Starting phenix.real_space_refine on Tue Aug 4 20:33:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z2r_73776/08_2026/9z2r_73776.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z2r_73776/08_2026/9z2r_73776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z2r_73776/08_2026/9z2r_73776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z2r_73776/08_2026/9z2r_73776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z2r_73776/08_2026/9z2r_73776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z2r_73776/08_2026/9z2r_73776.map" } resolution = 3.71 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= 0.005 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 75 5.49 5 S 31 5.16 5 C 3811 2.51 5 N 1125 2.21 5 O 1407 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6449 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4822 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 555} Chain breaks: 1 Chain: "B" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1600 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 9, 'rna3p': 65} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 1.51, per 1000 atoms: 0.23 Number of scatterers: 6449 At special positions: 0 Unit cell: (74.784, 93.48, 105.288, 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 75 15.00 O 1407 8.00 N 1125 7.00 C 3811 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: 0.56 Conformation dependent library (CDL) restraints added in 319.3 milliseconds 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1136 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 42.7% alpha, 17.6% beta 21 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 0.89 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 98 through 103 removed outlier: 3.709A pdb=" N GLU A 103 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 124 removed outlier: 3.676A 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 162 through 165 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.549A pdb=" N LEU A 170 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 removed outlier: 4.039A 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: 3.795A pdb=" N ILE A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.824A 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: 4.600A pdb=" N GLY A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 340 removed outlier: 4.042A 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: 3.711A 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: 4.459A pdb=" N GLN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 538 removed outlier: 3.706A 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 651 removed outlier: 3.820A pdb=" N ASP A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) 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: 8.222A pdb=" N TRP A 127 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE A 80 " --> pdb=" O TRP A 127 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR A 129 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU A 78 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 5.292A 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 Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345 removed outlier: 4.473A pdb=" N GLY A 314 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ASP A 263 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LYS A 179 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU A 266 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 181 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE A 236 " --> pdb=" O THR A 583 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N THR A 583 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 7.028A 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: 6.726A 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 622 195 hydrogen bonds defined for protein. 513 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 0.78 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: 1810 1.34 - 1.46: 1663 1.46 - 1.58: 3085 1.58 - 1.70: 149 1.70 - 1.82: 50 Bond restraints: 6757 Sorted by residual: bond pdb=" N1 C B 48 " pdb=" C2 C B 48 " ideal model delta sigma weight residual 1.397 1.419 -0.022 1.00e-02 1.00e+04 5.04e+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 1.60e+00 bond pdb=" C2' C B 48 " pdb=" C1' C B 48 " ideal model delta sigma weight residual 1.529 1.542 -0.013 1.10e-02 8.26e+03 1.50e+00 bond pdb=" C3' C B 48 " pdb=" C2' C B 48 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.10e-02 8.26e+03 1.22e+00 bond pdb=" CA SFG A 801 " pdb=" C SFG A 801 " ideal model delta sigma weight residual 1.553 1.532 0.021 2.00e-02 2.50e+03 1.08e+00 ... (remaining 6752 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 9140 1.27 - 2.55: 265 2.55 - 3.82: 106 3.82 - 5.09: 3 5.09 - 6.36: 3 Bond angle restraints: 9517 Sorted by residual: angle pdb=" O4' C B 48 " pdb=" C1' C B 48 " pdb=" N1 C B 48 " ideal model delta sigma weight residual 108.50 111.10 -2.60 7.00e-01 2.04e+00 1.38e+01 angle pdb=" O5' A B 21 " pdb=" C5' A B 21 " pdb=" C4' A B 21 " ideal model delta sigma weight residual 109.40 112.23 -2.83 8.00e-01 1.56e+00 1.25e+01 angle pdb=" O5' G B 73 " pdb=" C5' G B 73 " pdb=" C4' G B 73 " ideal model delta sigma weight residual 109.40 112.16 -2.76 8.00e-01 1.56e+00 1.19e+01 angle pdb=" O5' G B 66 " pdb=" C5' G B 66 " pdb=" C4' G B 66 " ideal model delta sigma weight residual 109.40 112.08 -2.68 8.00e-01 1.56e+00 1.12e+01 angle pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sigma weight residual 118.80 122.35 -3.55 1.10e+00 8.26e-01 1.04e+01 ... (remaining 9512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 4059 35.78 - 71.57: 176 71.57 - 107.35: 27 107.35 - 143.13: 2 143.13 - 178.92: 1 Dihedral angle restraints: 4265 sinusoidal: 2518 harmonic: 1747 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 72.81 127.19 1 1.50e+01 4.44e-03 6.85e+01 dihedral pdb=" O4' U B 20 " pdb=" C1' U B 20 " pdb=" N1 U B 20 " pdb=" C2 U B 20 " ideal model delta sinusoidal sigma weight residual -128.00 50.92 -178.92 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' G B 15 " pdb=" C1' G B 15 " pdb=" N9 G B 15 " pdb=" C4 G B 15 " ideal model delta sinusoidal sigma weight residual -90.00 -20.55 -69.45 1 2.00e+01 2.50e-03 1.56e+01 ... (remaining 4262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 865 0.047 - 0.093: 123 0.093 - 0.140: 120 0.140 - 0.187: 1 0.187 - 0.234: 1 Chirality restraints: 1110 Sorted by residual: 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 -2.64 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C2' C B 48 " pdb=" C3' C B 48 " pdb=" O2' C B 48 " pdb=" C1' C B 48 " both_signs ideal model delta sigma weight residual False -2.62 -2.78 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" C2' G B 29 " pdb=" C3' G B 29 " pdb=" O2' G B 29 " pdb=" C1' G B 29 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 1107 not shown) Planarity restraints: 938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 531 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO A 532 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 532 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 532 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 167 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO A 168 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 530 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A 531 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 531 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 531 " -0.016 5.00e-02 4.00e+02 ... (remaining 935 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1124 2.77 - 3.30: 5865 3.30 - 3.83: 11617 3.83 - 4.37: 13416 4.37 - 4.90: 20974 Nonbonded interactions: 52996 Sorted by model distance: nonbonded pdb=" OP2 U B 50 " pdb=" N2 G B 59 " model vdw 2.236 3.120 nonbonded pdb=" OG SER A 151 " pdb=" NH1 ARG A 700 " model vdw 2.243 3.120 nonbonded pdb=" N2 G B 29 " pdb=" O2 C B 41 " model vdw 2.258 3.120 nonbonded pdb=" NH2 ARG A 438 " pdb=" OP2 U B 33 " model vdw 2.284 3.120 nonbonded pdb=" OD1 ASN A 569 " pdb=" ND2 ASN A 573 " model vdw 2.284 3.120 ... (remaining 52991 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: 1.320 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.260 Find NCS groups from input model: 0.020 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 0.026 6757 Z= 0.132 Angle : 0.548 6.363 9517 Z= 0.389 Chirality : 0.049 0.234 1110 Planarity : 0.004 0.037 938 Dihedral : 17.258 178.918 3129 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 2.34 (0.36), residues: 593 helix: 2.40 (0.42), residues: 192 sheet: 0.47 (0.51), residues: 104 loop : 1.62 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 248 TYR 0.008 0.001 TYR A 38 PHE 0.007 0.001 PHE A 48 TRP 0.007 0.001 TRP A 287 HIS 0.003 0.000 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.13 ( 6757) covalent geometry : angle 0.54763 / 0.39 ( 9517) hydrogen bonds : bond 0.16819 / 11.44 ( 249) hydrogen bonds : angle 5.60212 / 3.80 ( 613) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0799 time to fit residues: 6.3438 Evaluate side-chains 31 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 50.0000 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.080970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.054467 restraints weight = 26766.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.056237 restraints weight = 15570.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.056659 restraints weight = 9958.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.056843 restraints weight = 9638.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.057060 restraints weight = 8883.176| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6757 Z= 0.167 Angle : 0.563 9.059 9517 Z= 0.290 Chirality : 0.039 0.158 1110 Planarity : 0.005 0.037 938 Dihedral : 20.878 178.589 1881 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.74 % Allowed : 4.28 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 2.09 (0.36), residues: 593 helix: 2.10 (0.41), residues: 198 sheet: 0.09 (0.49), residues: 106 loop : 1.66 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 639 TYR 0.014 0.002 TYR A 51 PHE 0.009 0.001 PHE A 145 TRP 0.010 0.001 TRP A 435 HIS 0.005 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 6757) covalent geometry : angle 0.56266 / 0.29 ( 9517) hydrogen bonds : bond 0.04572 / 3.09 ( 249) hydrogen bonds : angle 4.81180 / 3.33 ( 613) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 277 MET cc_start: 0.8497 (mtp) cc_final: 0.8177 (mtp) outliers start: 4 outliers final: 1 residues processed: 33 average time/residue: 0.0394 time to fit residues: 2.0835 Evaluate side-chains 28 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 17 optimal weight: 0.3980 chunk 64 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 62 optimal weight: 50.0000 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.080702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054006 restraints weight = 27460.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.055968 restraints weight = 15870.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.056171 restraints weight = 10219.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.056496 restraints weight = 9968.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.056578 restraints weight = 9449.714| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6757 Z= 0.208 Angle : 0.553 8.982 9517 Z= 0.283 Chirality : 0.038 0.165 1110 Planarity : 0.005 0.038 938 Dihedral : 20.844 179.064 1881 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.12 % Allowed : 5.76 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.85 (0.36), residues: 593 helix: 1.75 (0.39), residues: 199 sheet: 0.04 (0.49), residues: 103 loop : 1.58 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 315 TYR 0.012 0.001 TYR A 52 PHE 0.008 0.001 PHE A 48 TRP 0.013 0.001 TRP A 127 HIS 0.005 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 ( 6757) covalent geometry : angle 0.55297 / 0.28 ( 9517) hydrogen bonds : bond 0.04636 / 3.08 ( 249) hydrogen bonds : angle 4.63999 / 3.24 ( 613) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.9299 (mmm) cc_final: 0.8284 (mmm) REVERT: A 202 MET cc_start: 0.8537 (tpp) cc_final: 0.8109 (tpp) REVERT: A 701 MET cc_start: 0.8520 (mmp) cc_final: 0.8224 (mmp) outliers start: 6 outliers final: 1 residues processed: 33 average time/residue: 0.0474 time to fit residues: 2.4684 Evaluate side-chains 24 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 63 optimal weight: 30.0000 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 61 optimal weight: 40.0000 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.080829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054426 restraints weight = 26879.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.056025 restraints weight = 15344.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.056386 restraints weight = 10182.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.056726 restraints weight = 9647.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.056817 restraints weight = 9321.721| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6757 Z= 0.108 Angle : 0.482 8.052 9517 Z= 0.247 Chirality : 0.037 0.164 1110 Planarity : 0.004 0.039 938 Dihedral : 20.819 178.677 1881 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.19 % Allowed : 7.06 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 593 helix: 1.81 (0.40), residues: 198 sheet: 0.04 (0.49), residues: 103 loop : 1.61 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 639 TYR 0.009 0.001 TYR A 51 PHE 0.008 0.001 PHE A 48 TRP 0.010 0.001 TRP A 435 HIS 0.003 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 6757) covalent geometry : angle 0.48221 / 0.25 ( 9517) hydrogen bonds : bond 0.03824 / 2.56 ( 249) hydrogen bonds : angle 4.28467 / 3.01 ( 613) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.8507 (tpp) cc_final: 0.8077 (tpp) REVERT: A 277 MET cc_start: 0.8430 (mtp) cc_final: 0.8092 (mtp) outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.0530 time to fit residues: 2.4175 Evaluate side-chains 25 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 13 optimal weight: 0.0770 chunk 5 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.0470 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.081285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.055240 restraints weight = 26769.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.057207 restraints weight = 13884.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.057637 restraints weight = 8966.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.057902 restraints weight = 8932.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.057966 restraints weight = 8285.825| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6757 Z= 0.093 Angle : 0.468 7.745 9517 Z= 0.238 Chirality : 0.036 0.163 1110 Planarity : 0.004 0.039 938 Dihedral : 20.752 178.297 1881 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.37 % Allowed : 7.25 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 593 helix: 1.99 (0.40), residues: 192 sheet: -0.04 (0.48), residues: 106 loop : 1.67 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 639 TYR 0.011 0.001 TYR A 51 PHE 0.011 0.001 PHE A 145 TRP 0.010 0.001 TRP A 435 HIS 0.002 0.000 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 ( 6757) covalent geometry : angle 0.46804 / 0.24 ( 9517) hydrogen bonds : bond 0.03565 / 2.36 ( 249) hydrogen bonds : angle 4.09658 / 2.88 ( 613) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 433 MET cc_start: 0.9250 (tpp) cc_final: 0.9004 (tpp) REVERT: A 702 MET cc_start: 0.8220 (tpp) cc_final: 0.7873 (tpp) outliers start: 2 outliers final: 1 residues processed: 29 average time/residue: 0.0456 time to fit residues: 2.1689 Evaluate side-chains 26 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 40.0000 chunk 14 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 63 optimal weight: 30.0000 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.082382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.056075 restraints weight = 26944.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.057851 restraints weight = 15948.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.058631 restraints weight = 10059.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.058866 restraints weight = 9569.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.058939 restraints weight = 9086.221| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6757 Z= 0.113 Angle : 0.476 9.639 9517 Z= 0.242 Chirality : 0.036 0.165 1110 Planarity : 0.004 0.039 938 Dihedral : 20.716 178.305 1881 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.56 % Allowed : 7.62 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.94 (0.36), residues: 593 helix: 1.91 (0.40), residues: 192 sheet: 0.01 (0.49), residues: 103 loop : 1.60 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 639 TYR 0.010 0.001 TYR A 51 PHE 0.012 0.001 PHE A 145 TRP 0.008 0.001 TRP A 435 HIS 0.003 0.001 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 6757) covalent geometry : angle 0.47609 / 0.24 ( 9517) hydrogen bonds : bond 0.03636 / 2.43 ( 249) hydrogen bonds : angle 4.06231 / 2.86 ( 613) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 702 MET cc_start: 0.8187 (tpp) cc_final: 0.7860 (tpp) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 0.0523 time to fit residues: 2.3858 Evaluate side-chains 26 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 64 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.080372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.053605 restraints weight = 26476.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.055517 restraints weight = 13754.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.056674 restraints weight = 9761.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.057238 restraints weight = 8189.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.057701 restraints weight = 7500.716| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6757 Z= 0.098 Angle : 0.482 12.738 9517 Z= 0.240 Chirality : 0.036 0.166 1110 Planarity : 0.004 0.039 938 Dihedral : 20.685 178.230 1881 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.56 % Allowed : 7.81 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.94 (0.36), residues: 593 helix: 1.90 (0.40), residues: 192 sheet: 0.01 (0.49), residues: 103 loop : 1.62 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 639 TYR 0.013 0.001 TYR A 51 PHE 0.013 0.001 PHE A 145 TRP 0.010 0.001 TRP A 435 HIS 0.002 0.000 HIS A 697 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 6757) covalent geometry : angle 0.48197 / 0.24 ( 9517) hydrogen bonds : bond 0.03448 / 2.30 ( 249) hydrogen bonds : angle 4.01523 / 2.84 ( 613) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 702 MET cc_start: 0.8075 (tpp) cc_final: 0.7818 (tpp) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 0.0473 time to fit residues: 2.2308 Evaluate side-chains 26 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.0670 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.080502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.053760 restraints weight = 26463.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.055672 restraints weight = 13784.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.056841 restraints weight = 9767.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.057419 restraints weight = 8180.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.057852 restraints weight = 7482.782| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6757 Z= 0.094 Angle : 0.465 9.371 9517 Z= 0.234 Chirality : 0.036 0.168 1110 Planarity : 0.004 0.038 938 Dihedral : 20.646 178.122 1881 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.56 % Allowed : 7.62 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 593 helix: 1.84 (0.40), residues: 193 sheet: 0.05 (0.49), residues: 103 loop : 1.58 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 639 TYR 0.010 0.001 TYR A 51 PHE 0.017 0.001 PHE A 145 TRP 0.010 0.001 TRP A 435 HIS 0.002 0.000 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 6757) covalent geometry : angle 0.46488 / 0.23 ( 9517) hydrogen bonds : bond 0.03390 / 2.25 ( 249) hydrogen bonds : angle 3.95267 / 2.80 ( 613) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 702 MET cc_start: 0.8038 (tpp) cc_final: 0.7821 (tpp) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 0.0515 time to fit residues: 2.3352 Evaluate side-chains 26 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 65 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 62 optimal weight: 50.0000 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.081293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.055304 restraints weight = 27172.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057152 restraints weight = 15222.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.057723 restraints weight = 10089.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.057989 restraints weight = 9567.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.058052 restraints weight = 9160.827| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6757 Z= 0.159 Angle : 0.516 7.920 9517 Z= 0.255 Chirality : 0.037 0.169 1110 Planarity : 0.004 0.040 938 Dihedral : 20.666 178.585 1881 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.19 % Allowed : 8.55 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 593 helix: 1.89 (0.40), residues: 192 sheet: 0.06 (0.50), residues: 103 loop : 1.48 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 278 TYR 0.015 0.001 TYR A 52 PHE 0.012 0.001 PHE A 145 TRP 0.011 0.001 TRP A 435 HIS 0.004 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 6757) covalent geometry : angle 0.51609 / 0.26 ( 9517) hydrogen bonds : bond 0.03876 / 2.61 ( 249) hydrogen bonds : angle 4.11033 / 2.92 ( 613) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.0456 time to fit residues: 1.9089 Evaluate side-chains 25 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 30.0000 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 40.0000 chunk 13 optimal weight: 0.0020 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.081832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055677 restraints weight = 26342.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.057582 restraints weight = 15163.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.058103 restraints weight = 9447.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.058342 restraints weight = 9109.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.058501 restraints weight = 8755.858| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6757 Z= 0.095 Angle : 0.503 10.297 9517 Z= 0.247 Chirality : 0.036 0.168 1110 Planarity : 0.004 0.038 938 Dihedral : 20.677 178.407 1881 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.19 % Allowed : 8.92 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.92 (0.36), residues: 593 helix: 1.79 (0.40), residues: 195 sheet: 0.05 (0.50), residues: 105 loop : 1.66 (0.39), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 384 TYR 0.012 0.001 TYR A 51 PHE 0.015 0.001 PHE A 145 TRP 0.013 0.001 TRP A 435 HIS 0.002 0.000 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 6757) covalent geometry : angle 0.50324 / 0.25 ( 9517) hydrogen bonds : bond 0.03431 / 2.30 ( 249) hydrogen bonds : angle 3.96100 / 2.81 ( 613) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.9267 (mmm) cc_final: 0.8018 (mmm) outliers start: 1 outliers final: 1 residues processed: 27 average time/residue: 0.0434 time to fit residues: 1.8922 Evaluate side-chains 26 residues out of total 538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 22 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 61 optimal weight: 50.0000 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.081694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.055890 restraints weight = 26509.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.057697 restraints weight = 15033.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.058508 restraints weight = 9491.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.058655 restraints weight = 8893.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.058762 restraints weight = 8578.073| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6757 Z= 0.104 Angle : 0.527 14.670 9517 Z= 0.253 Chirality : 0.036 0.169 1110 Planarity : 0.004 0.039 938 Dihedral : 20.664 178.342 1881 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.37 % Allowed : 9.29 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.94 (0.36), residues: 593 helix: 1.85 (0.40), residues: 194 sheet: 0.04 (0.50), residues: 105 loop : 1.65 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 278 TYR 0.015 0.001 TYR A 51 PHE 0.009 0.001 PHE A 48 TRP 0.013 0.001 TRP A 435 HIS 0.002 0.000 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 ( 6757) covalent geometry : angle 0.52704 / 0.25 ( 9517) hydrogen bonds : bond 0.03476 / 2.33 ( 249) hydrogen bonds : angle 3.98954 / 2.84 ( 613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 917.63 seconds wall clock time: 16 minutes 36.06 seconds (996.06 seconds total)