Starting phenix.real_space_refine on Tue Mar 11 14:30:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smp_40598/03_2025/8smp_40598.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smp_40598/03_2025/8smp_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_40598/03_2025/8smp_40598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smp_40598/03_2025/8smp_40598.map" model { file = "/net/cci-nas-00/data/ceres_data/8smp_40598/03_2025/8smp_40598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smp_40598/03_2025/8smp_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-5624/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: 4.43, per 1000 atoms: 0.73 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: 1.61 Conformation dependent library (CDL) restraints added in 876.8 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: 0.68 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: 1.95 Time building geometry restraints manager: 1.87 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: 1.350 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 18.980 Find NCS groups from input model: 0.070 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.580 ------------------------------------------------------------------------------- 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 : 0.683 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: 0.1863 time to fit residues: 30.1546 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 : 0.697 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.136300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.116339 restraints weight = 7801.725| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.57 r_work: 0.3080 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.699 Fit side-chains REVERT: A 284 SER cc_start: 0.9001 (m) cc_final: 0.8753 (m) REVERT: A 436 TRP cc_start: 0.8443 (m100) cc_final: 0.8195 (m100) REVERT: L 93 SER cc_start: 0.8224 (t) cc_final: 0.7939 (p) outliers start: 15 outliers final: 7 residues processed: 126 average time/residue: 0.1970 time to fit residues: 32.0881 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 : 0.693 ------------------------------------------------------------------------------- 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 23 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 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 213 GLN A 260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.131269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.111829 restraints weight = 7891.776| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.47 r_work: 0.3020 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6261 Z= 0.305 Angle : 0.572 11.278 8495 Z= 0.304 Chirality : 0.043 0.149 921 Planarity : 0.004 0.052 1036 Dihedral : 4.652 37.054 869 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Rotamer: Outliers : 3.33 % Allowed : 21.82 % 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: 0.77 (0.31), residues: 747 helix: 2.05 (0.28), residues: 334 sheet: 0.16 (0.40), residues: 172 loop : -1.46 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 432 HIS 0.004 0.001 HIS A 398 PHE 0.023 0.002 PHE A 323 TYR 0.022 0.001 TYR H 83 ARG 0.003 0.000 ARG A 496 *********************** 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 133 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.699 Fit side-chains REVERT: A 60 PHE cc_start: 0.5604 (OUTLIER) cc_final: 0.4952 (m-10) REVERT: A 194 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7424 (pt0) REVERT: A 436 TRP cc_start: 0.8424 (m100) cc_final: 0.8200 (m100) outliers start: 22 outliers final: 13 residues processed: 127 average time/residue: 0.1843 time to fit residues: 30.7720 Evaluate side-chains 120 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 426 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 511 ILE 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 65 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.132296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.112761 restraints weight = 7908.886| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.48 r_work: 0.3033 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1909 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 : 0.536 11.330 8495 Z= 0.283 Chirality : 0.041 0.141 921 Planarity : 0.004 0.051 1036 Dihedral : 4.561 35.031 869 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.31 % Rotamer: Outliers : 3.48 % Allowed : 23.18 % Favored : 73.33 % 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: 0.82 (0.31), residues: 747 helix: 2.09 (0.28), residues: 335 sheet: 0.19 (0.40), residues: 171 loop : -1.44 (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 0.023 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 : 0.727 Fit side-chains REVERT: A 60 PHE cc_start: 0.5461 (OUTLIER) cc_final: 0.4892 (m-10) REVERT: A 436 TRP cc_start: 0.8434 (m100) cc_final: 0.8224 (m100) REVERT: L 80 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8264 (mm-40) outliers start: 23 outliers final: 15 residues processed: 125 average time/residue: 0.1891 time to fit residues: 31.1186 Evaluate side-chains 125 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 171 THR Chi-restraints excluded: chain A residue 338 THR 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 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 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 35 optimal weight: 0.0770 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 59 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.134054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.114830 restraints weight = 7809.673| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.41 r_work: 0.3068 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6261 Z= 0.168 Angle : 0.513 11.269 8495 Z= 0.267 Chirality : 0.040 0.135 921 Planarity : 0.004 0.049 1036 Dihedral : 4.411 33.618 869 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.31 % Rotamer: Outliers : 3.18 % Allowed : 25.61 % 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: 1.05 (0.32), residues: 747 helix: 2.28 (0.28), residues: 336 sheet: 0.29 (0.40), residues: 171 loop : -1.32 (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 72 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: 21 poor density : 113 time to evaluate : 0.691 Fit side-chains REVERT: A 60 PHE cc_start: 0.5370 (OUTLIER) cc_final: 0.4821 (m-10) outliers start: 21 outliers final: 14 residues processed: 126 average time/residue: 0.1850 time to fit residues: 30.5519 Evaluate side-chains 124 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 chunk 49 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.133608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.114481 restraints weight = 7723.502| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.41 r_work: 0.3063 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1904 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= 0.180 Angle : 0.516 11.159 8495 Z= 0.269 Chirality : 0.040 0.136 921 Planarity : 0.004 0.049 1036 Dihedral : 4.397 33.886 869 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.42 % Favored : 95.45 % 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: 1.07 (0.32), residues: 747 helix: 2.26 (0.28), residues: 336 sheet: 0.37 (0.40), residues: 171 loop : -1.33 (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 0.014 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 132 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.745 Fit side-chains REVERT: A 60 PHE cc_start: 0.5257 (OUTLIER) cc_final: 0.4710 (m-10) REVERT: A 194 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7500 (pt0) REVERT: A 436 TRP cc_start: 0.8380 (m100) cc_final: 0.7985 (m100) REVERT: L 80 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8243 (mm-40) outliers start: 22 outliers final: 16 residues processed: 124 average time/residue: 0.1855 time to fit residues: 30.3175 Evaluate side-chains 127 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 73 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.132565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.113488 restraints weight = 7846.665| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.43 r_work: 0.3056 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2039 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= 0.212 Angle : 0.541 11.167 8495 Z= 0.281 Chirality : 0.041 0.140 921 Planarity : 0.004 0.050 1036 Dihedral : 4.474 34.277 869 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Rotamer: Outliers : 3.79 % Allowed : 25.15 % Favored : 71.06 % 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: 0.99 (0.31), residues: 747 helix: 2.18 (0.28), residues: 336 sheet: 0.38 (0.39), residues: 171 loop : -1.39 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 432 HIS 0.003 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 135 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.648 Fit side-chains REVERT: A 60 PHE cc_start: 0.5384 (OUTLIER) cc_final: 0.4771 (m-10) REVERT: A 194 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7564 (pt0) REVERT: A 436 TRP cc_start: 0.8432 (m100) cc_final: 0.8006 (m100) outliers start: 25 outliers final: 18 residues processed: 126 average time/residue: 0.1892 time to fit residues: 31.5352 Evaluate side-chains 126 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 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 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 71 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.131928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.112716 restraints weight = 7796.331| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.41 r_work: 0.3037 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2131 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 : 0.556 11.106 8495 Z= 0.289 Chirality : 0.041 0.141 921 Planarity : 0.004 0.050 1036 Dihedral : 4.551 34.426 869 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Rotamer: Outliers : 3.64 % Allowed : 25.15 % 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: 0.93 (0.31), residues: 747 helix: 2.09 (0.28), residues: 336 sheet: 0.43 (0.40), residues: 171 loop : -1.44 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 432 HIS 0.003 0.001 HIS A 398 PHE 0.022 0.002 PHE A 323 TYR 0.017 0.001 TYR H 83 ARG 0.002 0.000 ARG A 388 *********************** 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 132 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.758 Fit side-chains REVERT: A 60 PHE cc_start: 0.5496 (OUTLIER) cc_final: 0.4736 (m-10) REVERT: A 194 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: A 436 TRP cc_start: 0.8423 (m100) cc_final: 0.8005 (m100) outliers start: 24 outliers final: 18 residues processed: 125 average time/residue: 0.1914 time to fit residues: 31.4310 Evaluate side-chains 124 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 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 426 ILE Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 475 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 20 SER Chi-restraints excluded: chain H residue 120 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.132516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.112757 restraints weight = 7787.659| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.53 r_work: 0.3031 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2160 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= 0.219 Angle : 0.558 11.101 8495 Z= 0.288 Chirality : 0.041 0.139 921 Planarity : 0.004 0.050 1036 Dihedral : 4.534 33.864 869 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.42 % Favored : 95.45 % Rotamer: Outliers : 3.33 % Allowed : 25.61 % Favored : 71.06 % 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: 0.95 (0.31), residues: 747 helix: 2.12 (0.28), residues: 336 sheet: 0.46 (0.40), residues: 171 loop : -1.45 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 432 HIS 0.003 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 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 127 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.688 Fit side-chains REVERT: A 60 PHE cc_start: 0.5523 (OUTLIER) cc_final: 0.4756 (m-10) REVERT: A 436 TRP cc_start: 0.8501 (m100) cc_final: 0.8120 (m100) outliers start: 22 outliers final: 18 residues processed: 120 average time/residue: 0.1834 time to fit residues: 29.0297 Evaluate side-chains 123 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 171 THR Chi-restraints excluded: chain A residue 251 VAL 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 20 SER Chi-restraints excluded: chain H residue 120 THR 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 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.132447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.113403 restraints weight = 7834.172| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.40 r_work: 0.3047 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2173 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= 0.211 Angle : 0.559 11.053 8495 Z= 0.288 Chirality : 0.041 0.137 921 Planarity : 0.004 0.050 1036 Dihedral : 4.503 33.767 869 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.31 % Rotamer: Outliers : 3.03 % Allowed : 25.76 % 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: 0.95 (0.31), residues: 747 helix: 2.17 (0.28), residues: 334 sheet: 0.45 (0.40), residues: 171 loop : -1.49 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 432 HIS 0.003 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 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 124 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.711 Fit side-chains REVERT: A 60 PHE cc_start: 0.5391 (OUTLIER) cc_final: 0.4633 (m-10) REVERT: A 436 TRP cc_start: 0.8475 (m100) cc_final: 0.8024 (m100) outliers start: 20 outliers final: 18 residues processed: 117 average time/residue: 0.1923 time to fit residues: 29.6813 Evaluate side-chains 123 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 171 THR Chi-restraints excluded: chain A residue 251 VAL 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 20 SER Chi-restraints excluded: chain H residue 120 THR 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 64 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 45 optimal weight: 0.0060 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.133953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.112507 restraints weight = 7992.848| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.66 r_work: 0.3021 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2178 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= 0.197 Angle : 0.557 11.057 8495 Z= 0.285 Chirality : 0.041 0.136 921 Planarity : 0.004 0.050 1036 Dihedral : 4.468 33.643 869 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.42 % Favored : 95.45 % Rotamer: Outliers : 3.18 % Allowed : 25.45 % 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: 0.99 (0.31), residues: 747 helix: 2.21 (0.28), residues: 334 sheet: 0.48 (0.40), residues: 171 loop : -1.49 (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 0.002 0.000 ARG L 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3370.61 seconds wall clock time: 58 minutes 25.86 seconds (3505.86 seconds total)