc_start: 0.8144 (p) cc_final: 0.7932 (t) outliers start: 16 outliers final: 14 residues processed: 146 average time/residue: 0.4021 time to fit residues: 77.5810 Evaluate side-chains 145 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 23 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.7072 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6946 Z= 0.203 Angle : 0.552 5.093 9448 Z= 0.294 Chirality : 0.039 0.182 1015 Planarity : 0.005 0.037 1173 Dihedral : 14.707 174.243 1096 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.52 % Favored : 92.11 % Rotamer: Outliers : 2.30 % Allowed : 11.80 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.28), residues: 798 helix: 0.04 (0.32), residues: 278 sheet: -0.78 (0.44), residues: 119 loop : -2.77 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 88 HIS 0.002 0.001 HIS A 298 PHE 0.013 0.001 PHE B 110 TYR 0.010 0.001 TYR A 277 ARG 0.003 0.000 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.7718 (p0) cc_final: 0.7388 (p0) REVERT: C 188 MET cc_start: 0.6621 (mmp) cc_final: 0.6192 (mmt) outliers start: 16 outliers final: 16 residues processed: 143 average time/residue: 0.4085 time to fit residues: 77.0912 Evaluate side-chains 145 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 23 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6946 Z= 0.213 Angle : 0.544 4.652 9448 Z= 0.288 Chirality : 0.039 0.180 1015 Planarity : 0.004 0.038 1173 Dihedral : 14.583 172.782 1096 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.27 % Favored : 90.23 % Rotamer: Outliers : 2.88 % Allowed : 13.81 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.29), residues: 798 helix: 0.16 (0.32), residues: 279 sheet: -0.77 (0.44), residues: 119 loop : -2.73 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 248 HIS 0.002 0.001 HIS B 192 PHE 0.014 0.001 PHE B 110 TYR 0.011 0.001 TYR A 277 ARG 0.005 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.7774 (p0) cc_final: 0.7448 (p0) REVERT: C 188 MET cc_start: 0.6609 (mmp) cc_final: 0.6086 (mmt) outliers start: 20 outliers final: 17 residues processed: 140 average time/residue: 0.3968 time to fit residues: 73.4791 Evaluate side-chains 145 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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: 0.7141 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6946 Z= 0.268 Angle : 0.575 5.001 9448 Z= 0.306 Chirality : 0.040 0.180 1015 Planarity : 0.005 0.037 1173 Dihedral : 14.571 172.580 1096 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.65 % Favored : 88.85 % Rotamer: Outliers : 3.02 % Allowed : 14.96 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.28), residues: 798 helix: 0.08 (0.32), residues: 279 sheet: -0.79 (0.45), residues: 119 loop : -2.75 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 248 HIS 0.003 0.001 HIS B 192 PHE 0.011 0.001 PHE B 110 TYR 0.013 0.001 TYR B 140 ARG 0.003 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.7792 (p0) cc_final: 0.7483 (p0) REVERT: C 188 MET cc_start: 0.6632 (mmp) cc_final: 0.6037 (mmt) outliers start: 21 outliers final: 21 residues processed: 139 average time/residue: 0.4025 time to fit residues: 74.5233 Evaluate side-chains 146 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 125 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.7072 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6946 Z= 0.167 Angle : 0.527 4.420 9448 Z= 0.277 Chirality : 0.039 0.186 1015 Planarity : 0.004 0.038 1173 Dihedral : 14.478 174.432 1096 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.90 % Favored : 90.60 % Rotamer: Outliers : 2.30 % Allowed : 16.55 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.74 (0.29), residues: 798 helix: 0.34 (0.32), residues: 282 sheet: -0.69 (0.45), residues: 119 loop : -2.51 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 248 HIS 0.002 0.001 HIS A 298 PHE 0.010 0.001 PHE C 208 TYR 0.010 0.001 TYR A 277 ARG 0.002 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.7746 (p0) cc_final: 0.7422 (p0) REVERT: C 188 MET cc_start: 0.6546 (mmp) cc_final: 0.5927 (mmt) outliers start: 16 outliers final: 16 residues processed: 140 average time/residue: 0.4033 time to fit residues: 75.6226 Evaluate side-chains 143 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.0470 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.9880 ------------------------------------------------------------------------------- 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: 0.7083 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6946 Z= 0.182 Angle : 0.528 4.513 9448 Z= 0.276 Chirality : 0.039 0.175 1015 Planarity : 0.004 0.037 1173 Dihedral : 14.475 172.874 1096 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.65 % Favored : 89.85 % Rotamer: Outliers : 2.45 % Allowed : 16.40 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.64 (0.29), residues: 798 helix: 0.46 (0.32), residues: 284 sheet: -0.62 (0.46), residues: 119 loop : -2.51 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 248 HIS 0.002 0.001 HIS C 227 PHE 0.013 0.001 PHE B 110 TYR 0.012 0.001 TYR C 167 ARG 0.003 0.000 ARG E 373 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6352 (tmm) REVERT: B 92 ASP cc_start: 0.7728 (p0) cc_final: 0.7387 (p0) REVERT: C 188 MET cc_start: 0.6532 (mmp) cc_final: 0.5802 (mmt) outliers start: 17 outliers final: 14 residues processed: 143 average time/residue: 0.3935 time to fit residues: 74.8472 Evaluate side-chains 143 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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: 0.7100 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6946 Z= 0.201 Angle : 0.538 4.590 9448 Z= 0.282 Chirality : 0.039 0.172 1015 Planarity : 0.004 0.037 1173 Dihedral : 14.466 172.801 1096 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.77 % Favored : 89.72 % Rotamer: Outliers : 2.59 % Allowed : 16.69 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.70 (0.29), residues: 798 helix: 0.36 (0.32), residues: 291 sheet: -0.63 (0.46), residues: 119 loop : -2.56 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 248 HIS 0.002 0.001 HIS A 298 PHE 0.017 0.001 PHE B 110 TYR 0.017 0.001 TYR C 167 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6347 (tmm) REVERT: B 92 ASP cc_start: 0.7753 (p0) cc_final: 0.7415 (p0) REVERT: C 188 MET cc_start: 0.6550 (mmp) cc_final: 0.5808 (mmt) outliers start: 18 outliers final: 16 residues processed: 139 average time/residue: 0.4002 time to fit residues: 73.7713 Evaluate side-chains 147 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.7113 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6946 Z= 0.214 Angle : 0.544 4.619 9448 Z= 0.286 Chirality : 0.040 0.172 1015 Planarity : 0.004 0.038 1173 Dihedral : 14.472 172.621 1096 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.90 % Favored : 89.60 % Rotamer: Outliers : 2.73 % Allowed : 16.83 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.73 (0.29), residues: 798 helix: 0.35 (0.32), residues: 290 sheet: -0.71 (0.46), residues: 119 loop : -2.56 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 190 HIS 0.002 0.001 HIS A 298 PHE 0.015 0.001 PHE B 110 TYR 0.016 0.001 TYR C 167 ARG 0.005 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.7763 (p0) cc_final: 0.7420 (p0) REVERT: C 188 MET cc_start: 0.6558 (mmp) cc_final: 0.6003 (mmt) outliers start: 19 outliers final: 17 residues processed: 135 average time/residue: 0.4249 time to fit residues: 76.9336 Evaluate side-chains 142 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 19 optimal weight: 0.0070 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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: 0.7037 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6946 Z= 0.149 Angle : 0.523 4.947 9448 Z= 0.271 Chirality : 0.039 0.174 1015 Planarity : 0.004 0.039 1173 Dihedral : 14.440 174.150 1096 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.65 % Favored : 90.98 % Rotamer: Outliers : 2.01 % Allowed : 17.70 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.44 (0.30), residues: 798 helix: 0.67 (0.32), residues: 290 sheet: -0.49 (0.48), residues: 113 loop : -2.45 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 190 HIS 0.004 0.001 HIS C 143 PHE 0.016 0.001 PHE B 78 TYR 0.020 0.001 TYR C 167 ARG 0.002 0.000 ARG E 373 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.7628 (p0) cc_final: 0.7290 (p0) REVERT: C 188 MET cc_start: 0.6532 (mmp) cc_final: 0.5972 (mmt) outliers start: 14 outliers final: 13 residues processed: 134 average time/residue: 0.3769 time to fit residues: 67.2522 Evaluate side-chains 137 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 163 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 46 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.9980 chunk 62 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 0.0570 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.191815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165891 restraints weight = 31086.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.170573 restraints weight = 14019.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.173568 restraints weight = 8162.556| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4062 r_free = 0.4062 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4061 r_free = 0.4061 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6946 Z= 0.169 Angle : 0.533 4.679 9448 Z= 0.276 Chirality : 0.039 0.163 1015 Planarity : 0.005 0.090 1173 Dihedral : 14.454 172.649 1096 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.52 % Favored : 90.10 % Rotamer: Outliers : 1.58 % Allowed : 18.42 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -1.40 (0.30), residues: 798 helix: 0.67 (0.32), residues: 293 sheet: -0.40 (0.48), residues: 113 loop : -2.45 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 190 HIS 0.003 0.001 HIS A 298 PHE 0.028 0.001 PHE C 110 TYR 0.011 0.001 TYR A 277 ARG 0.006 0.000 ARG A 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3392.29 seconds wall clock time: 60 minutes 18.40 seconds (3618.40 seconds total)