Starting phenix.real_space_refine on Fri Oct 10 13:33:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smp_40598/10_2025/8smp_40598.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smp_40598/10_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_40598/10_2025/8smp_40598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smp_40598/10_2025/8smp_40598.map" model { file = "/net/cci-nas-00/data/ceres_data/8smp_40598/10_2025/8smp_40598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smp_40598/10_2025/8smp_40598.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.61, per 1000 atoms: 0.26 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: 0.48 Conformation dependent library (CDL) restraints added in 375.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.22 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: 0.94 Time building geometry restraints manager: 0.67 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: 2.740 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.490 ------------------------------------------------------------------------------- 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 6263 Z= 0.117 Angle : 0.526 9.475 8499 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 456 TYR 0.011 0.001 TYR A 451 PHE 0.022 0.001 PHE A 323 TRP 0.022 0.001 TRP A 432 HIS 0.002 0.000 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 6261) covalent geometry : angle 0.52594 ( 8495) SS BOND : bond 0.00247 ( 2) SS BOND : angle 0.71426 ( 4) hydrogen bonds : bond 0.12115 ( 338) hydrogen bonds : angle 4.85189 ( 966) *********************** 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 : 0.183 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: 0.0856 time to fit residues: 13.9190 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 : 0.249 ------------------------------------------------------------------------------- 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 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.0020 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 overall best weight: 1.2072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 347 ASN L 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.132418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.112499 restraints weight = 7984.066| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.40 r_work: 0.3040 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6263 Z= 0.206 Angle : 0.587 11.446 8499 Z= 0.315 Chirality : 0.043 0.148 921 Planarity : 0.005 0.053 1036 Dihedral : 4.849 40.097 872 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 2.88 % Allowed : 20.76 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.32), residues: 747 helix: 2.10 (0.28), residues: 334 sheet: 0.23 (0.40), residues: 171 loop : -1.39 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 496 TYR 0.021 0.001 TYR H 83 PHE 0.022 0.002 PHE A 323 TRP 0.017 0.002 TRP A 432 HIS 0.004 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 6261) covalent geometry : angle 0.58652 ( 8495) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.59643 ( 4) hydrogen bonds : bond 0.04788 ( 338) hydrogen bonds : angle 4.16948 ( 966) *********************** 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 134 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.238 Fit side-chains REVERT: A 436 TRP cc_start: 0.8443 (m100) cc_final: 0.8223 (m100) REVERT: L 93 SER cc_start: 0.8364 (t) cc_final: 0.8153 (p) outliers start: 19 outliers final: 11 residues processed: 127 average time/residue: 0.0867 time to fit residues: 14.4705 Evaluate side-chains 122 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR 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 511 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 121 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 chunk 3 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN L 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.133523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.114502 restraints weight = 7800.342| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.39 r_work: 0.3067 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6263 Z= 0.138 Angle : 0.531 11.335 8499 Z= 0.279 Chirality : 0.041 0.140 921 Planarity : 0.004 0.050 1036 Dihedral : 4.459 35.551 869 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.42 % Favored : 95.45 % Rotamer: Outliers : 2.73 % Allowed : 23.03 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.32), residues: 747 helix: 2.13 (0.28), residues: 337 sheet: 0.24 (0.40), residues: 171 loop : -1.31 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 496 TYR 0.017 0.001 TYR H 83 PHE 0.022 0.001 PHE A 323 TRP 0.015 0.001 TRP A 432 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6261) covalent geometry : angle 0.53125 ( 8495) SS BOND : bond 0.00314 ( 2) SS BOND : angle 0.53198 ( 4) hydrogen bonds : bond 0.04191 ( 338) hydrogen bonds : angle 3.92732 ( 966) *********************** 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: 18 poor density : 114 time to evaluate : 0.229 Fit side-chains REVERT: A 60 PHE cc_start: 0.5466 (OUTLIER) cc_final: 0.4948 (m-10) REVERT: A 436 TRP cc_start: 0.8394 (m100) cc_final: 0.8138 (m100) outliers start: 18 outliers final: 11 residues processed: 124 average time/residue: 0.0834 time to fit residues: 13.6623 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 : 0.228 ------------------------------------------------------------------------------- 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 400 HIS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 469 MET 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 72 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.131751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.112743 restraints weight = 7877.796| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.36 r_work: 0.3041 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6263 Z= 0.161 Angle : 0.547 11.323 8499 Z= 0.290 Chirality : 0.041 0.143 921 Planarity : 0.004 0.052 1036 Dihedral : 4.536 36.138 869 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.22 % Favored : 94.65 % Rotamer: Outliers : 3.94 % Allowed : 23.18 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.31), residues: 747 helix: 2.10 (0.28), residues: 334 sheet: 0.19 (0.40), residues: 171 loop : -1.41 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 496 TYR 0.020 0.001 TYR H 83 PHE 0.022 0.001 PHE A 323 TRP 0.014 0.001 TRP A 432 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6261) covalent geometry : angle 0.54719 ( 8495) SS BOND : bond 0.00171 ( 2) SS BOND : angle 0.65262 ( 4) hydrogen bonds : bond 0.04396 ( 338) hydrogen bonds : angle 3.95550 ( 966) *********************** 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 137 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.221 Fit side-chains REVERT: A 60 PHE cc_start: 0.5467 (OUTLIER) cc_final: 0.4894 (m-10) REVERT: A 194 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7528 (pt0) REVERT: A 436 TRP cc_start: 0.8401 (m100) cc_final: 0.8179 (m100) REVERT: L 80 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8313 (mm-40) outliers start: 26 outliers final: 16 residues processed: 126 average time/residue: 0.0872 time to fit residues: 14.4196 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 : 0.242 ------------------------------------------------------------------------------- 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 75 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 256 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 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 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 18 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.131829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.112354 restraints weight = 7881.565| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.42 r_work: 0.3024 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6263 Z= 0.157 Angle : 0.549 11.270 8499 Z= 0.288 Chirality : 0.041 0.141 921 Planarity : 0.004 0.052 1036 Dihedral : 4.572 34.775 869 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.69 % Favored : 95.18 % Rotamer: Outliers : 3.94 % Allowed : 24.24 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.31), residues: 747 helix: 2.10 (0.28), residues: 334 sheet: 0.26 (0.40), residues: 171 loop : -1.43 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 496 TYR 0.020 0.001 TYR H 83 PHE 0.023 0.001 PHE A 323 TRP 0.014 0.001 TRP A 432 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 6261) covalent geometry : angle 0.54846 ( 8495) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.64876 ( 4) hydrogen bonds : bond 0.04345 ( 338) hydrogen bonds : angle 3.94448 ( 966) *********************** 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 135 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.277 Fit side-chains REVERT: A 60 PHE cc_start: 0.5497 (OUTLIER) cc_final: 0.4753 (m-10) REVERT: A 194 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7519 (pt0) REVERT: A 565 TRP cc_start: 0.4190 (OUTLIER) cc_final: 0.3748 (m-90) outliers start: 26 outliers final: 18 residues processed: 125 average time/residue: 0.0866 time to fit residues: 14.2696 Evaluate side-chains 128 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 256 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 565 TRP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 16 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 48 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.134285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.115224 restraints weight = 7761.876| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.18 r_work: 0.3080 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6263 Z= 0.123 Angle : 0.524 11.121 8499 Z= 0.273 Chirality : 0.040 0.142 921 Planarity : 0.004 0.050 1036 Dihedral : 4.460 33.477 869 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.42 % Favored : 95.45 % Rotamer: Outliers : 3.64 % Allowed : 24.55 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.31), residues: 747 helix: 2.19 (0.28), residues: 336 sheet: 0.34 (0.40), residues: 171 loop : -1.38 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 329 TYR 0.015 0.001 TYR H 83 PHE 0.022 0.001 PHE A 323 TRP 0.013 0.001 TRP A 432 HIS 0.002 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6261) covalent geometry : angle 0.52346 ( 8495) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.61172 ( 4) hydrogen bonds : bond 0.03990 ( 338) hydrogen bonds : angle 3.84036 ( 966) *********************** 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 138 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.231 Fit side-chains REVERT: A 60 PHE cc_start: 0.5495 (OUTLIER) cc_final: 0.4806 (m-10) REVERT: A 194 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7422 (pt0) REVERT: A 436 TRP cc_start: 0.8326 (m100) cc_final: 0.7900 (m100) REVERT: A 565 TRP cc_start: 0.4110 (OUTLIER) cc_final: 0.3619 (m-90) REVERT: L 80 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8244 (mm-40) outliers start: 24 outliers final: 16 residues processed: 130 average time/residue: 0.0860 time to fit residues: 14.6788 Evaluate side-chains 130 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 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 565 TRP 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 70 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.132785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.112073 restraints weight = 7873.637| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.56 r_work: 0.3023 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6263 Z= 0.153 Angle : 0.553 11.142 8499 Z= 0.288 Chirality : 0.041 0.141 921 Planarity : 0.004 0.051 1036 Dihedral : 4.540 34.647 869 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 4.70 % Allowed : 23.79 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.31), residues: 747 helix: 2.08 (0.28), residues: 336 sheet: 0.38 (0.40), residues: 171 loop : -1.44 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 496 TYR 0.017 0.001 TYR H 83 PHE 0.022 0.001 PHE A 323 TRP 0.011 0.001 TRP A 432 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6261) covalent geometry : angle 0.55266 ( 8495) SS BOND : bond 0.00145 ( 2) SS BOND : angle 0.63924 ( 4) hydrogen bonds : bond 0.04258 ( 338) hydrogen bonds : angle 3.90889 ( 966) *********************** 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 139 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.235 Fit side-chains REVERT: A 30 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6805 (mt) REVERT: A 60 PHE cc_start: 0.5552 (OUTLIER) cc_final: 0.4752 (m-10) REVERT: A 194 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7598 (pt0) REVERT: A 436 TRP cc_start: 0.8459 (m100) cc_final: 0.8031 (m100) REVERT: A 565 TRP cc_start: 0.4134 (OUTLIER) cc_final: 0.3673 (m-90) outliers start: 31 outliers final: 22 residues processed: 130 average time/residue: 0.0867 time to fit residues: 14.8299 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 : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE 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 257 LEU 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 484 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 565 TRP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.133440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.111578 restraints weight = 7887.983| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.55 r_work: 0.3037 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6263 Z= 0.137 Angle : 0.540 11.087 8499 Z= 0.281 Chirality : 0.041 0.137 921 Planarity : 0.004 0.051 1036 Dihedral : 4.511 33.703 869 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.31 % Rotamer: Outliers : 4.09 % Allowed : 24.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.31), residues: 747 helix: 2.14 (0.28), residues: 336 sheet: 0.47 (0.40), residues: 171 loop : -1.41 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 19 TYR 0.016 0.001 TYR H 83 PHE 0.022 0.001 PHE A 323 TRP 0.011 0.001 TRP A 432 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6261) covalent geometry : angle 0.54025 ( 8495) SS BOND : bond 0.00171 ( 2) SS BOND : angle 0.63644 ( 4) hydrogen bonds : bond 0.04091 ( 338) hydrogen bonds : angle 3.86202 ( 966) *********************** 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: 27 poor density : 105 time to evaluate : 0.260 Fit side-chains REVERT: A 30 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6757 (mt) REVERT: A 60 PHE cc_start: 0.5522 (OUTLIER) cc_final: 0.4748 (m-10) REVERT: A 194 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7566 (pt0) REVERT: A 436 TRP cc_start: 0.8512 (m100) cc_final: 0.8121 (m100) REVERT: A 565 TRP cc_start: 0.4132 (OUTLIER) cc_final: 0.3678 (m-90) outliers start: 27 outliers final: 20 residues processed: 123 average time/residue: 0.0868 time to fit residues: 14.0794 Evaluate side-chains 130 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE 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 257 LEU 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 565 TRP Chi-restraints excluded: chain A residue 566 VAL 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 51 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.131044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.110822 restraints weight = 7928.877| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.55 r_work: 0.2997 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6263 Z= 0.193 Angle : 0.587 11.051 8499 Z= 0.308 Chirality : 0.042 0.146 921 Planarity : 0.004 0.053 1036 Dihedral : 4.713 35.599 869 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.22 % Favored : 94.65 % Rotamer: Outliers : 4.55 % Allowed : 24.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.31), residues: 747 helix: 1.95 (0.28), residues: 334 sheet: 0.32 (0.40), residues: 172 loop : -1.51 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 19 TYR 0.019 0.001 TYR H 83 PHE 0.023 0.002 PHE A 323 TRP 0.012 0.001 TRP A 432 HIS 0.004 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 6261) covalent geometry : angle 0.58719 ( 8495) SS BOND : bond 0.00108 ( 2) SS BOND : angle 0.67510 ( 4) hydrogen bonds : bond 0.04650 ( 338) hydrogen bonds : angle 4.03636 ( 966) *********************** 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: 30 poor density : 101 time to evaluate : 0.258 Fit side-chains REVERT: A 30 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6890 (mt) REVERT: A 60 PHE cc_start: 0.5628 (OUTLIER) cc_final: 0.4706 (m-10) REVERT: A 436 TRP cc_start: 0.8478 (m100) cc_final: 0.8121 (m100) REVERT: A 565 TRP cc_start: 0.4313 (OUTLIER) cc_final: 0.3872 (m-90) REVERT: L 80 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8419 (mm-40) outliers start: 30 outliers final: 23 residues processed: 121 average time/residue: 0.0936 time to fit residues: 14.6487 Evaluate side-chains 125 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE 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 251 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 LEU 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 488 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 565 TRP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 73 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.132532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.111635 restraints weight = 7910.529| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.59 r_work: 0.3018 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6263 Z= 0.148 Angle : 0.555 11.055 8499 Z= 0.288 Chirality : 0.041 0.138 921 Planarity : 0.004 0.051 1036 Dihedral : 4.610 34.522 869 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.42 % Favored : 95.45 % Rotamer: Outliers : 4.24 % Allowed : 24.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.31), residues: 747 helix: 2.03 (0.28), residues: 335 sheet: 0.38 (0.40), residues: 171 loop : -1.50 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 496 TYR 0.017 0.001 TYR H 83 PHE 0.022 0.001 PHE A 323 TRP 0.012 0.001 TRP A 432 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6261) covalent geometry : angle 0.55447 ( 8495) SS BOND : bond 0.00173 ( 2) SS BOND : angle 0.65043 ( 4) hydrogen bonds : bond 0.04249 ( 338) hydrogen bonds : angle 3.93342 ( 966) ********************** 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: 28 poor density : 104 time to evaluate : 0.246 Fit side-chains REVERT: A 30 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6816 (mt) REVERT: A 60 PHE cc_start: 0.5583 (OUTLIER) cc_final: 0.4713 (m-10) REVERT: A 436 TRP cc_start: 0.8502 (m100) cc_final: 0.8083 (m100) REVERT: A 565 TRP cc_start: 0.4300 (OUTLIER) cc_final: 0.3902 (m-90) outliers start: 28 outliers final: 23 residues processed: 123 average time/residue: 0.0876 time to fit residues: 14.0779 Evaluate side-chains 130 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE 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 251 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 400 HIS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 565 TRP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 38 optimal weight: 0.0770 chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 28 optimal weight: 0.9980 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.134615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.112827 restraints weight = 7839.126| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.53 r_work: 0.3047 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6263 Z= 0.117 Angle : 0.531 10.989 8499 Z= 0.275 Chirality : 0.040 0.132 921 Planarity : 0.004 0.050 1036 Dihedral : 4.443 33.398 869 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.42 % Favored : 95.45 % Rotamer: Outliers : 3.79 % Allowed : 25.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.31), residues: 747 helix: 2.24 (0.28), residues: 334 sheet: 0.49 (0.40), residues: 171 loop : -1.50 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 496 TYR 0.013 0.001 TYR H 83 PHE 0.022 0.001 PHE A 323 TRP 0.011 0.001 TRP A 432 HIS 0.002 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6261) covalent geometry : angle 0.53110 ( 8495) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.60919 ( 4) hydrogen bonds : bond 0.03839 ( 338) hydrogen bonds : angle 3.81756 ( 966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1761.09 seconds wall clock time: 30 minutes 58.86 seconds (1858.86 seconds total)