Starting phenix.real_space_refine on Mon Sep 23 19:47:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zb9_39898/09_2024/8zb9_39898.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zb9_39898/09_2024/8zb9_39898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zb9_39898/09_2024/8zb9_39898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zb9_39898/09_2024/8zb9_39898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zb9_39898/09_2024/8zb9_39898.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zb9_39898/09_2024/8zb9_39898.cif" } resolution = 3.31 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= 0.039 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 42 5.16 5 C 3075 2.51 5 N 848 2.21 5 O 939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4904 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2455 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain breaks: 4 Chain: "a" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2449 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 18, 'TRANS': 291} Chain breaks: 3 Time building chain proxies: 4.25, per 1000 atoms: 0.87 Number of scatterers: 4904 At special positions: 0 Unit cell: (86.7, 103.7, 64.6, 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 42 16.00 O 939 8.00 N 848 7.00 C 3075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.28 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 224 " distance=2.04 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=1.97 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 224 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=1.97 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: 1.00 Conformation dependent library (CDL) restraints added in 530.9 milliseconds 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 10 sheets defined 16.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 24 through 27 Processing helix chain 'A' and resid 40 through 52 Processing helix chain 'A' and resid 61 through 82 removed outlier: 5.341A pdb=" N ASP A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.814A pdb=" N ILE A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 24 through 27 Processing helix chain 'a' and resid 40 through 53 removed outlier: 3.570A pdb=" N GLY a 53 " --> pdb=" O SER a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 82 removed outlier: 5.317A pdb=" N ASP a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N GLU a 74 " --> pdb=" O SER a 70 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE a 75 " --> pdb=" O ARG a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 180 through 184 removed outlier: 4.044A pdb=" N ILE a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU a 184 " --> pdb=" O GLY a 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 184' Processing helix chain 'a' and resid 227 through 231 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 15 removed outlier: 3.567A pdb=" N GLU A 12 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 7 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 14 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 5 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN a 2 " --> pdb=" O ILE A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.247A pdb=" N GLY A 56 " --> pdb=" O VAL A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.860A pdb=" N SER A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 323 removed outlier: 3.569A pdb=" N LYS A 276 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 218 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU A 216 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ARG A 277 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N HIS A 214 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ILE A 213 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N HIS A 205 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 200 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 192 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 185 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY a 185 " --> pdb=" O GLY a 196 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS a 192 " --> pdb=" O ASN a 189 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE a 200 " --> pdb=" O SER a 197 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP a 201 " --> pdb=" O LEU a 216 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU a 216 " --> pdb=" O TRP a 201 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY a 203 " --> pdb=" O HIS a 214 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR a 210 " --> pdb=" O VAL a 207 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU a 216 " --> pdb=" O VAL a 275 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA a 218 " --> pdb=" O LEU a 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 285 through 287 removed outlier: 3.567A pdb=" N ILE A 286 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 34 through 35 Processing sheet with id=AA8, first strand: chain 'a' and resid 56 through 57 removed outlier: 7.456A pdb=" N GLY a 56 " --> pdb=" O VAL a 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'a' and resid 86 through 87 Processing sheet with id=AB1, first strand: chain 'a' and resid 285 through 287 removed outlier: 3.794A pdb=" N CYS a 313 " --> pdb=" O ILE a 286 " (cutoff:3.500A) 110 hydrogen bonds defined for protein. 303 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: 1.20 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 926 1.32 - 1.45: 1458 1.45 - 1.58: 2587 1.58 - 1.71: 0 1.71 - 1.85: 60 Bond restraints: 5031 Sorted by residual: bond pdb=" CA GLN a 2 " pdb=" C GLN a 2 " ideal model delta sigma weight residual 1.525 1.465 0.059 1.28e-02 6.10e+03 2.15e+01 bond pdb=" CA PRO A 93 " pdb=" C PRO A 93 " ideal model delta sigma weight residual 1.522 1.476 0.046 9.90e-03 1.02e+04 2.14e+01 bond pdb=" CA CYS a 4 " pdb=" C CYS a 4 " ideal model delta sigma weight residual 1.531 1.482 0.049 1.15e-02 7.56e+03 1.85e+01 bond pdb=" CA GLN A 91 " pdb=" C GLN A 91 " ideal model delta sigma weight residual 1.531 1.477 0.054 1.32e-02 5.74e+03 1.67e+01 bond pdb=" C TYR A 97 " pdb=" O TYR A 97 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.24e-02 6.50e+03 1.30e+01 ... (remaining 5026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 6417 1.71 - 3.43: 307 3.43 - 5.14: 60 5.14 - 6.86: 11 6.86 - 8.57: 4 Bond angle restraints: 6799 Sorted by residual: angle pdb=" N PRO A 93 " pdb=" CA PRO A 93 " pdb=" C PRO A 93 " ideal model delta sigma weight residual 110.50 101.93 8.57 1.57e+00 4.06e-01 2.98e+01 angle pdb=" C VAL A 96 " pdb=" CA VAL A 96 " pdb=" CB VAL A 96 " ideal model delta sigma weight residual 111.40 103.49 7.91 1.90e+00 2.77e-01 1.73e+01 angle pdb=" N LEU a 13 " pdb=" CA LEU a 13 " pdb=" C LEU a 13 " ideal model delta sigma weight residual 114.64 108.38 6.26 1.52e+00 4.33e-01 1.69e+01 angle pdb=" N CYS a 4 " pdb=" CA CYS a 4 " pdb=" C CYS a 4 " ideal model delta sigma weight residual 108.18 115.92 -7.74 2.01e+00 2.48e-01 1.48e+01 angle pdb=" N GLN A 98 " pdb=" CA GLN A 98 " pdb=" C GLN A 98 " ideal model delta sigma weight residual 109.94 115.97 -6.03 1.57e+00 4.06e-01 1.48e+01 ... (remaining 6794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 2511 16.98 - 33.97: 384 33.97 - 50.95: 89 50.95 - 67.93: 15 67.93 - 84.91: 9 Dihedral angle restraints: 3008 sinusoidal: 1247 harmonic: 1761 Sorted by residual: dihedral pdb=" CB CYS A 4 " pdb=" SG CYS A 4 " pdb=" SG CYS A 15 " pdb=" CB CYS A 15 " ideal model delta sinusoidal sigma weight residual 93.00 31.72 61.28 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CA ASP a 92 " pdb=" C ASP a 92 " pdb=" N PRO a 93 " pdb=" CA PRO a 93 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CB CYS A 280 " pdb=" SG CYS A 280 " pdb=" SG CYS A 329 " pdb=" CB CYS A 329 " ideal model delta sinusoidal sigma weight residual 93.00 131.00 -38.00 1 1.00e+01 1.00e-02 2.03e+01 ... (remaining 3005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 382 0.035 - 0.071: 206 0.071 - 0.106: 79 0.106 - 0.142: 26 0.142 - 0.177: 5 Chirality restraints: 698 Sorted by residual: chirality pdb=" CA GLN A 98 " pdb=" N GLN A 98 " pdb=" C GLN A 98 " pdb=" CB GLN A 98 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA VAL a 149 " pdb=" N VAL a 149 " pdb=" C VAL a 149 " pdb=" CB VAL a 149 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA VAL a 207 " pdb=" N VAL a 207 " pdb=" C VAL a 207 " pdb=" CB VAL a 207 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 695 not shown) Planarity restraints: 889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 280 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO A 281 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 314 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C ARG A 314 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG A 314 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 315 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP a 38 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO a 39 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO a 39 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO a 39 " 0.030 5.00e-02 4.00e+02 ... (remaining 886 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1354 2.79 - 3.32: 4194 3.32 - 3.85: 7481 3.85 - 4.37: 8734 4.37 - 4.90: 15828 Nonbonded interactions: 37591 Sorted by model distance: nonbonded pdb=" O LYS A 296 " pdb=" NH1 ARG A 336 " model vdw 2.267 3.120 nonbonded pdb=" O LYS a 296 " pdb=" NH1 ARG a 336 " model vdw 2.269 3.120 nonbonded pdb=" OG1 THR A 302 " pdb=" OD1 ASP A 303 " model vdw 2.301 3.040 nonbonded pdb=" O TYR a 34 " pdb=" NH1 ARG a 71 " model vdw 2.326 3.120 nonbonded pdb=" OD1 ASP a 17 " pdb=" N GLY a 18 " model vdw 2.331 3.120 ... (remaining 37586 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 82 or resid 85 through 159 or resid 166 through \ 337)) selection = (chain 'a' and (resid 1 through 94 or resid 96 through 235 or resid 238 through \ 337)) } 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 individual isotropic 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: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.870 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 5031 Z= 0.491 Angle : 0.874 8.572 6799 Z= 0.510 Chirality : 0.051 0.177 698 Planarity : 0.006 0.055 889 Dihedral : 16.830 84.914 1845 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.24 % Favored : 85.76 % Rotamer: Outliers : 0.37 % Allowed : 22.65 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.33), residues: 604 helix: 1.07 (0.59), residues: 71 sheet: -2.67 (0.55), residues: 89 loop : -2.68 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 226 HIS 0.009 0.002 HIS a 205 PHE 0.023 0.002 PHE A 104 TYR 0.012 0.002 TYR A 260 ARG 0.004 0.000 ARG a 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.537 Fit side-chains REVERT: a 4 CYS cc_start: 0.8501 (m) cc_final: 0.8287 (m) REVERT: a 208 ASN cc_start: 0.7951 (t0) cc_final: 0.7372 (t0) outliers start: 2 outliers final: 0 residues processed: 90 average time/residue: 0.1476 time to fit residues: 17.8073 Evaluate side-chains 76 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5031 Z= 0.221 Angle : 0.609 7.489 6799 Z= 0.322 Chirality : 0.046 0.198 698 Planarity : 0.005 0.055 889 Dihedral : 4.954 22.325 664 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 3.31 % Allowed : 22.47 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.34), residues: 604 helix: 1.45 (0.63), residues: 72 sheet: -2.04 (0.60), residues: 84 loop : -2.42 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 311 HIS 0.004 0.001 HIS a 205 PHE 0.014 0.001 PHE A 104 TYR 0.006 0.001 TYR A 97 ARG 0.002 0.000 ARG a 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.709 Fit side-chains REVERT: a 208 ASN cc_start: 0.7623 (t0) cc_final: 0.6998 (t0) outliers start: 18 outliers final: 11 residues processed: 92 average time/residue: 0.2003 time to fit residues: 23.6462 Evaluate side-chains 88 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 134 ILE Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 45 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN ** a 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5031 Z= 0.200 Angle : 0.570 7.135 6799 Z= 0.299 Chirality : 0.044 0.140 698 Planarity : 0.005 0.054 889 Dihedral : 4.629 22.001 664 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 4.24 % Allowed : 22.84 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.34), residues: 604 helix: 1.62 (0.62), residues: 72 sheet: -2.12 (0.54), residues: 95 loop : -2.25 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 226 HIS 0.003 0.001 HIS a 256 PHE 0.013 0.001 PHE A 104 TYR 0.007 0.001 TYR A 35 ARG 0.002 0.000 ARG a 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 104 average time/residue: 0.1424 time to fit residues: 19.7848 Evaluate side-chains 91 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 29 optimal weight: 0.0670 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5031 Z= 0.205 Angle : 0.569 7.175 6799 Z= 0.295 Chirality : 0.044 0.133 698 Planarity : 0.005 0.054 889 Dihedral : 4.503 21.317 664 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 4.79 % Allowed : 24.13 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.34), residues: 604 helix: 1.65 (0.61), residues: 72 sheet: -1.99 (0.55), residues: 95 loop : -2.15 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 226 HIS 0.003 0.001 HIS A 205 PHE 0.009 0.001 PHE A 104 TYR 0.006 0.001 TYR A 35 ARG 0.001 0.000 ARG a 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7824 (tt0) outliers start: 26 outliers final: 21 residues processed: 101 average time/residue: 0.1468 time to fit residues: 20.2043 Evaluate side-chains 97 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 229 THR Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.0670 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5031 Z= 0.188 Angle : 0.548 7.494 6799 Z= 0.284 Chirality : 0.043 0.130 698 Planarity : 0.005 0.053 889 Dihedral : 4.296 21.016 664 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 5.16 % Allowed : 23.57 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.34), residues: 604 helix: 1.80 (0.61), residues: 72 sheet: -1.78 (0.55), residues: 95 loop : -2.07 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 226 HIS 0.003 0.001 HIS A 205 PHE 0.009 0.001 PHE A 104 TYR 0.005 0.001 TYR A 260 ARG 0.001 0.000 ARG a 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 80 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 2 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7604 (mp10) REVERT: a 66 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7800 (tt0) outliers start: 28 outliers final: 21 residues processed: 100 average time/residue: 0.1362 time to fit residues: 18.5239 Evaluate side-chains 95 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 104 PHE Chi-restraints excluded: chain a residue 134 ILE Chi-restraints excluded: chain a residue 229 THR Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 31 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5031 Z= 0.271 Angle : 0.609 7.059 6799 Z= 0.318 Chirality : 0.045 0.132 698 Planarity : 0.005 0.054 889 Dihedral : 4.562 20.958 664 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 5.89 % Allowed : 23.20 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.34), residues: 604 helix: 1.74 (0.61), residues: 72 sheet: -1.75 (0.55), residues: 95 loop : -2.10 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 226 HIS 0.005 0.001 HIS a 205 PHE 0.010 0.001 PHE A 323 TYR 0.006 0.001 TYR a 32 ARG 0.003 0.000 ARG a 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 75 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7585 (mt-10) REVERT: a 2 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7755 (mp10) REVERT: a 52 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6940 (tp30) outliers start: 32 outliers final: 27 residues processed: 96 average time/residue: 0.1373 time to fit residues: 17.8759 Evaluate side-chains 98 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 70 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 52 GLU Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 134 ILE Chi-restraints excluded: chain a residue 229 THR Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5031 Z= 0.307 Angle : 0.631 8.130 6799 Z= 0.329 Chirality : 0.045 0.134 698 Planarity : 0.005 0.055 889 Dihedral : 4.719 21.180 664 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 6.26 % Allowed : 24.13 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.34), residues: 604 helix: 1.65 (0.61), residues: 72 sheet: -1.76 (0.55), residues: 95 loop : -2.20 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 226 HIS 0.006 0.001 HIS a 205 PHE 0.012 0.001 PHE A 323 TYR 0.007 0.001 TYR a 32 ARG 0.002 0.000 ARG a 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 79 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7609 (mt-10) REVERT: a 2 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7731 (mp10) outliers start: 34 outliers final: 29 residues processed: 103 average time/residue: 0.1465 time to fit residues: 20.1733 Evaluate side-chains 103 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 74 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 134 ILE Chi-restraints excluded: chain a residue 229 THR Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 321 VAL Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 54 optimal weight: 0.0050 chunk 57 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** a 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5031 Z= 0.238 Angle : 0.603 8.394 6799 Z= 0.313 Chirality : 0.044 0.142 698 Planarity : 0.005 0.056 889 Dihedral : 4.582 21.167 664 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 5.71 % Allowed : 24.86 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.34), residues: 604 helix: 1.59 (0.60), residues: 73 sheet: -1.74 (0.55), residues: 95 loop : -2.13 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 226 HIS 0.004 0.001 HIS a 205 PHE 0.009 0.001 PHE A 104 TYR 0.006 0.001 TYR A 35 ARG 0.004 0.000 ARG a 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 78 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 2 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7737 (mp10) outliers start: 31 outliers final: 28 residues processed: 102 average time/residue: 0.1462 time to fit residues: 20.1344 Evaluate side-chains 99 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 71 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 55 CYS Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 104 PHE Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 134 ILE Chi-restraints excluded: chain a residue 229 THR Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.0570 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.0570 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN a 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5031 Z= 0.217 Angle : 0.593 8.611 6799 Z= 0.306 Chirality : 0.044 0.131 698 Planarity : 0.005 0.055 889 Dihedral : 4.441 21.044 664 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 5.89 % Allowed : 24.68 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.34), residues: 604 helix: 1.82 (0.60), residues: 71 sheet: -1.70 (0.55), residues: 95 loop : -2.12 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 226 HIS 0.003 0.001 HIS a 205 PHE 0.009 0.001 PHE A 104 TYR 0.006 0.001 TYR A 35 ARG 0.003 0.000 ARG a 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 75 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 28 residues processed: 97 average time/residue: 0.1325 time to fit residues: 17.5226 Evaluate side-chains 99 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 71 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 104 PHE Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 134 ILE Chi-restraints excluded: chain a residue 229 THR Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5031 Z= 0.282 Angle : 0.627 8.448 6799 Z= 0.325 Chirality : 0.045 0.132 698 Planarity : 0.005 0.054 889 Dihedral : 4.656 20.969 664 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer: Outliers : 5.34 % Allowed : 25.05 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.34), residues: 604 helix: 1.57 (0.60), residues: 73 sheet: -1.75 (0.55), residues: 95 loop : -2.14 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 226 HIS 0.005 0.001 HIS a 205 PHE 0.010 0.001 PHE A 323 TYR 0.006 0.001 TYR a 32 ARG 0.002 0.000 ARG a 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 74 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 29 residues processed: 93 average time/residue: 0.1425 time to fit residues: 17.7926 Evaluate side-chains 100 residues out of total 543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 71 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 104 PHE Chi-restraints excluded: chain a residue 132 SER Chi-restraints excluded: chain a residue 134 ILE Chi-restraints excluded: chain a residue 229 THR Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 262 VAL Chi-restraints excluded: chain a residue 264 THR Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 43 optimal weight: 0.0980 chunk 2 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.182899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.148814 restraints weight = 5246.747| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.64 r_work: 0.3544 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5031 Z= 0.188 Angle : 0.572 8.902 6799 Z= 0.294 Chirality : 0.043 0.129 698 Planarity : 0.005 0.055 889 Dihedral : 4.268 20.807 664 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.97 % Allowed : 25.78 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.34), residues: 604 helix: 1.88 (0.59), residues: 72 sheet: -1.69 (0.55), residues: 95 loop : -2.06 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 211 HIS 0.002 0.001 HIS A 205 PHE 0.009 0.001 PHE A 104 TYR 0.006 0.001 TYR A 35 ARG 0.003 0.000 ARG a 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1614.98 seconds wall clock time: 29 minutes 52.22 seconds (1792.22 seconds total)