Starting phenix.real_space_refine on Fri Dec 27 17:05:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smp_40598/12_2024/8smp_40598.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smp_40598/12_2024/8smp_40598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8smp_40598/12_2024/8smp_40598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smp_40598/12_2024/8smp_40598.map" model { file = "/net/cci-nas-00/data/ceres_data/8smp_40598/12_2024/8smp_40598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smp_40598/12_2024/8smp_40598.cif" } resolution = 3.4 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 3949 2.51 5 N 989 2.21 5 O 1108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6097 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4339 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 14, 'TRANS': 512} Chain breaks: 2 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 937 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.60, per 1000 atoms: 0.75 Number of scatterers: 6097 At special positions: 0 Unit cell: (68.04, 78.84, 138.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 2 15.00 Mg 1 11.99 O 1108 8.00 N 989 7.00 C 3949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 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: 1.76 Conformation dependent library (CDL) restraints added in 976.2 milliseconds 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 46.2% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 27 through 52 Processing helix chain 'A' and resid 59 through 90 Processing helix chain 'A' and resid 110 through 123 Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 144 through 155 removed outlier: 4.027A pdb=" N MET A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 216 through 230 removed outlier: 3.980A pdb=" N GLU A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 230 " --> pdb=" O PHE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 259 Processing helix chain 'A' and resid 278 through 294 removed outlier: 3.632A pdb=" N PHE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.509A pdb=" N PHE A 302 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 removed outlier: 4.917A pdb=" N GLU A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ALA A 326 " --> pdb=" O VAL A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 Processing helix chain 'A' and resid 371 through 394 removed outlier: 3.883A pdb=" N LEU A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 428 Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 430 through 457 Processing helix chain 'A' and resid 459 through 465 removed outlier: 3.755A pdb=" N LEU A 462 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 465 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 removed outlier: 3.981A pdb=" N LEU A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 505 through 529 Processing helix chain 'A' and resid 534 through 568 Processing helix chain 'H' and resid 31 through 34 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.723A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.416A pdb=" N GLY A 161 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N MET A 212 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR A 163 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 100 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE A 134 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU A 102 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL A 136 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE A 104 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP A 138 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLY A 106 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 105 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 313 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLY A 264 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N TYR A 263 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N TYR A 358 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 10.868A pdb=" N ALA A 265 " --> pdb=" O TYR A 358 " (cutoff:3.500A) removed outlier: 11.457A pdb=" N HIS A 360 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 10.434A pdb=" N GLY A 267 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER A 362 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA3, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.586A pdb=" N ALA H 95 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 12 through 13 removed outlier: 6.561A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.575A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 966 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: 1.80 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1720 1.34 - 1.45: 1185 1.45 - 1.57: 3276 1.57 - 1.69: 3 1.69 - 1.81: 77 Bond restraints: 6261 Sorted by residual: bond pdb=" N THR A 25 " pdb=" CA THR A 25 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.63e+00 bond pdb=" N HIS A 23 " pdb=" CA HIS A 23 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.41e-02 5.03e+03 4.00e+00 bond pdb=" C HIS A 23 " pdb=" N PRO A 24 " ideal model delta sigma weight residual 1.326 1.351 -0.025 1.44e-02 4.82e+03 3.03e+00 bond pdb=" CG HIS A 23 " pdb=" CD2 HIS A 23 " ideal model delta sigma weight residual 1.354 1.338 0.016 1.10e-02 8.26e+03 2.08e+00 bond pdb=" N THR A 335 " pdb=" CA THR A 335 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.07e+00 ... (remaining 6256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 8384 1.89 - 3.79: 90 3.79 - 5.68: 17 5.68 - 7.58: 1 7.58 - 9.47: 3 Bond angle restraints: 8495 Sorted by residual: angle pdb=" C GLY A 334 " pdb=" N THR A 335 " pdb=" CA THR A 335 " ideal model delta sigma weight residual 121.54 131.01 -9.47 1.91e+00 2.74e-01 2.46e+01 angle pdb=" N ILE A 460 " pdb=" CA ILE A 460 " pdb=" C ILE A 460 " ideal model delta sigma weight residual 113.07 106.49 6.58 1.36e+00 5.41e-01 2.34e+01 angle pdb=" N VAL H 67 " pdb=" CA VAL H 67 " pdb=" C VAL H 67 " ideal model delta sigma weight residual 112.96 109.89 3.07 1.00e+00 1.00e+00 9.42e+00 angle pdb=" N THR A 335 " pdb=" CA THR A 335 " pdb=" CB THR A 335 " ideal model delta sigma weight residual 110.49 115.34 -4.85 1.69e+00 3.50e-01 8.23e+00 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 126.93 -5.39 1.91e+00 2.74e-01 7.96e+00 ... (remaining 8490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 3141 17.79 - 35.58: 379 35.58 - 53.37: 115 53.37 - 71.16: 13 71.16 - 88.95: 3 Dihedral angle restraints: 3651 sinusoidal: 1441 harmonic: 2210 Sorted by residual: dihedral pdb=" CA ASN A 458 " pdb=" C ASN A 458 " pdb=" N PHE A 459 " pdb=" CA PHE A 459 " ideal model delta harmonic sigma weight residual 180.00 162.33 17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" N ASN H 80 " pdb=" CA ASN H 80 " pdb=" CB ASN H 80 " pdb=" CG ASN H 80 " ideal model delta sinusoidal sigma weight residual -60.00 -119.96 59.96 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LYS A 537 " pdb=" CA LYS A 537 " pdb=" CB LYS A 537 " pdb=" CG LYS A 537 " ideal model delta sinusoidal sigma weight residual -180.00 -120.60 -59.40 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 642 0.035 - 0.069: 194 0.069 - 0.104: 61 0.104 - 0.139: 21 0.139 - 0.173: 3 Chirality restraints: 921 Sorted by residual: chirality pdb=" CA HIS A 23 " pdb=" N HIS A 23 " pdb=" C HIS A 23 " pdb=" CB HIS A 23 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA TRP A 436 " pdb=" N TRP A 436 " pdb=" C TRP A 436 " pdb=" CB TRP A 436 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA ILE A 460 " pdb=" N ILE A 460 " pdb=" C ILE A 460 " pdb=" CB ILE A 460 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 918 not shown) Planarity restraints: 1036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 59 " -0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO L 60 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 534 " -0.030 5.00e-02 4.00e+02 4.63e-02 3.42e+00 pdb=" N PRO A 535 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 310 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A 311 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " -0.025 5.00e-02 4.00e+02 ... (remaining 1033 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 291 2.73 - 3.27: 5741 3.27 - 3.81: 10224 3.81 - 4.36: 11622 4.36 - 4.90: 21170 Nonbonded interactions: 49048 Sorted by model distance: nonbonded pdb=" O GLY A 334 " pdb=" OG1 THR A 335 " model vdw 2.186 3.040 nonbonded pdb=" O LYS A 17 " pdb=" OH TYR A 354 " model vdw 2.261 3.040 nonbonded pdb=" O2B UDP A 601 " pdb="MG MG A 602 " model vdw 2.263 2.170 nonbonded pdb=" O MET A 469 " pdb=" OG1 THR A 473 " model vdw 2.278 3.040 nonbonded pdb=" OE2 GLU A 109 " pdb=" NH1 ARG A 496 " model vdw 2.286 3.120 ... (remaining 49043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.020 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.840 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.002 0.038 6261 Z= 0.142 Angle : 0.526 9.475 8495 Z= 0.285 Chirality : 0.040 0.173 921 Planarity : 0.004 0.066 1036 Dihedral : 16.401 88.946 2241 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.15 % Favored : 95.72 % Rotamer: Outliers : 0.30 % Allowed : 22.42 % Favored : 77.27 % 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: 1.14 (0.32), residues: 747 helix: 2.34 (0.29), residues: 338 sheet: 0.32 (0.41), residues: 168 loop : -1.27 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 432 HIS 0.002 0.000 HIS A 72 PHE 0.022 0.001 PHE A 323 TYR 0.011 0.001 TYR A 451 ARG 0.002 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.684 Fit side-chains REVERT: A 436 TRP cc_start: 0.8110 (m100) cc_final: 0.7854 (m100) REVERT: H 93 ASP cc_start: 0.8716 (m-30) cc_final: 0.8337 (m-30) outliers start: 2 outliers final: 1 residues processed: 123 average time/residue: 0.1827 time to fit residues: 29.8555 Evaluate side-chains 120 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 92 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.0370 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN L 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6261 Z= 0.220 Angle : 0.528 11.497 8495 Z= 0.281 Chirality : 0.041 0.141 921 Planarity : 0.005 0.049 1036 Dihedral : 4.527 41.309 872 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.95 % Favored : 94.91 % Rotamer: Outliers : 2.27 % Allowed : 21.21 % Favored : 76.52 % 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: 1.14 (0.32), residues: 747 helix: 2.31 (0.28), residues: 338 sheet: 0.39 (0.40), residues: 169 loop : -1.28 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 432 HIS 0.003 0.001 HIS A 72 PHE 0.022 0.001 PHE A 323 TYR 0.016 0.001 TYR H 83 ARG 0.006 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.824 Fit side-chains REVERT: A 284 SER cc_start: 0.8455 (m) cc_final: 0.8152 (m) REVERT: A 290 MET cc_start: 0.8879 (tpp) cc_final: 0.8647 (tpp) REVERT: A 404 MET cc_start: 0.7960 (ttp) cc_final: 0.7676 (ttm) REVERT: A 436 TRP cc_start: 0.8061 (m100) cc_final: 0.7685 (m100) REVERT: L 93 SER cc_start: 0.8000 (t) cc_final: 0.7575 (p) outliers start: 15 outliers final: 7 residues processed: 126 average time/residue: 0.2107 time to fit residues: 34.5893 Evaluate side-chains 123 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6261 Z= 0.225 Angle : 0.532 11.311 8495 Z= 0.281 Chirality : 0.041 0.142 921 Planarity : 0.004 0.050 1036 Dihedral : 4.462 35.664 869 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.95 % Favored : 94.91 % Rotamer: Outliers : 2.88 % Allowed : 22.27 % Favored : 74.85 % 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: 1.02 (0.32), residues: 747 helix: 2.22 (0.28), residues: 337 sheet: 0.30 (0.40), residues: 171 loop : -1.32 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 432 HIS 0.003 0.001 HIS A 398 PHE 0.022 0.001 PHE A 323 TYR 0.018 0.001 TYR H 83 ARG 0.003 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.798 Fit side-chains REVERT: A 60 PHE cc_start: 0.5370 (OUTLIER) cc_final: 0.4840 (m-10) REVERT: A 436 TRP cc_start: 0.8065 (m100) cc_final: 0.7678 (m100) REVERT: L 93 SER cc_start: 0.8237 (t) cc_final: 0.7893 (p) outliers start: 19 outliers final: 11 residues processed: 126 average time/residue: 0.1925 time to fit residues: 31.9201 Evaluate side-chains 122 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6261 Z= 0.229 Angle : 0.532 11.312 8495 Z= 0.281 Chirality : 0.041 0.142 921 Planarity : 0.004 0.051 1036 Dihedral : 4.465 35.849 869 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.95 % Favored : 94.91 % Rotamer: Outliers : 3.48 % Allowed : 23.33 % Favored : 73.18 % 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 (0.31), residues: 747 helix: 2.20 (0.28), residues: 335 sheet: 0.24 (0.40), residues: 171 loop : -1.40 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 432 HIS 0.003 0.001 HIS A 398 PHE 0.022 0.001 PHE A 323 TYR 0.018 0.001 TYR H 83 ARG 0.002 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.760 Fit side-chains REVERT: A 60 PHE cc_start: 0.5504 (OUTLIER) cc_final: 0.4869 (m-10) REVERT: A 194 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7242 (pt0) REVERT: A 289 TRP cc_start: 0.8374 (t60) cc_final: 0.8082 (t60) REVERT: A 436 TRP cc_start: 0.8072 (m100) cc_final: 0.7683 (m100) REVERT: L 80 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8282 (mm-40) outliers start: 23 outliers final: 13 residues processed: 125 average time/residue: 0.1926 time to fit residues: 32.2329 Evaluate side-chains 122 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6261 Z= 0.190 Angle : 0.520 11.273 8495 Z= 0.271 Chirality : 0.040 0.137 921 Planarity : 0.004 0.050 1036 Dihedral : 4.429 34.082 869 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.31 % Rotamer: Outliers : 3.33 % Allowed : 25.30 % Favored : 71.36 % 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: 1.05 (0.31), residues: 747 helix: 2.27 (0.28), residues: 336 sheet: 0.31 (0.40), residues: 171 loop : -1.34 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 432 HIS 0.002 0.001 HIS A 398 PHE 0.022 0.001 PHE A 323 TYR 0.016 0.001 TYR H 83 ARG 0.002 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.618 Fit side-chains REVERT: A 60 PHE cc_start: 0.5271 (OUTLIER) cc_final: 0.4758 (m-10) REVERT: A 194 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7286 (pt0) REVERT: A 289 TRP cc_start: 0.8342 (t60) cc_final: 0.8069 (t60) REVERT: A 436 TRP cc_start: 0.8049 (m100) cc_final: 0.7668 (m100) outliers start: 22 outliers final: 16 residues processed: 125 average time/residue: 0.1977 time to fit residues: 32.2275 Evaluate side-chains 129 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN L 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6261 Z= 0.211 Angle : 0.533 11.086 8495 Z= 0.279 Chirality : 0.041 0.139 921 Planarity : 0.004 0.050 1036 Dihedral : 4.456 34.570 869 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.69 % Favored : 95.18 % Rotamer: Outliers : 4.24 % Allowed : 24.55 % Favored : 71.21 % 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: 1.01 (0.31), residues: 747 helix: 2.24 (0.28), residues: 336 sheet: 0.31 (0.39), residues: 171 loop : -1.37 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 432 HIS 0.003 0.001 HIS A 398 PHE 0.022 0.001 PHE A 323 TYR 0.018 0.001 TYR H 83 ARG 0.002 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.665 Fit side-chains REVERT: A 60 PHE cc_start: 0.5285 (OUTLIER) cc_final: 0.4706 (m-10) REVERT: A 194 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7337 (pt0) REVERT: A 289 TRP cc_start: 0.8377 (t60) cc_final: 0.8136 (t60) REVERT: A 436 TRP cc_start: 0.8043 (m100) cc_final: 0.7645 (m100) REVERT: L 80 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8299 (mm-40) outliers start: 28 outliers final: 20 residues processed: 125 average time/residue: 0.1888 time to fit residues: 30.8948 Evaluate side-chains 130 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6261 Z= 0.202 Angle : 0.533 11.139 8495 Z= 0.276 Chirality : 0.041 0.137 921 Planarity : 0.004 0.050 1036 Dihedral : 4.462 33.912 869 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.69 % Favored : 95.18 % Rotamer: Outliers : 4.09 % Allowed : 25.00 % Favored : 70.91 % 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: 1.04 (0.31), residues: 747 helix: 2.26 (0.28), residues: 336 sheet: 0.34 (0.39), residues: 171 loop : -1.37 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 432 HIS 0.002 0.001 HIS A 398 PHE 0.022 0.001 PHE A 323 TYR 0.016 0.001 TYR H 83 ARG 0.002 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.737 Fit side-chains REVERT: A 60 PHE cc_start: 0.5371 (OUTLIER) cc_final: 0.4728 (m-10) REVERT: A 194 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7291 (pt0) REVERT: A 289 TRP cc_start: 0.8379 (t60) cc_final: 0.8118 (t60) REVERT: A 436 TRP cc_start: 0.8068 (m100) cc_final: 0.7642 (m100) outliers start: 27 outliers final: 20 residues processed: 128 average time/residue: 0.1881 time to fit residues: 31.3716 Evaluate side-chains 129 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6261 Z= 0.204 Angle : 0.540 11.101 8495 Z= 0.279 Chirality : 0.040 0.137 921 Planarity : 0.004 0.050 1036 Dihedral : 4.466 33.901 869 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.31 % Rotamer: Outliers : 3.94 % Allowed : 25.15 % Favored : 70.91 % 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: 1.05 (0.31), residues: 747 helix: 2.28 (0.28), residues: 334 sheet: 0.43 (0.40), residues: 171 loop : -1.44 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 432 HIS 0.002 0.001 HIS A 398 PHE 0.022 0.001 PHE A 323 TYR 0.016 0.001 TYR H 83 ARG 0.001 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.666 Fit side-chains REVERT: A 60 PHE cc_start: 0.5350 (OUTLIER) cc_final: 0.4658 (m-10) REVERT: A 194 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7262 (pt0) REVERT: A 289 TRP cc_start: 0.8395 (t60) cc_final: 0.8123 (t60) REVERT: A 436 TRP cc_start: 0.8066 (m100) cc_final: 0.7607 (m100) outliers start: 26 outliers final: 21 residues processed: 125 average time/residue: 0.1968 time to fit residues: 32.3433 Evaluate side-chains 127 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 0.0060 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6261 Z= 0.196 Angle : 0.541 11.108 8495 Z= 0.279 Chirality : 0.040 0.136 921 Planarity : 0.004 0.050 1036 Dihedral : 4.442 33.589 869 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.42 % Favored : 95.45 % Rotamer: Outliers : 3.94 % Allowed : 25.15 % Favored : 70.91 % 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: 1.09 (0.31), residues: 747 helix: 2.32 (0.28), residues: 334 sheet: 0.47 (0.40), residues: 171 loop : -1.42 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 432 HIS 0.002 0.001 HIS A 398 PHE 0.022 0.001 PHE A 323 TYR 0.015 0.001 TYR H 83 ARG 0.001 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.709 Fit side-chains REVERT: A 60 PHE cc_start: 0.5330 (OUTLIER) cc_final: 0.4669 (m-10) REVERT: A 194 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7254 (pt0) REVERT: A 289 TRP cc_start: 0.8383 (t60) cc_final: 0.8098 (t60) REVERT: A 436 TRP cc_start: 0.8101 (m100) cc_final: 0.7662 (m100) outliers start: 26 outliers final: 23 residues processed: 122 average time/residue: 0.1901 time to fit residues: 30.5631 Evaluate side-chains 130 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6261 Z= 0.234 Angle : 0.565 11.034 8495 Z= 0.291 Chirality : 0.041 0.141 921 Planarity : 0.004 0.051 1036 Dihedral : 4.533 34.466 869 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 4.09 % Allowed : 25.00 % Favored : 70.91 % 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: 0.97 (0.31), residues: 747 helix: 2.21 (0.28), residues: 333 sheet: 0.42 (0.40), residues: 171 loop : -1.46 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 432 HIS 0.003 0.001 HIS A 398 PHE 0.022 0.001 PHE A 323 TYR 0.017 0.001 TYR H 83 ARG 0.002 0.000 ARG L 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.666 Fit side-chains REVERT: A 60 PHE cc_start: 0.5478 (OUTLIER) cc_final: 0.4665 (m-10) REVERT: A 194 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7272 (pt0) REVERT: A 436 TRP cc_start: 0.8049 (m100) cc_final: 0.7598 (m100) outliers start: 27 outliers final: 23 residues processed: 123 average time/residue: 0.1856 time to fit residues: 30.1241 Evaluate side-chains 130 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 60 PHE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.131810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.112314 restraints weight = 7724.196| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.46 r_work: 0.3026 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6261 Z= 0.237 Angle : 0.565 11.005 8495 Z= 0.291 Chirality : 0.041 0.140 921 Planarity : 0.004 0.051 1036 Dihedral : 4.558 34.277 869 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Rotamer: Outliers : 3.94 % Allowed : 24.85 % Favored : 71.21 % 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: 0.92 (0.31), residues: 747 helix: 2.18 (0.28), residues: 332 sheet: 0.41 (0.40), residues: 171 loop : -1.52 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 432 HIS 0.003 0.001 HIS A 398 PHE 0.022 0.001 PHE A 323 TYR 0.017 0.001 TYR H 83 ARG 0.002 0.000 ARG L 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1692.21 seconds wall clock time: 31 minutes 50.02 seconds (1910.02 seconds total)