Starting phenix.real_space_refine on Fri Apr 5 13:45:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/04_2024/5lii_4053.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/04_2024/5lii_4053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/04_2024/5lii_4053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/04_2024/5lii_4053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/04_2024/5lii_4053.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/04_2024/5lii_4053.pdb" } resolution = 3.8 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= 0.270 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: 4 Type Number sf(0) Gaussians S 11 5.16 5 C 1947 2.51 5 N 545 2.21 5 O 595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3098 Number of models: 1 Model: "" Number of chains: 1 Chain: "P" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3098 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 414} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 154 Time building chain proxies: 2.27, per 1000 atoms: 0.73 Number of scatterers: 3098 At special positions: 0 Unit cell: (66.24, 100.74, 97.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 11 16.00 O 595 8.00 N 545 7.00 C 1947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 569.7 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 806 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 5 sheets defined 11.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'P' and resid 63 through 68 Processing helix chain 'P' and resid 125 through 131 Processing helix chain 'P' and resid 137 through 159 removed outlier: 3.620A pdb=" N THR P 142 " --> pdb=" O SER P 138 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU P 154 " --> pdb=" O ALA P 150 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR P 159 " --> pdb=" O TRP P 155 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 210 removed outlier: 3.528A pdb=" N ASN P 201 " --> pdb=" O GLU P 197 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY P 210 " --> pdb=" O ARG P 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 70 through 72 removed outlier: 6.829A pdb=" N ARG P 71 " --> pdb=" O GLU P 418 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 82 through 84 Processing sheet with id=AA3, first strand: chain 'P' and resid 325 through 326 removed outlier: 3.509A pdb=" N SER P 326 " --> pdb=" O ILE P 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'P' and resid 348 through 350 Processing sheet with id=AA5, first strand: chain 'P' and resid 404 through 407 41 hydrogen bonds defined for protein. 114 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.64 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 542 1.27 - 1.41: 749 1.41 - 1.55: 1832 1.55 - 1.69: 3 1.69 - 1.83: 22 Bond restraints: 3148 Sorted by residual: bond pdb=" C ALA P 101 " pdb=" N PRO P 102 " ideal model delta sigma weight residual 1.334 1.134 0.200 2.34e-02 1.83e+03 7.32e+01 bond pdb=" CA MET P 409 " pdb=" CB MET P 409 " ideal model delta sigma weight residual 1.528 1.420 0.109 1.35e-02 5.49e+03 6.47e+01 bond pdb=" CB TYR P 441 " pdb=" CG TYR P 441 " ideal model delta sigma weight residual 1.512 1.445 0.067 2.20e-02 2.07e+03 9.31e+00 bond pdb=" CG LEU P 181 " pdb=" CD1 LEU P 181 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.04e+00 bond pdb=" CB PRO P 137 " pdb=" CG PRO P 137 " ideal model delta sigma weight residual 1.506 1.400 0.106 3.90e-02 6.57e+02 7.41e+00 ... (remaining 3143 not shown) Histogram of bond angle deviations from ideal: 65.95 - 85.26: 4 85.26 - 104.56: 78 104.56 - 123.86: 4090 123.86 - 143.16: 112 143.16 - 162.47: 2 Bond angle restraints: 4286 Sorted by residual: angle pdb=" N PRO P 399 " pdb=" CA PRO P 399 " pdb=" CB PRO P 399 " ideal model delta sigma weight residual 102.60 65.95 36.65 1.10e+00 8.26e-01 1.11e+03 angle pdb=" N VAL P 118 " pdb=" CA VAL P 118 " pdb=" CB VAL P 118 " ideal model delta sigma weight residual 110.49 78.16 32.33 1.15e+00 7.56e-01 7.90e+02 angle pdb=" N LEU P 398 " pdb=" CA LEU P 398 " pdb=" C LEU P 398 " ideal model delta sigma weight residual 107.91 149.33 -41.42 2.05e+00 2.38e-01 4.08e+02 angle pdb=" N PRO P 399 " pdb=" CD PRO P 399 " pdb=" CG PRO P 399 " ideal model delta sigma weight residual 103.80 79.83 23.97 1.20e+00 6.94e-01 3.99e+02 angle pdb=" N PRO P 399 " pdb=" CA PRO P 399 " pdb=" C PRO P 399 " ideal model delta sigma weight residual 112.10 162.47 -50.37 2.60e+00 1.48e-01 3.75e+02 ... (remaining 4281 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 10.87: 1509 10.87 - 21.73: 277 21.73 - 32.60: 73 32.60 - 43.46: 16 43.46 - 54.32: 6 Dihedral angle restraints: 1881 sinusoidal: 631 harmonic: 1250 Sorted by residual: dihedral pdb=" N VAL P 118 " pdb=" C VAL P 118 " pdb=" CA VAL P 118 " pdb=" CB VAL P 118 " ideal model delta harmonic sigma weight residual 123.40 88.32 35.08 0 2.50e+00 1.60e-01 1.97e+02 dihedral pdb=" CA LYS P 394 " pdb=" C LYS P 394 " pdb=" N ASN P 395 " pdb=" CA ASN P 395 " ideal model delta harmonic sigma weight residual 180.00 -129.42 -50.58 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" N LEU P 398 " pdb=" C LEU P 398 " pdb=" CA LEU P 398 " pdb=" CB LEU P 398 " ideal model delta harmonic sigma weight residual 122.80 144.26 -21.46 0 2.50e+00 1.60e-01 7.37e+01 ... (remaining 1878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.366: 500 0.366 - 0.732: 1 0.732 - 1.098: 1 1.098 - 1.464: 0 1.464 - 1.829: 2 Chirality restraints: 504 Sorted by residual: chirality pdb=" CA PRO P 399 " pdb=" N PRO P 399 " pdb=" C PRO P 399 " pdb=" CB PRO P 399 " both_signs ideal model delta sigma weight residual False 2.72 0.89 1.83 2.00e-01 2.50e+01 8.37e+01 chirality pdb=" CA LEU P 398 " pdb=" N LEU P 398 " pdb=" C LEU P 398 " pdb=" CB LEU P 398 " both_signs ideal model delta sigma weight residual False 2.51 0.99 1.52 2.00e-01 2.50e+01 5.79e+01 chirality pdb=" CA ASN P 133 " pdb=" N ASN P 133 " pdb=" C ASN P 133 " pdb=" CB ASN P 133 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 501 not shown) Planarity restraints: 564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU P 398 " 0.143 5.00e-02 4.00e+02 2.09e-01 7.02e+01 pdb=" N PRO P 399 " -0.359 5.00e-02 4.00e+02 pdb=" CA PRO P 399 " 0.147 5.00e-02 4.00e+02 pdb=" CD PRO P 399 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 261 " 0.029 2.00e-02 2.50e+03 2.01e-02 7.10e+00 pdb=" CG PHE P 261 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE P 261 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE P 261 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE P 261 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE P 261 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE P 261 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 256 " 0.023 2.00e-02 2.50e+03 1.86e-02 6.89e+00 pdb=" CG TYR P 256 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR P 256 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR P 256 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR P 256 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR P 256 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR P 256 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR P 256 " -0.001 2.00e-02 2.50e+03 ... (remaining 561 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 45 2.46 - 3.07: 2532 3.07 - 3.68: 4232 3.68 - 4.29: 5645 4.29 - 4.90: 8788 Nonbonded interactions: 21242 Sorted by model distance: nonbonded pdb=" O ASN P 229 " pdb=" OD1 ASN P 229 " model vdw 1.855 3.040 nonbonded pdb=" CE2 TYR P 117 " pdb=" CG2 THR P 152 " model vdw 1.987 3.760 nonbonded pdb=" O LEU P 398 " pdb=" CD PRO P 399 " model vdw 2.081 2.752 nonbonded pdb=" O GLY P 233 " pdb=" NH1 ARG P 234 " model vdw 2.082 2.520 nonbonded pdb=" OG SER P 75 " pdb=" O VAL P 78 " model vdw 2.093 2.440 ... (remaining 21237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.610 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.020 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 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 : 0.015 0.200 3148 Z= 0.963 Angle : 2.407 50.367 4286 Z= 1.473 Chirality : 0.139 1.829 504 Planarity : 0.012 0.209 564 Dihedral : 12.691 54.322 1075 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 42.83 Ramachandran Plot: Outliers : 1.16 % Allowed : 16.94 % Favored : 81.90 % Rotamer: Outliers : 1.41 % Allowed : 6.01 % Favored : 92.58 % Cbeta Deviations : 1.49 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 16.67 % Twisted General : 1.93 % 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: -6.10 (0.25), residues: 431 helix: -4.70 (0.36), residues: 55 sheet: -1.38 (0.90), residues: 28 loop : -4.65 (0.20), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP P 440 HIS 0.011 0.005 HIS P 86 PHE 0.044 0.006 PHE P 94 TYR 0.046 0.005 TYR P 256 ARG 0.010 0.002 ARG P 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 37 GLN cc_start: 0.8674 (pm20) cc_final: 0.8415 (pm20) REVERT: P 65 TYR cc_start: 0.8667 (t80) cc_final: 0.8349 (t80) REVERT: P 109 ARG cc_start: 0.7061 (mtp180) cc_final: 0.6511 (mtt90) REVERT: P 133 ASN cc_start: 0.7821 (m-40) cc_final: 0.7415 (m-40) REVERT: P 184 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7947 (mtpt) REVERT: P 268 THR cc_start: 0.8176 (p) cc_final: 0.7792 (p) REVERT: P 393 ASP cc_start: 0.7378 (m-30) cc_final: 0.7103 (m-30) REVERT: P 424 LYS cc_start: 0.8253 (ptmt) cc_final: 0.8004 (ptmt) outliers start: 4 outliers final: 2 residues processed: 84 average time/residue: 0.1566 time to fit residues: 15.9140 Evaluate side-chains 59 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 207 ILE Chi-restraints excluded: chain P residue 399 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 229 ASN ** P 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3148 Z= 0.209 Angle : 0.896 10.261 4286 Z= 0.475 Chirality : 0.049 0.190 504 Planarity : 0.006 0.074 564 Dihedral : 9.352 33.239 464 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.46 % Favored : 85.85 % Rotamer: Outliers : 5.30 % Allowed : 12.01 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.34 (0.30), residues: 431 helix: -2.61 (0.63), residues: 54 sheet: -0.87 (1.24), residues: 23 loop : -4.35 (0.23), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 452 HIS 0.003 0.001 HIS P 265 PHE 0.018 0.002 PHE P 373 TYR 0.022 0.003 TYR P 441 ARG 0.002 0.001 ARG P 459 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: P 37 GLN cc_start: 0.8670 (pm20) cc_final: 0.8258 (pm20) REVERT: P 154 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6291 (pm20) REVERT: P 184 LYS cc_start: 0.7500 (mtmm) cc_final: 0.7272 (mtpt) REVERT: P 219 MET cc_start: 0.6621 (tpp) cc_final: 0.6167 (mmt) REVERT: P 268 THR cc_start: 0.7903 (p) cc_final: 0.7389 (p) REVERT: P 431 ASN cc_start: 0.8052 (m-40) cc_final: 0.7680 (m-40) outliers start: 15 outliers final: 6 residues processed: 79 average time/residue: 0.1634 time to fit residues: 15.4493 Evaluate side-chains 62 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 433 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 3148 Z= 0.396 Angle : 1.000 11.433 4286 Z= 0.532 Chirality : 0.054 0.217 504 Planarity : 0.007 0.105 564 Dihedral : 9.305 27.278 459 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.70 % Allowed : 19.26 % Favored : 80.05 % Rotamer: Outliers : 7.77 % Allowed : 16.61 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -5.32 (0.32), residues: 431 helix: -2.58 (0.63), residues: 61 sheet: -0.19 (1.44), residues: 22 loop : -4.40 (0.23), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP P 452 HIS 0.005 0.002 HIS P 91 PHE 0.025 0.004 PHE P 261 TYR 0.027 0.004 TYR P 441 ARG 0.005 0.001 ARG P 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 60 time to evaluate : 0.375 Fit side-chains REVERT: P 71 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7674 (ptp-170) REVERT: P 93 ARG cc_start: 0.7810 (tpp80) cc_final: 0.7509 (tpp80) REVERT: P 154 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6577 (pm20) REVERT: P 198 LYS cc_start: 0.8539 (ttpp) cc_final: 0.6967 (tppt) REVERT: P 263 LYS cc_start: 0.7777 (pttm) cc_final: 0.7560 (ptpp) REVERT: P 431 ASN cc_start: 0.8516 (m-40) cc_final: 0.8097 (m-40) outliers start: 22 outliers final: 15 residues processed: 79 average time/residue: 0.1707 time to fit residues: 16.1741 Evaluate side-chains 72 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 181 LEU Chi-restraints excluded: chain P residue 183 ASP Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 388 THR Chi-restraints excluded: chain P residue 433 SER Chi-restraints excluded: chain P residue 454 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 0.0370 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 229 ASN P 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3148 Z= 0.177 Angle : 0.782 12.864 4286 Z= 0.403 Chirality : 0.045 0.149 504 Planarity : 0.006 0.090 564 Dihedral : 7.824 28.556 459 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.23 % Favored : 86.08 % Rotamer: Outliers : 8.83 % Allowed : 16.61 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -5.17 (0.31), residues: 431 helix: -2.44 (0.60), residues: 61 sheet: -0.66 (1.10), residues: 28 loop : -4.31 (0.24), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP P 57 HIS 0.002 0.001 HIS P 91 PHE 0.014 0.002 PHE P 373 TYR 0.015 0.002 TYR P 441 ARG 0.002 0.000 ARG P 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 64 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: P 37 GLN cc_start: 0.8633 (pm20) cc_final: 0.8187 (pm20) REVERT: P 93 ARG cc_start: 0.7732 (tpp80) cc_final: 0.7416 (tpp80) REVERT: P 154 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6384 (pm20) REVERT: P 263 LYS cc_start: 0.7838 (pttm) cc_final: 0.7392 (ptmm) REVERT: P 395 ASN cc_start: 0.4847 (t0) cc_final: 0.3678 (p0) REVERT: P 458 VAL cc_start: 0.6638 (OUTLIER) cc_final: 0.6412 (t) REVERT: P 459 ARG cc_start: 0.6912 (mtp-110) cc_final: 0.6632 (ttp-170) REVERT: P 460 TYR cc_start: 0.2997 (OUTLIER) cc_final: 0.0770 (p90) outliers start: 25 outliers final: 14 residues processed: 81 average time/residue: 0.1529 time to fit residues: 14.9651 Evaluate side-chains 71 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 54 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 161 ASP Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 433 SER Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Chi-restraints excluded: chain P residue 460 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 0.0030 chunk 28 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9792 ------------------------------------------------------------------------------- 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: 0.6671 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3148 Z= 0.208 Angle : 0.811 13.040 4286 Z= 0.414 Chirality : 0.045 0.160 504 Planarity : 0.006 0.088 564 Dihedral : 7.514 26.266 459 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.31 % Favored : 83.99 % Rotamer: Outliers : 8.48 % Allowed : 19.79 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.88 (0.32), residues: 431 helix: -1.92 (0.68), residues: 54 sheet: -0.25 (1.20), residues: 28 loop : -4.15 (0.24), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP P 57 HIS 0.002 0.001 HIS P 91 PHE 0.018 0.002 PHE P 373 TYR 0.019 0.002 TYR P 441 ARG 0.002 0.000 ARG P 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 0.364 Fit side-chains REVERT: P 30 TYR cc_start: 0.3616 (OUTLIER) cc_final: 0.3109 (m-80) REVERT: P 37 GLN cc_start: 0.8570 (pm20) cc_final: 0.8103 (pm20) REVERT: P 71 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7189 (ttm110) REVERT: P 154 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6353 (pm20) REVERT: P 173 LEU cc_start: 0.7502 (tp) cc_final: 0.7287 (tt) REVERT: P 198 LYS cc_start: 0.8449 (ttpp) cc_final: 0.6798 (tppt) REVERT: P 263 LYS cc_start: 0.7794 (pttm) cc_final: 0.7423 (ptmm) REVERT: P 371 MET cc_start: 0.5851 (mtt) cc_final: 0.5337 (mmm) REVERT: P 395 ASN cc_start: 0.4750 (t0) cc_final: 0.3865 (p0) REVERT: P 459 ARG cc_start: 0.6980 (mtp-110) cc_final: 0.6752 (ttp-170) REVERT: P 460 TYR cc_start: 0.3484 (OUTLIER) cc_final: 0.1122 (p90) outliers start: 24 outliers final: 18 residues processed: 75 average time/residue: 0.1778 time to fit residues: 15.8521 Evaluate side-chains 78 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 57 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 161 ASP Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 433 SER Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 460 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.0270 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3148 Z= 0.227 Angle : 0.809 13.222 4286 Z= 0.414 Chirality : 0.046 0.157 504 Planarity : 0.006 0.087 564 Dihedral : 7.485 26.521 459 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.70 % Allowed : 17.17 % Favored : 82.13 % Rotamer: Outliers : 8.83 % Allowed : 19.79 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.86 (0.33), residues: 431 helix: -2.31 (0.62), residues: 61 sheet: -0.13 (1.21), residues: 28 loop : -4.10 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP P 57 HIS 0.002 0.001 HIS P 91 PHE 0.016 0.002 PHE P 261 TYR 0.018 0.003 TYR P 441 ARG 0.002 0.000 ARG P 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 61 time to evaluate : 0.333 Fit side-chains REVERT: P 30 TYR cc_start: 0.3569 (OUTLIER) cc_final: 0.3173 (m-10) REVERT: P 37 GLN cc_start: 0.8559 (pm20) cc_final: 0.8088 (pm20) REVERT: P 71 ARG cc_start: 0.7779 (mtm110) cc_final: 0.7402 (ttm110) REVERT: P 154 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6392 (pm20) REVERT: P 263 LYS cc_start: 0.7891 (pttm) cc_final: 0.7517 (ptmm) REVERT: P 371 MET cc_start: 0.5877 (mtt) cc_final: 0.5547 (mmm) REVERT: P 395 ASN cc_start: 0.5191 (t0) cc_final: 0.3839 (p0) REVERT: P 458 VAL cc_start: 0.6619 (OUTLIER) cc_final: 0.6352 (t) REVERT: P 459 ARG cc_start: 0.7024 (mtp-110) cc_final: 0.6683 (ttp-170) REVERT: P 460 TYR cc_start: 0.2896 (OUTLIER) cc_final: 0.0467 (p90) outliers start: 25 outliers final: 18 residues processed: 78 average time/residue: 0.1386 time to fit residues: 13.2530 Evaluate side-chains 81 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 59 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 126 ILE Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 161 ASP Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Chi-restraints excluded: chain P residue 460 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 0.2980 chunk 35 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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: 0.6577 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3148 Z= 0.161 Angle : 0.755 13.361 4286 Z= 0.376 Chirality : 0.043 0.137 504 Planarity : 0.006 0.081 564 Dihedral : 6.769 25.532 459 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.69 % Favored : 85.61 % Rotamer: Outliers : 8.83 % Allowed : 20.49 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.54 (0.33), residues: 431 helix: -1.82 (0.67), residues: 55 sheet: -0.35 (1.12), residues: 28 loop : -3.85 (0.26), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP P 57 HIS 0.002 0.001 HIS P 415 PHE 0.013 0.002 PHE P 373 TYR 0.013 0.002 TYR P 218 ARG 0.001 0.000 ARG P 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 61 time to evaluate : 0.356 Fit side-chains REVERT: P 30 TYR cc_start: 0.3614 (OUTLIER) cc_final: 0.3045 (m-80) REVERT: P 37 GLN cc_start: 0.8555 (pm20) cc_final: 0.8126 (pm20) REVERT: P 71 ARG cc_start: 0.7838 (mtm110) cc_final: 0.7502 (ttm110) REVERT: P 109 ARG cc_start: 0.6991 (mtp180) cc_final: 0.6426 (mpt180) REVERT: P 154 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6235 (pm20) REVERT: P 198 LYS cc_start: 0.8425 (ttpp) cc_final: 0.6833 (tppt) REVERT: P 263 LYS cc_start: 0.7545 (pttm) cc_final: 0.7278 (ptmm) REVERT: P 265 HIS cc_start: 0.6911 (OUTLIER) cc_final: 0.6503 (t-90) REVERT: P 395 ASN cc_start: 0.4703 (t0) cc_final: 0.3360 (p0) REVERT: P 431 ASN cc_start: 0.7606 (m-40) cc_final: 0.7359 (t0) REVERT: P 454 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.7066 (ptm-80) REVERT: P 458 VAL cc_start: 0.6390 (OUTLIER) cc_final: 0.6159 (t) outliers start: 25 outliers final: 15 residues processed: 81 average time/residue: 0.1591 time to fit residues: 15.6437 Evaluate side-chains 75 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 55 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 161 ASP Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 265 HIS Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 0.0070 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 37 optimal weight: 0.0370 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.2980 chunk 30 optimal weight: 0.3980 overall best weight: 0.3076 ------------------------------------------------------------------------------- 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: 0.6499 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3148 Z= 0.147 Angle : 0.736 13.597 4286 Z= 0.366 Chirality : 0.042 0.135 504 Planarity : 0.007 0.108 564 Dihedral : 6.327 24.890 459 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.23 % Favored : 86.08 % Rotamer: Outliers : 8.13 % Allowed : 21.55 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.29 (0.34), residues: 431 helix: -1.60 (0.66), residues: 55 sheet: -0.37 (1.10), residues: 28 loop : -3.65 (0.27), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 57 HIS 0.001 0.000 HIS P 415 PHE 0.009 0.001 PHE P 373 TYR 0.012 0.001 TYR P 218 ARG 0.001 0.000 ARG P 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 65 time to evaluate : 0.363 Fit side-chains REVERT: P 37 GLN cc_start: 0.8542 (pm20) cc_final: 0.8157 (pm20) REVERT: P 51 GLN cc_start: 0.7481 (mm-40) cc_final: 0.7004 (mm110) REVERT: P 71 ARG cc_start: 0.7635 (mtm110) cc_final: 0.7400 (ttm110) REVERT: P 109 ARG cc_start: 0.6954 (mtp180) cc_final: 0.6453 (mpt180) REVERT: P 154 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6204 (pm20) REVERT: P 198 LYS cc_start: 0.8340 (ttpp) cc_final: 0.6745 (tppt) REVERT: P 265 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6211 (t-90) REVERT: P 395 ASN cc_start: 0.4009 (t0) cc_final: 0.3281 (p0) REVERT: P 412 GLN cc_start: 0.7749 (mp10) cc_final: 0.7541 (mp10) REVERT: P 431 ASN cc_start: 0.7472 (m-40) cc_final: 0.7165 (t0) REVERT: P 454 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6876 (ptm-80) REVERT: P 458 VAL cc_start: 0.6343 (OUTLIER) cc_final: 0.6094 (t) outliers start: 23 outliers final: 14 residues processed: 84 average time/residue: 0.1653 time to fit residues: 16.6514 Evaluate side-chains 77 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 265 HIS Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 38 optimal weight: 0.0570 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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: 0.6528 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3148 Z= 0.169 Angle : 0.784 15.857 4286 Z= 0.386 Chirality : 0.044 0.165 504 Planarity : 0.006 0.108 564 Dihedral : 6.293 21.327 459 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.23 % Favored : 86.08 % Rotamer: Outliers : 7.77 % Allowed : 21.91 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.40 (0.33), residues: 431 helix: -2.11 (0.57), residues: 67 sheet: 0.16 (1.39), residues: 18 loop : -3.63 (0.27), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 57 HIS 0.002 0.001 HIS P 265 PHE 0.011 0.001 PHE P 261 TYR 0.012 0.002 TYR P 441 ARG 0.001 0.000 ARG P 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 0.344 Fit side-chains REVERT: P 30 TYR cc_start: 0.3442 (OUTLIER) cc_final: 0.2838 (m-10) REVERT: P 37 GLN cc_start: 0.8496 (pm20) cc_final: 0.7942 (pm20) REVERT: P 71 ARG cc_start: 0.7705 (mtm110) cc_final: 0.7458 (ttm110) REVERT: P 395 ASN cc_start: 0.4064 (t0) cc_final: 0.3829 (p0) REVERT: P 396 GLU cc_start: 0.6718 (mm-30) cc_final: 0.6382 (tm-30) REVERT: P 431 ASN cc_start: 0.7558 (m-40) cc_final: 0.7312 (t0) REVERT: P 454 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6742 (ptm-80) REVERT: P 458 VAL cc_start: 0.6383 (OUTLIER) cc_final: 0.6140 (t) outliers start: 22 outliers final: 17 residues processed: 73 average time/residue: 0.1254 time to fit residues: 11.5541 Evaluate side-chains 77 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 57 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 126 ILE Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.6560 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3148 Z= 0.181 Angle : 0.749 13.226 4286 Z= 0.380 Chirality : 0.044 0.130 504 Planarity : 0.007 0.106 564 Dihedral : 6.401 22.093 459 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.70 % Allowed : 14.62 % Favored : 84.69 % Rotamer: Outliers : 8.13 % Allowed : 21.91 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.39 (0.34), residues: 431 helix: -2.13 (0.57), residues: 67 sheet: 0.22 (1.39), residues: 18 loop : -3.62 (0.27), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP P 57 HIS 0.004 0.001 HIS P 265 PHE 0.011 0.002 PHE P 261 TYR 0.014 0.002 TYR P 441 ARG 0.001 0.000 ARG P 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 55 time to evaluate : 0.363 Fit side-chains REVERT: P 30 TYR cc_start: 0.3423 (OUTLIER) cc_final: 0.2865 (m-10) REVERT: P 37 GLN cc_start: 0.8489 (pm20) cc_final: 0.7998 (pm20) REVERT: P 71 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7467 (ttm110) REVERT: P 154 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.5950 (pm20) REVERT: P 250 TYR cc_start: 0.6601 (OUTLIER) cc_final: 0.5443 (m-80) REVERT: P 395 ASN cc_start: 0.3923 (t0) cc_final: 0.3641 (p0) REVERT: P 396 GLU cc_start: 0.6475 (mm-30) cc_final: 0.6105 (tm-30) REVERT: P 454 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6739 (ptm-80) REVERT: P 458 VAL cc_start: 0.6365 (OUTLIER) cc_final: 0.6127 (t) outliers start: 23 outliers final: 17 residues processed: 71 average time/residue: 0.1371 time to fit residues: 12.3445 Evaluate side-chains 76 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 54 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 126 ILE Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 250 TYR Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 5.9990 chunk 4 optimal weight: 0.1980 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.0670 chunk 16 optimal weight: 0.0670 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.214091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.199686 restraints weight = 4757.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.202448 restraints weight = 2737.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.204473 restraints weight = 1800.205| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3148 Z= 0.148 Angle : 0.710 13.303 4286 Z= 0.357 Chirality : 0.042 0.123 504 Planarity : 0.006 0.102 564 Dihedral : 5.968 20.787 459 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.70 % Allowed : 12.06 % Favored : 87.24 % Rotamer: Outliers : 7.07 % Allowed : 23.32 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -4.25 (0.34), residues: 431 helix: -1.86 (0.59), residues: 67 sheet: 0.32 (1.40), residues: 18 loop : -3.56 (0.27), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP P 57 HIS 0.004 0.001 HIS P 265 PHE 0.010 0.001 PHE P 373 TYR 0.009 0.001 TYR P 441 ARG 0.001 0.000 ARG P 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1136.90 seconds wall clock time: 21 minutes 14.07 seconds (1274.07 seconds total)