Starting phenix.real_space_refine on Thu Jul 2 03:11:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z2t_73777/07_2026/9z2t_73777.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z2t_73777/07_2026/9z2t_73777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z2t_73777/07_2026/9z2t_73777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z2t_73777/07_2026/9z2t_73777.map" model { file = "/net/cci-nas-00/data/ceres_data/9z2t_73777/07_2026/9z2t_73777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z2t_73777/07_2026/9z2t_73777.cif" } resolution = 3.7 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 56 5.49 5 S 31 5.16 5 C 3617 2.51 5 N 1043 2.21 5 O 1274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6021 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4802 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 554} Chain breaks: 1 Chain: "B" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1192 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 22, 'rna3p_pyr': 27} Link IDs: {'rna2p': 7, 'rna3p': 48} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 1.21, per 1000 atoms: 0.20 Number of scatterers: 6021 At special positions: 0 Unit cell: (70.848, 83.64, 106.272, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 56 15.00 O 1274 8.00 N 1043 7.00 C 3617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 233.1 milliseconds 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 41.5% alpha, 17.6% beta 17 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 121 through 124 removed outlier: 3.679A pdb=" N GLU A 124 " --> pdb=" O TYR A 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 142 through 155 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.510A pdb=" N LEU A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 removed outlier: 4.035A pdb=" N GLN A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.800A pdb=" N ILE A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.833A pdb=" N MET A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 309 removed outlier: 4.595A pdb=" N GLY A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 340 removed outlier: 4.034A pdb=" N ILE A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 405 removed outlier: 3.723A pdb=" N HIS A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 413 through 418 removed outlier: 4.464A pdb=" N GLN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 538 removed outlier: 3.768A pdb=" N ILE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 623 through 633 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 642 through 650 Processing helix chain 'A' and resid 691 through 702 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 117 removed outlier: 8.371A pdb=" N TRP A 127 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE A 80 " --> pdb=" O TRP A 127 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N THR A 129 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU A 78 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU A 131 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA3, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.502A pdb=" N PHE A 422 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345 removed outlier: 4.511A pdb=" N GLY A 314 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ASP A 263 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS A 179 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU A 266 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 181 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE A 236 " --> pdb=" O THR A 583 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR A 583 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL A 238 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 367 Processing sheet with id=AA7, first strand: chain 'A' and resid 521 through 522 removed outlier: 6.908A pdb=" N LEU A 560 " --> pdb=" O VAL A 587 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 619 through 622 191 hydrogen bonds defined for protein. 513 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 0.46 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: 1744 1.34 - 1.46: 1409 1.46 - 1.58: 2966 1.58 - 1.70: 110 1.70 - 1.81: 50 Bond restraints: 6279 Sorted by residual: bond pdb=" N1 C B 48 " pdb=" C2 C B 48 " ideal model delta sigma weight residual 1.397 1.420 -0.023 1.00e-02 1.00e+04 5.49e+00 bond pdb=" CD SFG A 801 " pdb=" NE SFG A 801 " ideal model delta sigma weight residual 1.471 1.496 -0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" C1' C B 48 " pdb=" N1 C B 48 " ideal model delta sigma weight residual 1.480 1.497 -0.017 1.50e-02 4.44e+03 1.34e+00 bond pdb=" CA SFG A 801 " pdb=" C SFG A 801 " ideal model delta sigma weight residual 1.553 1.533 0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" N1 C B 48 " pdb=" C6 C B 48 " ideal model delta sigma weight residual 1.367 1.361 0.006 6.00e-03 2.78e+04 9.41e-01 ... (remaining 6274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 8599 1.25 - 2.51: 115 2.51 - 3.76: 47 3.76 - 5.02: 9 5.02 - 6.27: 3 Bond angle restraints: 8773 Sorted by residual: angle pdb=" C1' G B 45 " pdb=" N9 G B 45 " pdb=" C8 G B 45 " ideal model delta sigma weight residual 127.00 122.44 4.56 1.30e+00 5.92e-01 1.23e+01 angle pdb=" C1' G B 45 " pdb=" N9 G B 45 " pdb=" C4 G B 45 " ideal model delta sigma weight residual 126.50 130.71 -4.21 1.30e+00 5.92e-01 1.05e+01 angle pdb=" C8 G B 46 " pdb=" N9 G B 46 " pdb=" C4 G B 46 " ideal model delta sigma weight residual 106.40 105.22 1.18 4.00e-01 6.25e+00 8.64e+00 angle pdb=" C4' G B 46 " pdb=" C3' G B 46 " pdb=" O3' G B 46 " ideal model delta sigma weight residual 113.00 117.41 -4.41 1.50e+00 4.44e-01 8.63e+00 angle pdb=" C8 G B 45 " pdb=" N9 G B 45 " pdb=" C4 G B 45 " ideal model delta sigma weight residual 106.40 105.30 1.10 4.00e-01 6.25e+00 7.60e+00 ... (remaining 8768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.68: 3698 25.68 - 51.36: 157 51.36 - 77.04: 88 77.04 - 102.71: 2 102.71 - 128.39: 1 Dihedral angle restraints: 3946 sinusoidal: 2207 harmonic: 1739 Sorted by residual: dihedral pdb=" O4' C B 48 " pdb=" C1' C B 48 " pdb=" N1 C B 48 " pdb=" C2 C B 48 " ideal model delta sinusoidal sigma weight residual 200.00 71.61 128.39 1 1.50e+01 4.44e-03 6.92e+01 dihedral pdb=" O4' G B 45 " pdb=" C1' G B 45 " pdb=" N9 G B 45 " pdb=" C4 G B 45 " ideal model delta sinusoidal sigma weight residual -78.00 -20.65 -57.35 1 1.70e+01 3.46e-03 1.53e+01 dihedral pdb=" CB LYS A 579 " pdb=" CG LYS A 579 " pdb=" CD LYS A 579 " pdb=" CE LYS A 579 " ideal model delta sinusoidal sigma weight residual -180.00 -122.81 -57.19 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 3943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 757 0.036 - 0.072: 174 0.072 - 0.108: 58 0.108 - 0.144: 17 0.144 - 0.180: 5 Chirality restraints: 1011 Sorted by residual: chirality pdb=" C4' G B 45 " pdb=" C5' G B 45 " pdb=" O4' G B 45 " pdb=" C3' G B 45 " both_signs ideal model delta sigma weight residual False -2.50 -2.32 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" P G B 46 " pdb=" OP1 G B 46 " pdb=" OP2 G B 46 " pdb=" O5' G B 46 " both_signs ideal model delta sigma weight residual True 2.41 -2.59 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" P C B 48 " pdb=" OP1 C B 48 " pdb=" OP2 C B 48 " pdb=" O5' C B 48 " both_signs ideal model delta sigma weight residual True 2.41 -2.56 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 1008 not shown) Planarity restraints: 916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 46 " -0.071 2.00e-02 2.50e+03 3.59e-02 3.87e+01 pdb=" N9 G B 46 " 0.100 2.00e-02 2.50e+03 pdb=" C8 G B 46 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B 46 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G B 46 " -0.007 2.00e-02 2.50e+03 pdb=" C6 G B 46 " -0.010 2.00e-02 2.50e+03 pdb=" O6 G B 46 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G B 46 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G B 46 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 46 " 0.005 2.00e-02 2.50e+03 pdb=" N3 G B 46 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G B 46 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 45 " -0.033 2.00e-02 2.50e+03 2.61e-02 2.04e+01 pdb=" N9 G B 45 " 0.076 2.00e-02 2.50e+03 pdb=" C8 G B 45 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G B 45 " -0.008 2.00e-02 2.50e+03 pdb=" C5 G B 45 " -0.007 2.00e-02 2.50e+03 pdb=" C6 G B 45 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G B 45 " 0.005 2.00e-02 2.50e+03 pdb=" N1 G B 45 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G B 45 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G B 45 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 45 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B 45 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 63 " 0.024 2.00e-02 2.50e+03 1.48e-02 4.91e+00 pdb=" N1 C B 63 " -0.031 2.00e-02 2.50e+03 pdb=" C2 C B 63 " 0.015 2.00e-02 2.50e+03 pdb=" O2 C B 63 " -0.008 2.00e-02 2.50e+03 pdb=" N3 C B 63 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C B 63 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C B 63 " 0.005 2.00e-02 2.50e+03 pdb=" C5 C B 63 " 0.005 2.00e-02 2.50e+03 pdb=" C6 C B 63 " -0.009 2.00e-02 2.50e+03 ... (remaining 913 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1934 2.85 - 3.36: 5308 3.36 - 3.88: 10389 3.88 - 4.39: 11598 4.39 - 4.90: 18804 Nonbonded interactions: 48033 Sorted by model distance: nonbonded pdb=" NH1 ARG A 301 " pdb=" OP1 G B 30 " model vdw 2.341 3.120 nonbonded pdb=" OD2 ASP A 268 " pdb=" N SFG A 801 " model vdw 2.358 3.120 nonbonded pdb=" OP2 U B 50 " pdb=" N2 G B 59 " model vdw 2.402 3.120 nonbonded pdb=" N2 G B 5 " pdb=" O2 U B 68 " model vdw 2.417 3.120 nonbonded pdb=" O ILE A 246 " pdb=" NH2 ARG A 305 " model vdw 2.418 3.120 ... (remaining 48028 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 group one per residue 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: 0.880 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.000 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 0.025 6279 Z= 0.107 Angle : 0.448 6.272 8773 Z= 0.289 Chirality : 0.039 0.180 1011 Planarity : 0.004 0.036 916 Dihedral : 16.242 128.392 2816 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 2.15 (0.36), residues: 591 helix: 2.31 (0.41), residues: 193 sheet: 0.28 (0.51), residues: 107 loop : 1.50 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 248 TYR 0.006 0.001 TYR A 52 PHE 0.011 0.001 PHE A 48 TRP 0.004 0.001 TRP A 588 HIS 0.002 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00174 / 0.11 ( 6279) covalent geometry : angle 0.44770 / 0.29 ( 8773) hydrogen bonds : bond 0.17146 / 10.42 ( 235) hydrogen bonds : angle 5.66247 / 3.78 ( 597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 HIS cc_start: 0.7862 (m90) cc_final: 0.6422 (m90) REVERT: A 249 LEU cc_start: 0.8650 (mt) cc_final: 0.8414 (mt) REVERT: A 367 MET cc_start: 0.8667 (ttp) cc_final: 0.8413 (tmm) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0683 time to fit residues: 5.8302 Evaluate side-chains 36 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0060 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 HIS A 240 ASN A 416 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.087263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.059649 restraints weight = 20487.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.061652 restraints weight = 10816.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.062933 restraints weight = 7639.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.063757 restraints weight = 6302.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.063937 restraints weight = 5674.920| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6279 Z= 0.148 Angle : 0.528 6.372 8773 Z= 0.275 Chirality : 0.040 0.290 1011 Planarity : 0.005 0.043 916 Dihedral : 18.674 120.744 1579 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.93 % Allowed : 4.11 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 2.15 (0.36), residues: 591 helix: 2.40 (0.41), residues: 193 sheet: -0.01 (0.48), residues: 111 loop : 1.59 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 315 TYR 0.008 0.001 TYR A 52 PHE 0.011 0.001 PHE A 206 TRP 0.008 0.001 TRP A 435 HIS 0.009 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 6279) covalent geometry : angle 0.52831 / 0.28 ( 8773) hydrogen bonds : bond 0.04626 / 2.91 ( 235) hydrogen bonds : angle 4.71792 / 3.22 ( 597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.125 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.0703 time to fit residues: 3.7939 Evaluate side-chains 35 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 236 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.086206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.058481 restraints weight = 20331.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.060532 restraints weight = 10147.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.061862 restraints weight = 6986.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.062483 restraints weight = 5718.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.062939 restraints weight = 5183.373| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6279 Z= 0.144 Angle : 0.522 7.599 8773 Z= 0.264 Chirality : 0.039 0.286 1011 Planarity : 0.004 0.044 916 Dihedral : 18.668 118.130 1579 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.31 % Allowed : 6.17 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 1.90 (0.36), residues: 591 helix: 2.09 (0.40), residues: 193 sheet: -0.14 (0.48), residues: 111 loop : 1.52 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 248 TYR 0.005 0.001 TYR A 51 PHE 0.011 0.001 PHE A 48 TRP 0.007 0.001 TRP A 435 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 6279) covalent geometry : angle 0.52229 / 0.26 ( 8773) hydrogen bonds : bond 0.03967 / 2.55 ( 235) hydrogen bonds : angle 4.46626 / 3.09 ( 597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8398 (ttt180) cc_final: 0.8142 (ttt-90) outliers start: 7 outliers final: 4 residues processed: 36 average time/residue: 0.0578 time to fit residues: 2.9582 Evaluate side-chains 35 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 86 HIS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 277 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 62 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 0.0170 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.085989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.058328 restraints weight = 20544.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.060247 restraints weight = 10815.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.061569 restraints weight = 7670.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.062336 restraints weight = 6333.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.062622 restraints weight = 5741.093| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6279 Z= 0.121 Angle : 0.490 7.655 8773 Z= 0.246 Chirality : 0.039 0.294 1011 Planarity : 0.004 0.045 916 Dihedral : 18.655 115.862 1579 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.93 % Allowed : 8.22 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 1.87 (0.36), residues: 591 helix: 2.09 (0.40), residues: 192 sheet: -0.25 (0.47), residues: 112 loop : 1.54 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 700 TYR 0.006 0.001 TYR A 52 PHE 0.012 0.001 PHE A 48 TRP 0.011 0.001 TRP A 435 HIS 0.004 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 6279) covalent geometry : angle 0.48977 / 0.25 ( 8773) hydrogen bonds : bond 0.03540 / 2.30 ( 235) hydrogen bonds : angle 4.26948 / 2.95 ( 597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8453 (ttt180) cc_final: 0.7613 (ttt-90) REVERT: A 367 MET cc_start: 0.8523 (ttp) cc_final: 0.8159 (tmm) outliers start: 5 outliers final: 2 residues processed: 37 average time/residue: 0.0571 time to fit residues: 3.0703 Evaluate side-chains 33 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 158 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 50 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.0370 chunk 46 optimal weight: 0.9980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.086518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.058939 restraints weight = 20678.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.060909 restraints weight = 10775.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.062250 restraints weight = 7588.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.062919 restraints weight = 6264.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.063416 restraints weight = 5686.539| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6279 Z= 0.098 Angle : 0.493 14.167 8773 Z= 0.242 Chirality : 0.039 0.296 1011 Planarity : 0.004 0.045 916 Dihedral : 18.621 114.280 1579 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.75 % Allowed : 8.79 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 1.87 (0.36), residues: 591 helix: 2.06 (0.40), residues: 192 sheet: -0.20 (0.47), residues: 112 loop : 1.52 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 545 TYR 0.006 0.001 TYR A 52 PHE 0.012 0.001 PHE A 48 TRP 0.010 0.001 TRP A 435 HIS 0.003 0.000 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 6279) covalent geometry : angle 0.49343 / 0.24 ( 8773) hydrogen bonds : bond 0.03307 / 2.19 ( 235) hydrogen bonds : angle 4.15301 / 2.86 ( 597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 86 HIS cc_start: 0.7851 (m90) cc_final: 0.7208 (m90) REVERT: A 367 MET cc_start: 0.8465 (ttp) cc_final: 0.8249 (tmm) REVERT: A 702 MET cc_start: 0.8613 (mmm) cc_final: 0.8313 (mmm) outliers start: 4 outliers final: 1 residues processed: 36 average time/residue: 0.0465 time to fit residues: 2.4512 Evaluate side-chains 33 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 0.0770 chunk 54 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.086399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.058866 restraints weight = 20481.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.060844 restraints weight = 10769.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.062133 restraints weight = 7618.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.062893 restraints weight = 6328.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.063104 restraints weight = 5711.430| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6279 Z= 0.095 Angle : 0.505 15.799 8773 Z= 0.243 Chirality : 0.038 0.298 1011 Planarity : 0.004 0.045 916 Dihedral : 18.581 113.001 1579 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.93 % Allowed : 9.35 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 1.86 (0.36), residues: 591 helix: 2.07 (0.40), residues: 192 sheet: -0.16 (0.48), residues: 112 loop : 1.49 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 545 TYR 0.007 0.001 TYR A 52 PHE 0.012 0.001 PHE A 48 TRP 0.009 0.001 TRP A 435 HIS 0.003 0.000 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 ( 6279) covalent geometry : angle 0.50456 / 0.24 ( 8773) hydrogen bonds : bond 0.03160 / 2.11 ( 235) hydrogen bonds : angle 4.03545 / 2.77 ( 597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 86 HIS cc_start: 0.7939 (m90) cc_final: 0.7323 (m90) REVERT: A 133 ARG cc_start: 0.8409 (ttt180) cc_final: 0.8135 (ttt-90) REVERT: A 367 MET cc_start: 0.8466 (ttp) cc_final: 0.8220 (tmm) REVERT: A 702 MET cc_start: 0.8672 (mmm) cc_final: 0.8397 (mmm) outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 0.0588 time to fit residues: 3.0844 Evaluate side-chains 38 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 6 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 39 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.086153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.058643 restraints weight = 20470.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.060612 restraints weight = 10817.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.061937 restraints weight = 7664.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062665 restraints weight = 6332.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.062884 restraints weight = 5738.094| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6279 Z= 0.095 Angle : 0.510 13.748 8773 Z= 0.242 Chirality : 0.038 0.303 1011 Planarity : 0.004 0.044 916 Dihedral : 18.548 111.061 1579 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.75 % Allowed : 10.09 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 1.89 (0.36), residues: 591 helix: 2.13 (0.40), residues: 192 sheet: -0.10 (0.48), residues: 112 loop : 1.46 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 700 TYR 0.007 0.001 TYR A 52 PHE 0.012 0.001 PHE A 48 TRP 0.009 0.001 TRP A 435 HIS 0.003 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 6279) covalent geometry : angle 0.51038 / 0.24 ( 8773) hydrogen bonds : bond 0.03085 / 2.05 ( 235) hydrogen bonds : angle 3.88430 / 2.69 ( 597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8436 (ttt180) cc_final: 0.8160 (ttt-90) REVERT: A 367 MET cc_start: 0.8439 (ttp) cc_final: 0.8191 (tmm) REVERT: A 702 MET cc_start: 0.8722 (mmm) cc_final: 0.8445 (mmm) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.0537 time to fit residues: 2.8178 Evaluate side-chains 33 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 0.0870 chunk 47 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.086308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.058714 restraints weight = 20487.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.060689 restraints weight = 10810.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.062014 restraints weight = 7649.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.062764 restraints weight = 6329.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.063059 restraints weight = 5722.826| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6279 Z= 0.091 Angle : 0.517 15.625 8773 Z= 0.244 Chirality : 0.038 0.304 1011 Planarity : 0.004 0.043 916 Dihedral : 18.524 109.929 1579 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.75 % Allowed : 10.09 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 1.93 (0.36), residues: 591 helix: 2.12 (0.40), residues: 192 sheet: -0.01 (0.48), residues: 112 loop : 1.48 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 700 TYR 0.007 0.001 TYR A 52 PHE 0.012 0.001 PHE A 48 TRP 0.009 0.001 TRP A 435 HIS 0.002 0.000 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 6279) covalent geometry : angle 0.51697 / 0.24 ( 8773) hydrogen bonds : bond 0.03000 / 2.02 ( 235) hydrogen bonds : angle 3.85374 / 2.65 ( 597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8390 (ttt180) cc_final: 0.8154 (ttt-90) REVERT: A 367 MET cc_start: 0.8433 (ttp) cc_final: 0.8187 (tmm) REVERT: A 702 MET cc_start: 0.8703 (mmm) cc_final: 0.8503 (mmm) outliers start: 4 outliers final: 4 residues processed: 36 average time/residue: 0.0510 time to fit residues: 2.6244 Evaluate side-chains 36 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 30.0000 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.085871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.058292 restraints weight = 20580.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.060268 restraints weight = 10895.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.061570 restraints weight = 7725.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.062333 restraints weight = 6403.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062689 restraints weight = 5787.527| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6279 Z= 0.095 Angle : 0.524 14.615 8773 Z= 0.244 Chirality : 0.038 0.304 1011 Planarity : 0.004 0.043 916 Dihedral : 18.489 108.439 1579 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.56 % Allowed : 10.28 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 1.99 (0.36), residues: 591 helix: 2.12 (0.40), residues: 193 sheet: 0.03 (0.48), residues: 112 loop : 1.55 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 545 TYR 0.006 0.001 TYR A 52 PHE 0.012 0.001 PHE A 48 TRP 0.008 0.001 TRP A 435 HIS 0.002 0.000 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 6279) covalent geometry : angle 0.52351 / 0.24 ( 8773) hydrogen bonds : bond 0.02964 / 1.99 ( 235) hydrogen bonds : angle 3.78092 / 2.59 ( 597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 367 MET cc_start: 0.8394 (ttp) cc_final: 0.8167 (tmm) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.0522 time to fit residues: 2.8752 Evaluate side-chains 34 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.085789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.058327 restraints weight = 20535.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.060310 restraints weight = 10807.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.061592 restraints weight = 7633.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.062319 restraints weight = 6324.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062628 restraints weight = 5738.289| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6279 Z= 0.091 Angle : 0.530 15.400 8773 Z= 0.245 Chirality : 0.038 0.304 1011 Planarity : 0.004 0.044 916 Dihedral : 18.452 107.415 1579 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.37 % Allowed : 10.84 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 1.97 (0.36), residues: 591 helix: 2.06 (0.40), residues: 194 sheet: 0.05 (0.47), residues: 112 loop : 1.56 (0.40), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 545 TYR 0.006 0.001 TYR A 52 PHE 0.012 0.001 PHE A 48 TRP 0.008 0.001 TRP A 435 HIS 0.002 0.000 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 ( 6279) covalent geometry : angle 0.52972 / 0.24 ( 8773) hydrogen bonds : bond 0.02932 / 1.98 ( 235) hydrogen bonds : angle 3.76162 / 2.57 ( 597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1182 Ramachandran restraints generated. 591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8223 (ttt-90) cc_final: 0.7872 (ttt-90) REVERT: A 326 ILE cc_start: 0.9335 (mm) cc_final: 0.8998 (mt) outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 0.0680 time to fit residues: 3.4479 Evaluate side-chains 34 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 63 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 0.0570 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.085425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.057830 restraints weight = 20503.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.059764 restraints weight = 10939.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.061038 restraints weight = 7858.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.061588 restraints weight = 6536.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.062147 restraints weight = 5978.293| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6279 Z= 0.106 Angle : 0.534 15.302 8773 Z= 0.248 Chirality : 0.038 0.304 1011 Planarity : 0.004 0.043 916 Dihedral : 18.425 105.913 1579 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.75 % Allowed : 10.47 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 are not related in a simple way. whole: 2.00 (0.36), residues: 591 helix: 2.07 (0.40), residues: 194 sheet: 0.09 (0.47), residues: 112 loop : 1.57 (0.40), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.007 0.001 TYR A 51 PHE 0.011 0.001 PHE A 48 TRP 0.007 0.001 TRP A 373 HIS 0.003 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 6279) covalent geometry : angle 0.53442 / 0.25 ( 8773) hydrogen bonds : bond 0.03017 / 2.02 ( 235) hydrogen bonds : angle 3.77094 / 2.59 ( 597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 857.96 seconds wall clock time: 15 minutes 34.13 seconds (934.13 seconds total)