Starting phenix.real_space_refine on Wed Mar 5 21:47:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7msx_23971/03_2025/7msx_23971.cif Found real_map, /net/cci-nas-00/data/ceres_data/7msx_23971/03_2025/7msx_23971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7msx_23971/03_2025/7msx_23971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7msx_23971/03_2025/7msx_23971.map" model { file = "/net/cci-nas-00/data/ceres_data/7msx_23971/03_2025/7msx_23971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7msx_23971/03_2025/7msx_23971.cif" } resolution = 3.15 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 26 5.16 5 C 2359 2.51 5 N 620 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3706 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3703 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 13, 'TRANS': 459} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1016 SG CYS A 143 13.882 35.673 58.737 1.00 38.05 S ATOM 1040 SG CYS A 146 12.818 36.968 62.628 1.00 47.40 S ATOM 1153 SG CYS A 161 16.687 37.445 59.660 1.00 42.84 S ATOM 1179 SG CYS A 164 15.449 34.581 62.038 1.00 44.32 S ATOM 1371 SG CYS A 190 28.609 18.258 44.496 1.00 54.40 S ATOM 1389 SG CYS A 193 30.905 15.408 45.275 1.00 70.39 S ATOM 1713 SG CYS A 236 31.982 19.316 43.189 1.00 52.65 S ATOM 136 SG CYS A 20 17.151 42.649 18.557 1.00 45.24 S ATOM 372 SG CYS A 51 16.203 45.352 15.948 1.00 45.63 S Time building chain proxies: 2.93, per 1000 atoms: 0.79 Number of scatterers: 3706 At special positions: 0 Unit cell: (57.546, 75.894, 114.258, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 26 16.00 O 698 8.00 N 620 7.00 C 2359 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: 0.81 Conformation dependent library (CDL) restraints added in 414.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 143 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 146 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 164 " pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 202 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 236 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 190 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 193 " pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 56 " pdb="ZN ZN A 703 " - pdb=" ND1 HIS A 54 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 51 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 20 " Number of angles added : 10 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 878 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 46.1% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 203 through 212 removed outlier: 4.250A pdb=" N GLY A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 275 removed outlier: 3.562A pdb=" N LEU A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 303 through 312 removed outlier: 3.732A pdb=" N LYS A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 378 through 394 Processing helix chain 'A' and resid 396 through 407 Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 424 through 438 Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.671A pdb=" N LEU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'A' and resid 492 through 503 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 removed outlier: 7.456A pdb=" N VAL A 6 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR A 61 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS A 78 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA A 184 " --> pdb=" O PRO A 245 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASN A 133 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS A 187 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 6 through 7 removed outlier: 7.456A pdb=" N VAL A 6 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR A 61 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS A 78 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 235 " --> pdb=" O TYR A 242 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 244 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR A 233 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG A 246 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N PHE A 231 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER A 248 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N CYS A 229 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR A 233 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ARG A 222 " --> pdb=" O TYR A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.678A pdb=" N LEU A 137 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 334 removed outlier: 6.106A pdb=" N VAL A 279 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR A 332 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 281 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY A 334 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 283 " --> pdb=" O GLY A 334 " (cutoff:3.500A) 181 hydrogen bonds defined for protein. 492 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: 1.03 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 722 1.33 - 1.45: 924 1.45 - 1.57: 2100 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3777 Sorted by residual: bond pdb=" N PRO A 91 " pdb=" CD PRO A 91 " ideal model delta sigma weight residual 1.473 1.400 0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" N PRO A 200 " pdb=" CD PRO A 200 " ideal model delta sigma weight residual 1.473 1.414 0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" N PRO A 13 " pdb=" CD PRO A 13 " ideal model delta sigma weight residual 1.473 1.414 0.059 1.40e-02 5.10e+03 1.76e+01 bond pdb=" N PRO A 17 " pdb=" CD PRO A 17 " ideal model delta sigma weight residual 1.473 1.416 0.057 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO A 74 " pdb=" CD PRO A 74 " ideal model delta sigma weight residual 1.473 1.417 0.056 1.40e-02 5.10e+03 1.58e+01 ... (remaining 3772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 4853 1.27 - 2.53: 203 2.53 - 3.80: 43 3.80 - 5.06: 1 5.06 - 6.33: 3 Bond angle restraints: 5103 Sorted by residual: angle pdb=" N GLY A 327 " pdb=" CA GLY A 327 " pdb=" C GLY A 327 " ideal model delta sigma weight residual 115.21 121.46 -6.25 1.30e+00 5.92e-01 2.31e+01 angle pdb=" C ALA A 26 " pdb=" N ARG A 27 " pdb=" CA ARG A 27 " ideal model delta sigma weight residual 120.28 116.58 3.70 1.34e+00 5.57e-01 7.63e+00 angle pdb=" CA TRP A 432 " pdb=" CB TRP A 432 " pdb=" CG TRP A 432 " ideal model delta sigma weight residual 113.60 118.78 -5.18 1.90e+00 2.77e-01 7.44e+00 angle pdb=" C VAL A 234 " pdb=" CA VAL A 234 " pdb=" CB VAL A 234 " ideal model delta sigma weight residual 111.44 109.09 2.35 9.50e-01 1.11e+00 6.11e+00 angle pdb=" C VAL A 157 " pdb=" CA VAL A 157 " pdb=" CB VAL A 157 " ideal model delta sigma weight residual 111.44 109.29 2.15 9.50e-01 1.11e+00 5.14e+00 ... (remaining 5098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.59: 2119 14.59 - 29.17: 99 29.17 - 43.76: 21 43.76 - 58.34: 7 58.34 - 72.92: 3 Dihedral angle restraints: 2249 sinusoidal: 885 harmonic: 1364 Sorted by residual: dihedral pdb=" CA GLY A 344 " pdb=" C GLY A 344 " pdb=" N GLU A 345 " pdb=" CA GLU A 345 " ideal model delta harmonic sigma weight residual 180.00 163.30 16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA SER A 351 " pdb=" C SER A 351 " pdb=" N PRO A 352 " pdb=" CA PRO A 352 " ideal model delta harmonic sigma weight residual 180.00 165.40 14.60 0 5.00e+00 4.00e-02 8.53e+00 dihedral pdb=" CA PHE A 329 " pdb=" C PHE A 329 " pdb=" N LYS A 330 " pdb=" CA LYS A 330 " ideal model delta harmonic sigma weight residual 180.00 165.44 14.56 0 5.00e+00 4.00e-02 8.48e+00 ... (remaining 2246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 375 0.033 - 0.067: 91 0.067 - 0.100: 56 0.100 - 0.134: 36 0.134 - 0.167: 15 Chirality restraints: 573 Sorted by residual: chirality pdb=" CA VAL A 186 " pdb=" N VAL A 186 " pdb=" C VAL A 186 " pdb=" CB VAL A 186 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA VAL A 230 " pdb=" N VAL A 230 " pdb=" C VAL A 230 " pdb=" CB VAL A 230 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA VAL A 6 " pdb=" N VAL A 6 " pdb=" C VAL A 6 " pdb=" CB VAL A 6 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 570 not shown) Planarity restraints: 649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 432 " -0.016 2.00e-02 2.50e+03 1.30e-02 4.20e+00 pdb=" CG TRP A 432 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 432 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 432 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 432 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 432 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 432 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 432 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 432 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 432 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 464 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C ASP A 464 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP A 464 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 465 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 463 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C ARG A 463 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG A 463 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP A 464 " -0.008 2.00e-02 2.50e+03 ... (remaining 646 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1457 2.89 - 3.39: 3529 3.39 - 3.89: 6079 3.89 - 4.40: 7034 4.40 - 4.90: 11643 Nonbonded interactions: 29742 Sorted by model distance: nonbonded pdb=" O GLU A 272 " pdb=" NZ LYS A 276 " model vdw 2.385 3.120 nonbonded pdb=" NZ LYS A 288 " pdb=" OD2 ASP A 409 " model vdw 2.388 3.120 nonbonded pdb=" OD2 ASP A 23 " pdb=" NH1 ARG A 27 " model vdw 2.476 3.120 nonbonded pdb=" NZ LYS A 320 " pdb=" OE2 GLU A 324 " model vdw 2.561 3.120 nonbonded pdb=" N GLU A 373 " pdb=" OE1 GLU A 373 " model vdw 2.566 3.120 ... (remaining 29737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.650 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.820 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.008 0.073 3777 Z= 0.519 Angle : 0.622 6.330 5103 Z= 0.397 Chirality : 0.052 0.167 573 Planarity : 0.003 0.023 649 Dihedral : 10.301 72.925 1371 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 0.06 (0.36), residues: 467 helix: 0.34 (0.34), residues: 180 sheet: -0.85 (0.52), residues: 74 loop : 0.34 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 432 HIS 0.001 0.000 HIS A 56 PHE 0.010 0.001 PHE A 93 TYR 0.013 0.001 TYR A 207 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8541 (pttt) cc_final: 0.8334 (pttm) REVERT: A 499 PHE cc_start: 0.7890 (t80) cc_final: 0.7633 (t80) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2123 time to fit residues: 25.1855 Evaluate side-chains 58 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 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 130 ASN A 152 GLN A 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.129094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097814 restraints weight = 4844.898| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.11 r_work: 0.3044 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3777 Z= 0.178 Angle : 0.497 5.600 5103 Z= 0.273 Chirality : 0.040 0.150 573 Planarity : 0.003 0.023 649 Dihedral : 4.325 20.756 502 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.21 % Allowed : 5.41 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.38), residues: 467 helix: 1.81 (0.36), residues: 180 sheet: -0.67 (0.53), residues: 74 loop : 0.42 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 432 HIS 0.003 0.001 HIS A 194 PHE 0.011 0.001 PHE A 41 TYR 0.016 0.001 TYR A 207 ARG 0.005 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.435 Fit side-chains REVERT: A 264 GLU cc_start: 0.8048 (pm20) cc_final: 0.7727 (mp0) REVERT: A 383 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: A 428 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8476 (tt) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 0.2199 time to fit residues: 15.9119 Evaluate side-chains 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.127724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.096490 restraints weight = 4833.899| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.09 r_work: 0.3014 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3777 Z= 0.208 Angle : 0.483 5.709 5103 Z= 0.262 Chirality : 0.040 0.179 573 Planarity : 0.003 0.027 649 Dihedral : 4.200 19.335 502 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.97 % Allowed : 7.13 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.38), residues: 467 helix: 1.96 (0.37), residues: 182 sheet: -0.78 (0.53), residues: 74 loop : 0.23 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 432 HIS 0.004 0.001 HIS A 194 PHE 0.013 0.001 PHE A 41 TYR 0.014 0.001 TYR A 207 ARG 0.005 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.435 Fit side-chains REVERT: A 218 ARG cc_start: 0.6910 (mmm160) cc_final: 0.6498 (mmm160) REVERT: A 383 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: A 428 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8561 (tt) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.1838 time to fit residues: 10.9040 Evaluate side-chains 47 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 40 optimal weight: 0.0770 chunk 6 optimal weight: 0.6980 overall best weight: 0.5940 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.128865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098779 restraints weight = 4852.586| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.06 r_work: 0.3041 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3777 Z= 0.159 Angle : 0.451 5.139 5103 Z= 0.244 Chirality : 0.039 0.167 573 Planarity : 0.003 0.028 649 Dihedral : 4.011 18.133 502 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.70 % Allowed : 5.65 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.38), residues: 467 helix: 2.07 (0.37), residues: 180 sheet: -0.82 (0.54), residues: 74 loop : 0.17 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 432 HIS 0.003 0.001 HIS A 194 PHE 0.009 0.001 PHE A 41 TYR 0.014 0.001 TYR A 207 ARG 0.004 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.468 Fit side-chains REVERT: A 55 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6233 (pp20) REVERT: A 383 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7988 (tt0) outliers start: 11 outliers final: 7 residues processed: 49 average time/residue: 0.1858 time to fit residues: 11.2885 Evaluate side-chains 49 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.127783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.096017 restraints weight = 4953.075| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.16 r_work: 0.3009 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3777 Z= 0.191 Angle : 0.453 6.210 5103 Z= 0.246 Chirality : 0.039 0.164 573 Planarity : 0.003 0.030 649 Dihedral : 4.000 19.009 502 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.70 % Allowed : 6.88 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.38), residues: 467 helix: 2.08 (0.37), residues: 180 sheet: -0.73 (0.54), residues: 74 loop : 0.17 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 432 HIS 0.003 0.001 HIS A 194 PHE 0.008 0.001 PHE A 41 TYR 0.013 0.001 TYR A 207 ARG 0.004 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.427 Fit side-chains REVERT: A 55 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6242 (pp20) REVERT: A 383 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.8046 (tt0) outliers start: 11 outliers final: 8 residues processed: 46 average time/residue: 0.1904 time to fit residues: 10.8672 Evaluate side-chains 49 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 383 GLN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 46 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.0570 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.129615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098406 restraints weight = 4868.226| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.12 r_work: 0.3053 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3777 Z= 0.137 Angle : 0.420 6.642 5103 Z= 0.226 Chirality : 0.038 0.156 573 Planarity : 0.003 0.030 649 Dihedral : 3.773 16.152 502 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.46 % Allowed : 7.37 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.38), residues: 467 helix: 1.87 (0.38), residues: 188 sheet: -0.67 (0.55), residues: 74 loop : 0.35 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 PHE 0.019 0.001 PHE A 41 TYR 0.012 0.001 TYR A 207 ARG 0.004 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.414 Fit side-chains REVERT: A 55 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6216 (pp20) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 0.1825 time to fit residues: 11.9534 Evaluate side-chains 52 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.126145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.094730 restraints weight = 4864.123| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.12 r_work: 0.2996 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3777 Z= 0.240 Angle : 0.467 4.868 5103 Z= 0.257 Chirality : 0.040 0.163 573 Planarity : 0.003 0.031 649 Dihedral : 4.077 19.951 502 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.46 % Allowed : 8.85 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.38), residues: 467 helix: 1.83 (0.38), residues: 188 sheet: -0.79 (0.56), residues: 74 loop : 0.28 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 432 HIS 0.003 0.001 HIS A 54 PHE 0.015 0.001 PHE A 41 TYR 0.013 0.001 TYR A 207 ARG 0.005 0.001 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.448 Fit side-chains REVERT: A 55 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6116 (pp20) outliers start: 10 outliers final: 7 residues processed: 48 average time/residue: 0.1782 time to fit residues: 10.6103 Evaluate side-chains 51 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.128051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.096499 restraints weight = 4932.699| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.14 r_work: 0.3016 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3777 Z= 0.167 Angle : 0.434 5.247 5103 Z= 0.240 Chirality : 0.038 0.158 573 Planarity : 0.003 0.031 649 Dihedral : 3.904 18.296 502 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.97 % Allowed : 9.83 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.38), residues: 467 helix: 1.83 (0.38), residues: 188 sheet: -0.76 (0.57), residues: 74 loop : 0.25 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 PHE 0.008 0.001 PHE A 41 TYR 0.012 0.001 TYR A 207 ARG 0.004 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.406 Fit side-chains REVERT: A 55 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6086 (pp20) outliers start: 8 outliers final: 7 residues processed: 48 average time/residue: 0.1984 time to fit residues: 11.8106 Evaluate side-chains 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.128436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.097145 restraints weight = 4827.873| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.11 r_work: 0.3027 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3777 Z= 0.166 Angle : 0.436 5.060 5103 Z= 0.244 Chirality : 0.039 0.157 573 Planarity : 0.003 0.031 649 Dihedral : 3.899 17.872 502 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.46 % Allowed : 10.32 % Favored : 87.22 % 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: 0.98 (0.38), residues: 467 helix: 2.00 (0.38), residues: 180 sheet: -0.75 (0.57), residues: 74 loop : 0.10 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 432 HIS 0.002 0.001 HIS A 194 PHE 0.016 0.001 PHE A 455 TYR 0.012 0.001 TYR A 207 ARG 0.005 0.001 ARG A 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.421 Fit side-chains REVERT: A 55 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6089 (pp20) outliers start: 10 outliers final: 9 residues processed: 45 average time/residue: 0.1972 time to fit residues: 11.4089 Evaluate side-chains 50 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.094721 restraints weight = 4864.373| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.12 r_work: 0.2991 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3777 Z= 0.240 Angle : 0.472 4.890 5103 Z= 0.263 Chirality : 0.040 0.162 573 Planarity : 0.004 0.031 649 Dihedral : 4.079 20.188 502 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.21 % Allowed : 10.32 % Favored : 87.47 % 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: 0.93 (0.38), residues: 467 helix: 1.94 (0.38), residues: 180 sheet: -0.71 (0.59), residues: 72 loop : 0.05 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 432 HIS 0.003 0.001 HIS A 54 PHE 0.015 0.001 PHE A 287 TYR 0.012 0.001 TYR A 207 ARG 0.005 0.001 ARG A 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 934 Ramachandran restraints generated. 467 Oldfield, 0 Emsley, 467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.442 Fit side-chains REVERT: A 55 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6066 (pp20) outliers start: 9 outliers final: 8 residues processed: 43 average time/residue: 0.1908 time to fit residues: 10.1890 Evaluate side-chains 49 residues out of total 407 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 495 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.097104 restraints weight = 4848.845| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.04 r_work: 0.3021 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3777 Z= 0.181 Angle : 0.442 4.803 5103 Z= 0.247 Chirality : 0.039 0.157 573 Planarity : 0.004 0.032 649 Dihedral : 3.949 18.451 502 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.46 % Allowed : 10.32 % Favored : 87.22 % 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: 0.86 (0.38), residues: 467 helix: 1.90 (0.37), residues: 180 sheet: -0.86 (0.58), residues: 74 loop : 0.05 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 432 HIS 0.002 0.001 HIS A 54 PHE 0.013 0.001 PHE A 287 TYR 0.012 0.001 TYR A 207 ARG 0.006 0.001 ARG A 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2526.78 seconds wall clock time: 43 minutes 56.88 seconds (2636.88 seconds total)