Starting phenix.real_space_refine on Wed Mar 5 22:34:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b6z_15893/03_2025/8b6z_15893.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b6z_15893/03_2025/8b6z_15893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b6z_15893/03_2025/8b6z_15893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b6z_15893/03_2025/8b6z_15893.map" model { file = "/net/cci-nas-00/data/ceres_data/8b6z_15893/03_2025/8b6z_15893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b6z_15893/03_2025/8b6z_15893.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 8 5.49 5 S 16 5.16 5 C 2240 2.51 5 N 624 2.21 5 O 693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3581 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3406 Classifications: {'peptide': 442} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 415} Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 175 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY A 50 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 50 " occ=0.00 Time building chain proxies: 3.97, per 1000 atoms: 1.11 Number of scatterers: 3581 At special positions: 0 Unit cell: (65.934, 93.906, 67.932, 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 16 16.00 P 8 15.00 O 693 8.00 N 624 7.00 C 2240 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: 0.88 Conformation dependent library (CDL) restraints added in 393.6 milliseconds 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 806 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 5 sheets defined 25.1% alpha, 33.3% beta 1 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.703A pdb=" N ILE A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.836A pdb=" N SER A 157 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 158 " --> pdb=" O MET A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 158' Processing helix chain 'A' and resid 163 through 182 removed outlier: 3.601A pdb=" N TYR A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.715A pdb=" N ALA A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.557A pdb=" N ILE A 8 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A 90 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 10 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N CYS A 111 " --> pdb=" O HIS A 7 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN A 9 " --> pdb=" O CYS A 111 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 113 " --> pdb=" O ASN A 9 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 11 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 115 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE A 13 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA A 117 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 191 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 216 Processing sheet with id=AA3, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.659A pdb=" N ASN A 311 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL A 292 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY A 309 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N MET A 294 " --> pdb=" O ASN A 307 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N ASN A 307 " --> pdb=" O MET A 294 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR A 261 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 249 Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389 removed outlier: 6.610A pdb=" N ALA A 373 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL A 405 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU A 375 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU A 403 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA A 338 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 339 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN A 343 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE A 438 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE A 345 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLY A 436 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP A 428 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 360 " --> pdb=" O ARG A 427 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 366 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 1.01 Time building geometry restraints manager: 1.05 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: 1126 1.34 - 1.46: 522 1.46 - 1.57: 1984 1.57 - 1.69: 15 1.69 - 1.81: 26 Bond restraints: 3673 Sorted by residual: bond pdb=" C ILE A 235 " pdb=" N LEU A 236 " ideal model delta sigma weight residual 1.327 1.339 -0.012 1.39e-02 5.18e+03 7.88e-01 bond pdb=" N VAL A 152 " pdb=" CA VAL A 152 " ideal model delta sigma weight residual 1.465 1.476 -0.011 1.38e-02 5.25e+03 5.94e-01 bond pdb=" CA GLY A 351 " pdb=" C GLY A 351 " ideal model delta sigma weight residual 1.514 1.505 0.010 1.41e-02 5.03e+03 4.55e-01 bond pdb=" CA HIS A 364 " pdb=" CB HIS A 364 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.69e-02 3.50e+03 4.23e-01 bond pdb=" C LYS A 165 " pdb=" O LYS A 165 " ideal model delta sigma weight residual 1.236 1.228 0.008 1.26e-02 6.30e+03 4.09e-01 ... (remaining 3668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 4915 1.47 - 2.93: 71 2.93 - 4.40: 20 4.40 - 5.86: 1 5.86 - 7.33: 1 Bond angle restraints: 5008 Sorted by residual: angle pdb=" N GLY A 182 " pdb=" CA GLY A 182 " pdb=" C GLY A 182 " ideal model delta sigma weight residual 113.18 120.51 -7.33 2.37e+00 1.78e-01 9.56e+00 angle pdb=" N SER A 157 " pdb=" CA SER A 157 " pdb=" C SER A 157 " ideal model delta sigma weight residual 112.88 115.26 -2.38 1.29e+00 6.01e-01 3.40e+00 angle pdb=" CB LYS A 172 " pdb=" CG LYS A 172 " pdb=" CD LYS A 172 " ideal model delta sigma weight residual 111.30 115.15 -3.85 2.30e+00 1.89e-01 2.80e+00 angle pdb=" CA GLY A 182 " pdb=" C GLY A 182 " pdb=" N TYR A 183 " ideal model delta sigma weight residual 116.69 119.99 -3.30 2.04e+00 2.40e-01 2.62e+00 angle pdb=" N ASN A 200 " pdb=" CA ASN A 200 " pdb=" CB ASN A 200 " ideal model delta sigma weight residual 113.15 110.58 2.57 1.63e+00 3.76e-01 2.48e+00 ... (remaining 5003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.56: 2078 14.56 - 29.12: 95 29.12 - 43.68: 36 43.68 - 58.25: 16 58.25 - 72.81: 11 Dihedral angle restraints: 2236 sinusoidal: 977 harmonic: 1259 Sorted by residual: dihedral pdb=" CA VAL A 152 " pdb=" C VAL A 152 " pdb=" N ASN A 153 " pdb=" CA ASN A 153 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PRO A 160 " pdb=" C PRO A 160 " pdb=" N ALA A 161 " pdb=" CA ALA A 161 " ideal model delta harmonic sigma weight residual -180.00 -162.08 -17.92 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ILE A 178 " pdb=" C ILE A 178 " pdb=" N LYS A 179 " pdb=" CA LYS A 179 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 309 0.025 - 0.050: 155 0.050 - 0.075: 37 0.075 - 0.100: 31 0.100 - 0.125: 37 Chirality restraints: 569 Sorted by residual: chirality pdb=" CA ILE A 401 " pdb=" N ILE A 401 " pdb=" C ILE A 401 " pdb=" CB ILE A 401 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL A 405 " pdb=" N VAL A 405 " pdb=" C VAL A 405 " pdb=" CB VAL A 405 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA VAL A 292 " pdb=" N VAL A 292 " pdb=" C VAL A 292 " pdb=" CB VAL A 292 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 566 not shown) Planarity restraints: 613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 419 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 420 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 420 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 420 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 418 " -0.021 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 419 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 419 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 419 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 358 " 0.016 5.00e-02 4.00e+02 2.43e-02 9.41e-01 pdb=" N PRO A 359 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 359 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 359 " 0.013 5.00e-02 4.00e+02 ... (remaining 610 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 924 2.81 - 3.33: 3215 3.33 - 3.85: 5926 3.85 - 4.38: 6908 4.38 - 4.90: 11870 Nonbonded interactions: 28843 Sorted by model distance: nonbonded pdb=" OD2 ASP A 74 " pdb=" OG SER A 76 " model vdw 2.286 3.040 nonbonded pdb=" O ALA A 231 " pdb=" OG1 THR A 234 " model vdw 2.388 3.040 nonbonded pdb=" O VAL A 277 " pdb=" OG SER A 329 " model vdw 2.390 3.040 nonbonded pdb=" OH TYR A 29 " pdb=" NE1 TRP A 58 " model vdw 2.391 3.120 nonbonded pdb=" OE2 GLU A 68 " pdb=" N ARG A 96 " model vdw 2.413 3.120 ... (remaining 28838 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=0.00 max=1.00 mean=0.70 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.140 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.790 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:10.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 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 0.023 3673 Z= 0.146 Angle : 0.507 7.329 5008 Z= 0.273 Chirality : 0.044 0.125 569 Planarity : 0.004 0.041 613 Dihedral : 12.065 72.808 1430 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.27 % Allowed : 2.14 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.37), residues: 440 helix: -0.07 (0.48), residues: 93 sheet: -0.11 (0.60), residues: 83 loop : -0.67 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.005 0.001 HIS A 364 PHE 0.005 0.001 PHE A 123 TYR 0.012 0.002 TYR A 167 ARG 0.003 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 THR cc_start: 0.6986 (p) cc_final: 0.5495 (t) REVERT: A 243 ASP cc_start: 0.5976 (m-30) cc_final: 0.5723 (t0) REVERT: A 254 TYR cc_start: 0.4476 (m-80) cc_final: 0.4154 (m-80) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 1.4097 time to fit residues: 101.4812 Evaluate side-chains 34 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 40.0000 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 11 optimal weight: 50.0000 chunk 22 optimal weight: 50.0000 chunk 17 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 13 optimal weight: 50.0000 chunk 20 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 overall best weight: 13.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.103914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.085661 restraints weight = 14109.203| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.53 r_work: 0.3744 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1041 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1056 | |-----------------------------------------------------------------------------| r_final: 0.3647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3673 Z= 0.341 Angle : 0.761 11.936 5008 Z= 0.391 Chirality : 0.050 0.164 569 Planarity : 0.005 0.044 613 Dihedral : 11.968 72.927 590 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.68 % Allowed : 12.87 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.38), residues: 440 helix: 0.41 (0.52), residues: 95 sheet: 0.02 (0.48), residues: 110 loop : -0.74 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 196 HIS 0.009 0.002 HIS A 295 PHE 0.008 0.001 PHE A 211 TYR 0.017 0.002 TYR A 183 ARG 0.007 0.001 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 LYS cc_start: 0.6051 (OUTLIER) cc_final: 0.5143 (tppt) REVERT: A 294 MET cc_start: 0.5361 (tpt) cc_final: 0.5102 (tmm) outliers start: 10 outliers final: 2 residues processed: 37 average time/residue: 1.4466 time to fit residues: 55.1736 Evaluate side-chains 26 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 330 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 14 optimal weight: 6.9990 chunk 39 optimal weight: 50.0000 chunk 4 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 30.0000 chunk 2 optimal weight: 50.0000 chunk 33 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** 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 = 0.4306 r_free = 0.4306 target = 0.102684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.084968 restraints weight = 13744.761| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.67 r_work: 0.3755 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3666 r_free = 0.3666 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1056 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1058 | |-----------------------------------------------------------------------------| r_final: 0.3665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3673 Z= 0.228 Angle : 0.675 12.923 5008 Z= 0.344 Chirality : 0.047 0.144 569 Planarity : 0.005 0.050 613 Dihedral : 11.804 73.449 590 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.88 % Allowed : 16.35 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.38), residues: 440 helix: 0.49 (0.52), residues: 95 sheet: 0.11 (0.54), residues: 97 loop : -0.76 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 196 HIS 0.006 0.001 HIS A 349 PHE 0.029 0.003 PHE A 211 TYR 0.012 0.002 TYR A 183 ARG 0.004 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: -0.2333 (mmt) cc_final: -0.2746 (mmm) REVERT: A 294 MET cc_start: 0.5254 (tpt) cc_final: 0.5041 (tmm) REVERT: A 310 PHE cc_start: 0.8691 (p90) cc_final: 0.7888 (p90) outliers start: 7 outliers final: 0 residues processed: 27 average time/residue: 1.2035 time to fit residues: 33.9020 Evaluate side-chains 20 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 33 optimal weight: 40.0000 chunk 40 optimal weight: 30.0000 chunk 15 optimal weight: 0.0060 chunk 27 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 2 optimal weight: 40.0000 chunk 37 optimal weight: 40.0000 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 overall best weight: 6.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.102168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.084305 restraints weight = 13906.285| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.62 r_work: 0.3746 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1058 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3673 Z= 0.213 Angle : 0.648 10.370 5008 Z= 0.327 Chirality : 0.046 0.142 569 Planarity : 0.005 0.052 613 Dihedral : 11.736 73.560 590 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.07 % Allowed : 15.55 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.38), residues: 440 helix: 0.62 (0.51), residues: 95 sheet: -0.07 (0.56), residues: 86 loop : -0.70 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 196 HIS 0.005 0.001 HIS A 364 PHE 0.030 0.002 PHE A 211 TYR 0.011 0.001 TYR A 183 ARG 0.003 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.6764 (mtm) cc_final: 0.6364 (pmm) REVERT: A 276 MET cc_start: 0.6077 (mtp) cc_final: 0.5519 (ttm) REVERT: A 294 MET cc_start: 0.5390 (tpt) cc_final: 0.5089 (tmm) REVERT: A 310 PHE cc_start: 0.8724 (p90) cc_final: 0.8002 (p90) outliers start: 4 outliers final: 0 residues processed: 23 average time/residue: 1.3450 time to fit residues: 32.2587 Evaluate side-chains 18 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 34 optimal weight: 50.0000 chunk 18 optimal weight: 20.0000 chunk 7 optimal weight: 50.0000 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.101849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.083976 restraints weight = 13989.947| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.60 r_work: 0.3750 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1060 | |-----------------------------------------------------------------------------| r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3673 Z= 0.169 Angle : 0.605 8.996 5008 Z= 0.304 Chirality : 0.045 0.144 569 Planarity : 0.005 0.051 613 Dihedral : 11.672 73.566 590 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.07 % Allowed : 15.55 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.38), residues: 440 helix: 0.84 (0.52), residues: 95 sheet: -0.10 (0.56), residues: 92 loop : -0.56 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 210 HIS 0.004 0.001 HIS A 364 PHE 0.034 0.002 PHE A 211 TYR 0.008 0.001 TYR A 357 ARG 0.002 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: -0.2531 (mmt) cc_final: -0.3094 (mmm) REVERT: A 155 MET cc_start: 0.6546 (OUTLIER) cc_final: 0.6145 (pmm) REVERT: A 165 LYS cc_start: 0.8450 (mmpt) cc_final: 0.8036 (pmtt) REVERT: A 276 MET cc_start: 0.6020 (mtp) cc_final: 0.5386 (ttm) REVERT: A 294 MET cc_start: 0.5332 (tpt) cc_final: 0.5048 (tmm) REVERT: A 310 PHE cc_start: 0.8740 (p90) cc_final: 0.7810 (p90) REVERT: A 404 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6967 (mmm) outliers start: 4 outliers final: 1 residues processed: 22 average time/residue: 1.2986 time to fit residues: 29.9168 Evaluate side-chains 23 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 404 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 12 optimal weight: 8.9990 chunk 4 optimal weight: 40.0000 chunk 34 optimal weight: 50.0000 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 35 optimal weight: 40.0000 chunk 17 optimal weight: 50.0000 chunk 30 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.101294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.082925 restraints weight = 13797.844| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.58 r_work: 0.3721 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1060 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3673 Z= 0.213 Angle : 0.604 8.726 5008 Z= 0.307 Chirality : 0.045 0.140 569 Planarity : 0.005 0.056 613 Dihedral : 11.602 73.590 590 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.88 % Allowed : 14.75 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.39), residues: 440 helix: 1.00 (0.53), residues: 95 sheet: 0.13 (0.54), residues: 97 loop : -0.53 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 210 HIS 0.005 0.001 HIS A 295 PHE 0.033 0.002 PHE A 211 TYR 0.011 0.001 TYR A 162 ARG 0.003 0.001 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 146 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7785 (pptt) REVERT: A 155 MET cc_start: 0.6438 (OUTLIER) cc_final: 0.6085 (pmm) REVERT: A 165 LYS cc_start: 0.8511 (mmpt) cc_final: 0.8137 (pmtt) REVERT: A 276 MET cc_start: 0.6106 (mtp) cc_final: 0.5561 (ttm) REVERT: A 294 MET cc_start: 0.5269 (tpt) cc_final: 0.4950 (tmm) REVERT: A 310 PHE cc_start: 0.8677 (p90) cc_final: 0.7807 (p90) REVERT: A 404 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7129 (mmm) outliers start: 7 outliers final: 2 residues processed: 24 average time/residue: 1.1970 time to fit residues: 30.0784 Evaluate side-chains 23 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 404 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 50.0000 chunk 19 optimal weight: 50.0000 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 50.0000 chunk 39 optimal weight: 50.0000 chunk 32 optimal weight: 40.0000 chunk 31 optimal weight: 3.9990 chunk 22 optimal weight: 40.0000 chunk 29 optimal weight: 30.0000 overall best weight: 10.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.100761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.082244 restraints weight = 13741.100| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.58 r_work: 0.3703 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3673 Z= 0.255 Angle : 0.627 7.883 5008 Z= 0.324 Chirality : 0.046 0.138 569 Planarity : 0.005 0.059 613 Dihedral : 11.394 73.472 590 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.88 % Allowed : 16.09 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.39), residues: 440 helix: 0.83 (0.52), residues: 95 sheet: 0.03 (0.52), residues: 105 loop : -0.57 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 58 HIS 0.007 0.002 HIS A 295 PHE 0.011 0.002 PHE A 340 TYR 0.011 0.002 TYR A 162 ARG 0.002 0.001 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 146 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7861 (pptt) REVERT: A 155 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.6118 (pmm) REVERT: A 165 LYS cc_start: 0.8499 (mmpt) cc_final: 0.8131 (pmtt) REVERT: A 276 MET cc_start: 0.6167 (mtp) cc_final: 0.5588 (ttm) REVERT: A 294 MET cc_start: 0.5406 (tpt) cc_final: 0.5018 (tmm) REVERT: A 310 PHE cc_start: 0.8601 (p90) cc_final: 0.7705 (p90) REVERT: A 404 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7053 (mmm) outliers start: 7 outliers final: 4 residues processed: 23 average time/residue: 1.2954 time to fit residues: 31.2291 Evaluate side-chains 25 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 429 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 34 optimal weight: 40.0000 chunk 32 optimal weight: 0.3980 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 0 optimal weight: 60.0000 chunk 38 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 6 optimal weight: 0.0970 chunk 16 optimal weight: 7.9990 overall best weight: 4.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.101053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.085482 restraints weight = 13548.864| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 4.25 r_work: 0.3694 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3673 Z= 0.165 Angle : 0.592 8.773 5008 Z= 0.301 Chirality : 0.045 0.141 569 Planarity : 0.005 0.056 613 Dihedral : 11.050 73.542 590 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.14 % Allowed : 15.82 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.39), residues: 440 helix: 1.00 (0.53), residues: 95 sheet: -0.07 (0.56), residues: 90 loop : -0.63 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 58 HIS 0.004 0.001 HIS A 364 PHE 0.012 0.001 PHE A 340 TYR 0.009 0.001 TYR A 162 ARG 0.002 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: -0.1700 (mmt) cc_final: -0.2026 (mpt) REVERT: A 165 LYS cc_start: 0.8490 (mmpt) cc_final: 0.8147 (pmtt) REVERT: A 217 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5643 (mm-30) REVERT: A 276 MET cc_start: 0.5837 (mtp) cc_final: 0.5244 (ttm) REVERT: A 294 MET cc_start: 0.5406 (tpt) cc_final: 0.5027 (tmm) REVERT: A 310 PHE cc_start: 0.8714 (p90) cc_final: 0.7810 (p90) REVERT: A 404 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6893 (mmm) outliers start: 8 outliers final: 2 residues processed: 25 average time/residue: 1.3099 time to fit residues: 34.1420 Evaluate side-chains 23 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 404 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 42 optimal weight: 8.9990 chunk 2 optimal weight: 40.0000 chunk 17 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 43 optimal weight: 40.0000 chunk 40 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.101158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.082857 restraints weight = 13569.162| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.47 r_work: 0.3728 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3673 Z= 0.179 Angle : 0.602 9.224 5008 Z= 0.303 Chirality : 0.045 0.137 569 Planarity : 0.005 0.060 613 Dihedral : 10.965 73.560 590 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.07 % Allowed : 17.43 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.39), residues: 440 helix: 0.94 (0.53), residues: 97 sheet: 0.02 (0.56), residues: 92 loop : -0.71 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 58 HIS 0.006 0.001 HIS A 26 PHE 0.011 0.001 PHE A 340 TYR 0.010 0.001 TYR A 162 ARG 0.002 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 26 HIS cc_start: 0.8046 (t70) cc_final: 0.7655 (t-90) REVERT: A 49 MET cc_start: -0.1737 (mmt) cc_final: -0.2055 (mpt) REVERT: A 165 LYS cc_start: 0.8488 (mmpt) cc_final: 0.8159 (pmtt) REVERT: A 217 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.5493 (mm-30) REVERT: A 276 MET cc_start: 0.6077 (mtp) cc_final: 0.5503 (ttm) REVERT: A 294 MET cc_start: 0.5373 (tpt) cc_final: 0.5015 (tmm) REVERT: A 310 PHE cc_start: 0.8704 (p90) cc_final: 0.7851 (p90) REVERT: A 404 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7059 (mmm) outliers start: 4 outliers final: 2 residues processed: 21 average time/residue: 1.3146 time to fit residues: 29.0184 Evaluate side-chains 22 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 404 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 0.0370 chunk 25 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 14 optimal weight: 40.0000 chunk 8 optimal weight: 50.0000 chunk 40 optimal weight: 40.0000 chunk 32 optimal weight: 20.0000 overall best weight: 6.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.100813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.082676 restraints weight = 13563.311| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.52 r_work: 0.3720 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| r_final: 0.3636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3673 Z= 0.179 Angle : 0.615 12.074 5008 Z= 0.305 Chirality : 0.045 0.136 569 Planarity : 0.005 0.059 613 Dihedral : 10.966 73.552 590 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.07 % Allowed : 17.96 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.39), residues: 440 helix: 1.03 (0.54), residues: 97 sheet: 0.09 (0.51), residues: 108 loop : -0.70 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 58 HIS 0.004 0.001 HIS A 26 PHE 0.012 0.002 PHE A 340 TYR 0.008 0.001 TYR A 357 ARG 0.002 0.000 ARG A 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 26 HIS cc_start: 0.8070 (t70) cc_final: 0.7666 (t-90) REVERT: A 49 MET cc_start: -0.1677 (mmt) cc_final: -0.1985 (mpt) REVERT: A 165 LYS cc_start: 0.8464 (mmpt) cc_final: 0.8140 (pmtt) REVERT: A 208 MET cc_start: 0.7021 (tmm) cc_final: 0.6703 (tpp) REVERT: A 276 MET cc_start: 0.6064 (mtp) cc_final: 0.5442 (ttm) REVERT: A 294 MET cc_start: 0.5454 (tpt) cc_final: 0.5093 (tmm) REVERT: A 310 PHE cc_start: 0.8701 (p90) cc_final: 0.7843 (p90) REVERT: A 404 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7089 (mmm) outliers start: 4 outliers final: 3 residues processed: 21 average time/residue: 1.3524 time to fit residues: 29.7158 Evaluate side-chains 22 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 404 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 8.9990 chunk 19 optimal weight: 30.0000 chunk 31 optimal weight: 7.9990 chunk 0 optimal weight: 60.0000 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 30.0000 chunk 7 optimal weight: 50.0000 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.100908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.082809 restraints weight = 13551.463| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.47 r_work: 0.3728 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1059 | |-----------------------------------------------------------------------------| r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.6360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3673 Z= 0.176 Angle : 0.607 11.630 5008 Z= 0.301 Chirality : 0.045 0.137 569 Planarity : 0.005 0.058 613 Dihedral : 10.935 73.546 590 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.07 % Allowed : 17.69 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.39), residues: 440 helix: 1.07 (0.54), residues: 97 sheet: 0.11 (0.52), residues: 106 loop : -0.64 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 58 HIS 0.004 0.001 HIS A 364 PHE 0.014 0.001 PHE A 211 TYR 0.008 0.001 TYR A 162 ARG 0.002 0.000 ARG A 423 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3785.60 seconds wall clock time: 65 minutes 16.11 seconds (3916.11 seconds total)