Starting phenix.real_space_refine on Tue Feb 11 05:49:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5msh_3565/02_2025/5msh_3565.cif Found real_map, /net/cci-nas-00/data/ceres_data/5msh_3565/02_2025/5msh_3565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5msh_3565/02_2025/5msh_3565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5msh_3565/02_2025/5msh_3565.map" model { file = "/net/cci-nas-00/data/ceres_data/5msh_3565/02_2025/5msh_3565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5msh_3565/02_2025/5msh_3565.cif" } resolution = 4.25 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= 0.003 sd= 0.022 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 31 5.16 5 C 2732 2.51 5 N 719 2.21 5 O 805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4287 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1422 Classifications: {'peptide': 182} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 163} Chain breaks: 1 Chain: "B" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2865 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 14, 'TRANS': 354} Time building chain proxies: 3.96, per 1000 atoms: 0.92 Number of scatterers: 4287 At special positions: 0 Unit cell: (92.4, 74.8, 99, 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 31 16.00 O 805 8.00 N 719 7.00 C 2732 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 - 3.00 Amino acid : True - 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: 1.08 Conformation dependent library (CDL) restraints added in 502.9 milliseconds 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 9 sheets defined 12.9% alpha, 46.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 58 through 65 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 300 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 5.732A pdb=" N MET A 163 " --> pdb=" O PRO A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 5.732A pdb=" N MET A 163 " --> pdb=" O PRO A 13 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA A 63 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN A 174 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 41 removed outlier: 3.654A pdb=" N ARG A 106 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 32 removed outlier: 5.989A pdb=" N LYS B 24 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 172 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 46 removed outlier: 6.330A pdb=" N VAL B 150 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP B 44 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET B 148 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N CYS B 87 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 111 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 202 removed outlier: 8.083A pdb=" N GLN B 188 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY B 356 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TRP B 190 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE B 354 " --> pdb=" O TRP B 190 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N LYS B 352 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASN B 194 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY B 350 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TRP B 196 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 348 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LYS B 347 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR B 251 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL B 349 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU B 249 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE B 351 " --> pdb=" O HIS B 247 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS B 247 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ASP B 353 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLU B 245 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 202 removed outlier: 8.083A pdb=" N GLN B 188 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY B 356 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TRP B 190 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE B 354 " --> pdb=" O TRP B 190 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N LYS B 352 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASN B 194 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY B 350 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TRP B 196 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 348 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LYS B 347 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR B 251 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL B 349 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU B 249 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE B 351 " --> pdb=" O HIS B 247 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS B 247 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ASP B 353 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLU B 245 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 210 through 214 174 hydrogen bonds defined for protein. 417 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: 1.27 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1083 1.32 - 1.45: 1049 1.45 - 1.57: 2218 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4398 Sorted by residual: bond pdb=" N PRO A 13 " pdb=" CA PRO A 13 " ideal model delta sigma weight residual 1.466 1.406 0.059 1.19e-02 7.06e+03 2.48e+01 bond pdb=" N PRO B 282 " pdb=" CA PRO B 282 " ideal model delta sigma weight residual 1.467 1.418 0.048 1.17e-02 7.31e+03 1.72e+01 bond pdb=" N PRO B 214 " pdb=" CA PRO B 214 " ideal model delta sigma weight residual 1.466 1.420 0.046 1.19e-02 7.06e+03 1.48e+01 bond pdb=" N PRO A 181 " pdb=" CA PRO A 181 " ideal model delta sigma weight residual 1.467 1.421 0.046 1.21e-02 6.83e+03 1.47e+01 bond pdb=" N PRO B 324 " pdb=" CA PRO B 324 " ideal model delta sigma weight residual 1.466 1.424 0.042 1.19e-02 7.06e+03 1.22e+01 ... (remaining 4393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 4957 1.80 - 3.61: 783 3.61 - 5.41: 178 5.41 - 7.22: 53 7.22 - 9.02: 19 Bond angle restraints: 5990 Sorted by residual: angle pdb=" CA ARG A 77 " pdb=" C ARG A 77 " pdb=" O ARG A 77 " ideal model delta sigma weight residual 120.80 113.22 7.58 1.11e+00 8.12e-01 4.67e+01 angle pdb=" C GLY A 126 " pdb=" N PRO A 127 " pdb=" CA PRO A 127 " ideal model delta sigma weight residual 119.64 125.81 -6.17 1.01e+00 9.80e-01 3.73e+01 angle pdb=" C GLY A 1 " pdb=" N PRO A 2 " pdb=" CA PRO A 2 " ideal model delta sigma weight residual 119.56 125.71 -6.15 1.01e+00 9.80e-01 3.71e+01 angle pdb=" C GLU B 178 " pdb=" N PRO B 179 " pdb=" CA PRO B 179 " ideal model delta sigma weight residual 120.31 126.08 -5.77 9.80e-01 1.04e+00 3.46e+01 angle pdb=" C ASN A 152 " pdb=" N PRO A 153 " pdb=" CA PRO A 153 " ideal model delta sigma weight residual 119.84 127.08 -7.24 1.25e+00 6.40e-01 3.35e+01 ... (remaining 5985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 2515 17.09 - 34.18: 44 34.18 - 51.27: 11 51.27 - 68.36: 7 68.36 - 85.44: 6 Dihedral angle restraints: 2583 sinusoidal: 998 harmonic: 1585 Sorted by residual: dihedral pdb=" CA ARG A 77 " pdb=" C ARG A 77 " pdb=" N GLY A 78 " pdb=" CA GLY A 78 " ideal model delta harmonic sigma weight residual 0.00 36.50 -36.50 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" C HIS B 66 " pdb=" N HIS B 66 " pdb=" CA HIS B 66 " pdb=" CB HIS B 66 " ideal model delta harmonic sigma weight residual -122.60 -131.97 9.37 0 2.50e+00 1.60e-01 1.40e+01 dihedral pdb=" N HIS B 66 " pdb=" C HIS B 66 " pdb=" CA HIS B 66 " pdb=" CB HIS B 66 " ideal model delta harmonic sigma weight residual 122.80 131.11 -8.31 0 2.50e+00 1.60e-01 1.11e+01 ... (remaining 2580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 505 0.083 - 0.166: 141 0.166 - 0.249: 17 0.249 - 0.333: 2 0.333 - 0.416: 1 Chirality restraints: 666 Sorted by residual: chirality pdb=" CA HIS B 66 " pdb=" N HIS B 66 " pdb=" C HIS B 66 " pdb=" CB HIS B 66 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CA MET B 231 " pdb=" N MET B 231 " pdb=" C MET B 231 " pdb=" CB MET B 231 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ASN B 233 " pdb=" N ASN B 233 " pdb=" C ASN B 233 " pdb=" CB ASN B 233 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 663 not shown) Planarity restraints: 772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 77 " -0.061 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C ARG A 77 " 0.216 2.00e-02 2.50e+03 pdb=" O ARG A 77 " -0.080 2.00e-02 2.50e+03 pdb=" N GLY A 78 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 128 " 0.052 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO B 129 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 47 " 0.036 2.00e-02 2.50e+03 1.75e-02 7.62e+00 pdb=" CG TRP A 47 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 47 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 47 " -0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP A 47 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 47 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 47 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 47 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 47 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 47 " 0.017 2.00e-02 2.50e+03 ... (remaining 769 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1481 2.84 - 3.35: 3794 3.35 - 3.87: 7265 3.87 - 4.38: 8569 4.38 - 4.90: 14240 Nonbonded interactions: 35349 Sorted by model distance: nonbonded pdb=" O ASN B 128 " pdb=" OD1 ASN B 128 " model vdw 2.323 3.040 nonbonded pdb=" N GLU B 279 " pdb=" OE1 GLU B 279 " model vdw 2.326 3.120 nonbonded pdb=" OG SER B 366 " pdb=" N ARG B 367 " model vdw 2.420 3.120 nonbonded pdb=" O PHE A 133 " pdb=" CD1 PHE A 133 " model vdw 2.429 3.340 nonbonded pdb=" N GLU A 101 " pdb=" OE1 GLU A 101 " model vdw 2.467 3.120 ... (remaining 35344 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.010 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.660 Find NCS groups from input model: 0.040 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0197 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 : 0.014 0.059 4398 Z= 0.942 Angle : 1.562 9.020 5990 Z= 1.032 Chirality : 0.074 0.416 666 Planarity : 0.009 0.125 772 Dihedral : 9.556 85.444 1561 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 1.47 % Allowed : 6.06 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.34), residues: 545 helix: -2.30 (0.58), residues: 57 sheet: 0.82 (0.38), residues: 181 loop : -1.20 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP A 47 HIS 0.003 0.001 HIS B 247 PHE 0.026 0.004 PHE B 202 TYR 0.031 0.005 TYR B 100 ARG 0.004 0.001 ARG B 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.6148 (tttt) cc_final: 0.4973 (mtmm) REVERT: A 89 GLN cc_start: 0.3743 (mt0) cc_final: 0.3304 (pt0) REVERT: B 24 LYS cc_start: -0.1135 (mttm) cc_final: -0.1570 (mttt) REVERT: B 200 LEU cc_start: 0.3159 (mt) cc_final: 0.2814 (mp) REVERT: B 347 LYS cc_start: 0.5153 (ttpt) cc_final: 0.4869 (pttt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2389 time to fit residues: 18.6848 Evaluate side-chains 42 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.0470 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 31 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 overall best weight: 3.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 GLN ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5335 r_free = 0.5335 target = 0.307616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.302645 restraints weight = 8549.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.5306 r_free = 0.5306 target = 0.304235 restraints weight = 5540.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5314 r_free = 0.5314 target = 0.305145 restraints weight = 3719.862| |-----------------------------------------------------------------------------| r_work (final): 0.5315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0484 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4398 Z= 0.196 Angle : 0.684 7.865 5990 Z= 0.368 Chirality : 0.049 0.157 666 Planarity : 0.005 0.045 772 Dihedral : 5.341 28.245 587 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.85 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.34), residues: 545 helix: -1.43 (0.69), residues: 52 sheet: 0.73 (0.40), residues: 176 loop : -0.75 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 47 HIS 0.006 0.002 HIS A 50 PHE 0.013 0.002 PHE A 133 TYR 0.012 0.002 TYR B 278 ARG 0.004 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.484 Fit side-chains REVERT: B 2 GLU cc_start: -0.0132 (mt-10) cc_final: -0.0591 (tm-30) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1896 time to fit residues: 12.1484 Evaluate side-chains 31 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 8.9990 chunk 28 optimal weight: 50.0000 chunk 19 optimal weight: 30.0000 chunk 46 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 50.0000 chunk 36 optimal weight: 0.0470 chunk 53 optimal weight: 50.0000 chunk 34 optimal weight: 50.0000 chunk 43 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 overall best weight: 7.8088 ------------------------------------------------------------------------------- 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 = 0.5299 r_free = 0.5299 target = 0.304426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.5280 r_free = 0.5280 target = 0.302511 restraints weight = 8685.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.5287 r_free = 0.5287 target = 0.303130 restraints weight = 6128.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5290 r_free = 0.5290 target = 0.303471 restraints weight = 4432.339| |-----------------------------------------------------------------------------| r_work (final): 0.5290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0975 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4398 Z= 0.267 Angle : 0.742 9.884 5990 Z= 0.402 Chirality : 0.054 0.534 666 Planarity : 0.006 0.065 772 Dihedral : 5.663 25.462 587 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.95 % Favored : 94.86 % Rotamer: Outliers : 0.21 % Allowed : 1.90 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.34), residues: 545 helix: -1.19 (0.77), residues: 46 sheet: 0.37 (0.39), residues: 181 loop : -0.75 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 86 HIS 0.016 0.003 HIS A 50 PHE 0.022 0.002 PHE A 32 TYR 0.015 0.002 TYR A 52 ARG 0.005 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: B 2 GLU cc_start: -0.0018 (mt-10) cc_final: -0.0551 (tm-30) outliers start: 1 outliers final: 1 residues processed: 45 average time/residue: 0.1412 time to fit residues: 8.7725 Evaluate side-chains 36 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 8.9990 chunk 22 optimal weight: 40.0000 chunk 38 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 51 optimal weight: 50.0000 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 50.0000 chunk 30 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 52 optimal weight: 50.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN B 183 HIS B 343 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.301039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5228 r_free = 0.5228 target = 0.295598 restraints weight = 8627.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5239 r_free = 0.5239 target = 0.296705 restraints weight = 6253.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5246 r_free = 0.5246 target = 0.297401 restraints weight = 4783.833| |-----------------------------------------------------------------------------| r_work (final): 0.5244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1292 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4398 Z= 0.269 Angle : 0.743 10.290 5990 Z= 0.396 Chirality : 0.052 0.396 666 Planarity : 0.006 0.048 772 Dihedral : 5.788 28.511 587 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.77 % Favored : 95.05 % Rotamer: Outliers : 0.63 % Allowed : 2.53 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.34), residues: 545 helix: -0.70 (0.76), residues: 46 sheet: 0.25 (0.38), residues: 186 loop : -0.88 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 86 HIS 0.005 0.001 HIS A 50 PHE 0.029 0.003 PHE A 24 TYR 0.013 0.002 TYR A 145 ARG 0.005 0.001 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.450 Fit side-chains REVERT: A 82 LYS cc_start: 0.6683 (tppt) cc_final: 0.6125 (ptpp) REVERT: B 2 GLU cc_start: -0.0293 (mt-10) cc_final: -0.0735 (tm-30) REVERT: B 343 ASN cc_start: 0.0804 (OUTLIER) cc_final: -0.3305 (m-40) outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.1636 time to fit residues: 11.1533 Evaluate side-chains 42 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5280 r_free = 0.5280 target = 0.301963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.5227 r_free = 0.5227 target = 0.296569 restraints weight = 8696.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.297569 restraints weight = 6197.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5241 r_free = 0.5241 target = 0.298002 restraints weight = 4691.825| |-----------------------------------------------------------------------------| r_work (final): 0.5241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1253 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4398 Z= 0.189 Angle : 0.643 9.516 5990 Z= 0.339 Chirality : 0.047 0.202 666 Planarity : 0.005 0.051 772 Dihedral : 5.157 22.002 587 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.59 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.35), residues: 545 helix: -0.82 (0.77), residues: 46 sheet: 0.32 (0.39), residues: 189 loop : -0.79 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 47 HIS 0.004 0.001 HIS A 50 PHE 0.013 0.002 PHE A 24 TYR 0.012 0.002 TYR A 145 ARG 0.003 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.434 Fit side-chains REVERT: A 56 ILE cc_start: 0.1628 (mt) cc_final: 0.1317 (mt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1419 time to fit residues: 9.0881 Evaluate side-chains 39 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 5.9990 chunk 38 optimal weight: 50.0000 chunk 4 optimal weight: 7.9990 chunk 48 optimal weight: 50.0000 chunk 14 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 6 optimal weight: 50.0000 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 50.0000 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 50.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5259 r_free = 0.5259 target = 0.300091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.5211 r_free = 0.5211 target = 0.295308 restraints weight = 8615.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5219 r_free = 0.5219 target = 0.296208 restraints weight = 6451.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5225 r_free = 0.5225 target = 0.296811 restraints weight = 5029.850| |-----------------------------------------------------------------------------| r_work (final): 0.5225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1374 moved from start: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4398 Z= 0.210 Angle : 0.661 8.141 5990 Z= 0.350 Chirality : 0.048 0.219 666 Planarity : 0.005 0.051 772 Dihedral : 5.265 24.079 587 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.24 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.35), residues: 545 helix: -0.99 (0.74), residues: 46 sheet: 0.10 (0.39), residues: 191 loop : -0.76 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 86 HIS 0.006 0.001 HIS A 50 PHE 0.018 0.002 PHE A 24 TYR 0.016 0.002 TYR A 93 ARG 0.004 0.000 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.485 Fit side-chains REVERT: A 56 ILE cc_start: 0.2074 (mt) cc_final: 0.1575 (mt) REVERT: A 163 MET cc_start: -0.0910 (tmm) cc_final: -0.3125 (ttp) REVERT: A 177 MET cc_start: 0.0970 (mmm) cc_final: 0.0505 (mmt) REVERT: B 59 THR cc_start: 0.3942 (t) cc_final: 0.3711 (t) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1483 time to fit residues: 9.4338 Evaluate side-chains 38 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 46 optimal weight: 50.0000 chunk 36 optimal weight: 30.0000 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.0370 chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 50.0000 overall best weight: 7.0068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.298850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.5234 r_free = 0.5234 target = 0.296339 restraints weight = 8619.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5236 r_free = 0.5236 target = 0.296634 restraints weight = 6642.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5236 r_free = 0.5236 target = 0.296634 restraints weight = 5491.349| |-----------------------------------------------------------------------------| r_work (final): 0.5237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1450 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4398 Z= 0.227 Angle : 0.679 7.309 5990 Z= 0.360 Chirality : 0.049 0.202 666 Planarity : 0.006 0.060 772 Dihedral : 5.411 24.087 587 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.79 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.35), residues: 545 helix: -1.01 (0.79), residues: 41 sheet: -0.11 (0.38), residues: 191 loop : -0.83 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 86 HIS 0.006 0.001 HIS A 50 PHE 0.017 0.002 PHE A 91 TYR 0.020 0.002 TYR A 93 ARG 0.004 0.001 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.461 Fit side-chains REVERT: A 82 LYS cc_start: 0.6641 (tppt) cc_final: 0.6259 (tptt) REVERT: A 127 PRO cc_start: 0.3400 (Cg_exo) cc_final: 0.3155 (Cg_endo) REVERT: A 163 MET cc_start: -0.0727 (tmm) cc_final: -0.3058 (mtp) REVERT: A 177 MET cc_start: 0.0627 (mmm) cc_final: 0.0327 (mmt) REVERT: B 59 THR cc_start: 0.4299 (t) cc_final: 0.4022 (t) REVERT: B 136 TRP cc_start: -0.0219 (p-90) cc_final: -0.0674 (p-90) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1660 time to fit residues: 10.0622 Evaluate side-chains 39 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 40.0000 chunk 37 optimal weight: 50.0000 chunk 44 optimal weight: 40.0000 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 50.0000 chunk 9 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.299269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.5239 r_free = 0.5239 target = 0.297367 restraints weight = 8520.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.5235 r_free = 0.5235 target = 0.297124 restraints weight = 7255.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.297368 restraints weight = 5619.180| |-----------------------------------------------------------------------------| r_work (final): 0.5241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1448 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4398 Z= 0.201 Angle : 0.650 6.438 5990 Z= 0.345 Chirality : 0.048 0.205 666 Planarity : 0.005 0.052 772 Dihedral : 5.247 24.083 587 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.24 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % 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: -1.01 (0.35), residues: 545 helix: -1.32 (0.79), residues: 41 sheet: -0.24 (0.38), residues: 193 loop : -0.80 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 86 HIS 0.005 0.001 HIS A 50 PHE 0.014 0.002 PHE A 91 TYR 0.015 0.002 TYR A 93 ARG 0.004 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.543 Fit side-chains REVERT: A 82 LYS cc_start: 0.6248 (tppt) cc_final: 0.5899 (tptt) REVERT: A 163 MET cc_start: -0.0695 (tmm) cc_final: -0.2860 (mtp) REVERT: B 20 LEU cc_start: -0.0214 (mt) cc_final: -0.0486 (tt) REVERT: B 136 TRP cc_start: -0.0218 (p-90) cc_final: -0.0727 (p-90) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.2085 time to fit residues: 12.0740 Evaluate side-chains 37 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 5.9990 chunk 24 optimal weight: 40.0000 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 30.0000 chunk 47 optimal weight: 50.0000 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5264 r_free = 0.5264 target = 0.299898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.5236 r_free = 0.5236 target = 0.297342 restraints weight = 8644.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5240 r_free = 0.5240 target = 0.297714 restraints weight = 6605.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.5244 r_free = 0.5244 target = 0.298139 restraints weight = 5423.680| |-----------------------------------------------------------------------------| r_work (final): 0.5244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1380 moved from start: 0.7482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4398 Z= 0.164 Angle : 0.609 6.469 5990 Z= 0.319 Chirality : 0.047 0.168 666 Planarity : 0.005 0.052 772 Dihedral : 4.843 21.535 587 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.87 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.35), residues: 545 helix: -0.54 (0.92), residues: 34 sheet: -0.03 (0.38), residues: 189 loop : -0.67 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.002 0.001 HIS A 50 PHE 0.011 0.002 PHE A 159 TYR 0.013 0.001 TYR B 325 ARG 0.003 0.001 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.444 Fit side-chains REVERT: A 82 LYS cc_start: 0.6360 (tppt) cc_final: 0.6038 (tptt) REVERT: A 163 MET cc_start: -0.0579 (tmm) cc_final: -0.2621 (mtp) REVERT: B 20 LEU cc_start: -0.0110 (mt) cc_final: -0.0379 (tt) REVERT: B 59 THR cc_start: 0.4009 (t) cc_final: 0.3778 (t) REVERT: B 136 TRP cc_start: -0.0244 (p-90) cc_final: -0.0672 (p-90) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1626 time to fit residues: 9.0939 Evaluate side-chains 36 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 50.0000 chunk 44 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 50.0000 chunk 19 optimal weight: 50.0000 chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 40.0000 chunk 28 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5259 r_free = 0.5259 target = 0.299556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.296871 restraints weight = 8474.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5234 r_free = 0.5234 target = 0.297371 restraints weight = 6661.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5236 r_free = 0.5236 target = 0.297576 restraints weight = 5318.779| |-----------------------------------------------------------------------------| r_work (final): 0.5237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1499 moved from start: 0.7792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4398 Z= 0.201 Angle : 0.658 6.166 5990 Z= 0.346 Chirality : 0.048 0.180 666 Planarity : 0.005 0.051 772 Dihedral : 5.093 24.220 587 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.06 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.35), residues: 545 helix: -0.82 (0.90), residues: 34 sheet: -0.10 (0.38), residues: 196 loop : -0.86 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 115 HIS 0.007 0.001 HIS A 50 PHE 0.015 0.002 PHE A 91 TYR 0.019 0.002 TYR B 325 ARG 0.006 0.001 ARG B 195 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.451 Fit side-chains REVERT: A 82 LYS cc_start: 0.6374 (tppt) cc_final: 0.6046 (tptt) REVERT: A 163 MET cc_start: -0.0522 (tmm) cc_final: -0.2098 (mtp) REVERT: B 20 LEU cc_start: -0.0093 (mt) cc_final: -0.0295 (tt) REVERT: B 59 THR cc_start: 0.4067 (t) cc_final: 0.3858 (t) REVERT: B 136 TRP cc_start: -0.0171 (p-90) cc_final: -0.0617 (p-90) REVERT: B 231 MET cc_start: 0.2366 (tpt) cc_final: 0.2155 (tpt) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1694 time to fit residues: 9.2005 Evaluate side-chains 37 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 30.0000 chunk 18 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 28 optimal weight: 30.0000 chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 50.0000 chunk 15 optimal weight: 0.0870 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 overall best weight: 4.8166 ------------------------------------------------------------------------------- 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 = 0.5261 r_free = 0.5261 target = 0.299941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.299681 restraints weight = 8604.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.299715 restraints weight = 6641.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5259 r_free = 0.5259 target = 0.299748 restraints weight = 4442.656| |-----------------------------------------------------------------------------| r_work (final): 0.5259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1454 moved from start: 0.8160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4398 Z= 0.188 Angle : 0.635 6.653 5990 Z= 0.334 Chirality : 0.048 0.185 666 Planarity : 0.005 0.053 772 Dihedral : 4.937 23.718 587 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.87 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.35), residues: 545 helix: -0.86 (0.92), residues: 34 sheet: -0.04 (0.39), residues: 191 loop : -0.96 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS A 50 PHE 0.012 0.002 PHE A 91 TYR 0.012 0.002 TYR A 145 ARG 0.004 0.001 ARG A 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1416.02 seconds wall clock time: 26 minutes 20.64 seconds (1580.64 seconds total)