Starting phenix.real_space_refine on Wed Mar 5 15:47:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkg_14041/03_2025/7qkg_14041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkg_14041/03_2025/7qkg_14041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qkg_14041/03_2025/7qkg_14041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkg_14041/03_2025/7qkg_14041.map" model { file = "/net/cci-nas-00/data/ceres_data/7qkg_14041/03_2025/7qkg_14041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkg_14041/03_2025/7qkg_14041.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 S 6 5.16 5 C 744 2.51 5 N 213 2.21 5 O 228 1.98 5 H 1278 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2469 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "A" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Time building chain proxies: 2.33, per 1000 atoms: 0.94 Number of scatterers: 2469 At special positions: 0 Unit cell: (74.984, 67.568, 35.432, 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 6 16.00 O 228 8.00 N 213 7.00 C 744 6.00 H 1278 1.00 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: 0.67 Conformation dependent library (CDL) restraints added in 183.8 milliseconds 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 288 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 277 through 278 removed outlier: 6.492A pdb=" N ILE B 277 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 282 through 283 removed outlier: 6.833A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 291 removed outlier: 9.111A pdb=" N ASN B 286 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N SER A 289 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN B 288 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N CYS A 291 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS B 290 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL B 287 " --> pdb=" O ASN C 286 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN C 288 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 removed outlier: 6.504A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.527A pdb=" N VAL B 306 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL A 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 308 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.516A pdb=" N VAL B 313 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 317 through 322 removed outlier: 6.401A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) 16 hydrogen bonds defined for protein. 48 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.71 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 1272 1.12 - 1.29: 201 1.29 - 1.47: 335 1.47 - 1.64: 664 1.64 - 1.81: 6 Bond restraints: 2478 Sorted by residual: bond pdb=" CE1 TYR A 310 " pdb=" HE1 TYR A 310 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASN B 327 " pdb=" H ASN B 327 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N VAL A 287 " pdb=" H VAL A 287 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N SER A 289 " pdb=" H SER A 289 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND2 ASN C 286 " pdb="HD21 ASN C 286 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 2473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 3724 2.51 - 5.02: 604 5.02 - 7.52: 185 7.52 - 10.03: 14 10.03 - 12.54: 6 Bond angle restraints: 4533 Sorted by residual: angle pdb=" CA ILE B 328 " pdb=" CB ILE B 328 " pdb=" CG1 ILE B 328 " ideal model delta sigma weight residual 110.40 118.04 -7.64 1.70e+00 3.46e-01 2.02e+01 angle pdb=" N PRO C 312 " pdb=" CA PRO C 312 " pdb=" CB PRO C 312 " ideal model delta sigma weight residual 103.31 107.26 -3.95 8.90e-01 1.26e+00 1.97e+01 angle pdb=" OE1 GLN C 276 " pdb=" CD GLN C 276 " pdb=" NE2 GLN C 276 " ideal model delta sigma weight residual 122.60 118.23 4.37 1.00e+00 1.00e+00 1.91e+01 angle pdb=" N PRO A 312 " pdb=" CA PRO A 312 " pdb=" CB PRO A 312 " ideal model delta sigma weight residual 103.31 107.19 -3.88 8.90e-01 1.26e+00 1.90e+01 angle pdb=" CA VAL B 287 " pdb=" C VAL B 287 " pdb=" N GLN B 288 " ideal model delta sigma weight residual 116.40 121.27 -4.87 1.12e+00 7.97e-01 1.89e+01 ... (remaining 4528 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 13.90: 983 13.90 - 27.79: 73 27.79 - 41.67: 29 41.67 - 55.56: 25 55.56 - 69.45: 30 Dihedral angle restraints: 1140 sinusoidal: 669 harmonic: 471 Sorted by residual: dihedral pdb=" CA ILE A 297 " pdb=" C ILE A 297 " pdb=" N LYS A 298 " pdb=" CA LYS A 298 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA VAL A 313 " pdb=" C VAL A 313 " pdb=" N ASP A 314 " pdb=" CA ASP A 314 " ideal model delta harmonic sigma weight residual 180.00 157.76 22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA VAL C 313 " pdb=" C VAL C 313 " pdb=" N ASP C 314 " pdb=" CA ASP C 314 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 1137 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.069: 119 0.069 - 0.138: 47 0.138 - 0.207: 19 0.207 - 0.275: 6 0.275 - 0.344: 4 Chirality restraints: 195 Sorted by residual: chirality pdb=" CA LYS B 311 " pdb=" N LYS B 311 " pdb=" C LYS B 311 " pdb=" CB LYS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA LYS C 311 " pdb=" N LYS C 311 " pdb=" C LYS C 311 " pdb=" CB LYS C 311 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA LYS A 311 " pdb=" N LYS A 311 " pdb=" C LYS A 311 " pdb=" CB LYS A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 192 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 307 " 0.082 2.00e-02 2.50e+03 8.02e-02 9.65e+01 pdb=" CD GLN B 307 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN B 307 " -0.079 2.00e-02 2.50e+03 pdb=" NE2 GLN B 307 " 0.025 2.00e-02 2.50e+03 pdb="HE21 GLN B 307 " -0.116 2.00e-02 2.50e+03 pdb="HE22 GLN B 307 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 297 " -0.031 2.00e-02 2.50e+03 5.67e-02 3.21e+01 pdb=" N LYS B 298 " 0.098 2.00e-02 2.50e+03 pdb=" CA LYS B 298 " -0.028 2.00e-02 2.50e+03 pdb=" H LYS B 298 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 313 " -0.030 2.00e-02 2.50e+03 5.64e-02 3.18e+01 pdb=" N ASP A 314 " 0.097 2.00e-02 2.50e+03 pdb=" CA ASP A 314 " -0.028 2.00e-02 2.50e+03 pdb=" H ASP A 314 " -0.040 2.00e-02 2.50e+03 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 209 2.17 - 2.78: 4235 2.78 - 3.39: 6470 3.39 - 3.99: 8308 3.99 - 4.60: 11399 Nonbonded interactions: 30621 Sorted by model distance: nonbonded pdb=" OD1 ASP A 283 " pdb=" HG SER A 285 " model vdw 1.569 2.450 nonbonded pdb=" OD1 ASP B 283 " pdb=" HG SER B 285 " model vdw 1.576 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.580 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.581 2.450 nonbonded pdb=" OD1 ASP C 283 " pdb=" HG SER C 285 " model vdw 1.636 2.450 ... (remaining 30616 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.050 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.800 Find NCS groups from input model: 0.060 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.010 0.036 1200 Z= 0.707 Angle : 2.027 8.738 1608 Z= 1.320 Chirality : 0.101 0.344 195 Planarity : 0.008 0.025 201 Dihedral : 10.758 42.499 462 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.58), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS A 299 TYR 0.041 0.010 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7728 (ttmt) REVERT: B 321 LYS cc_start: 0.8285 (mtmt) cc_final: 0.8075 (mtmm) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.4222 time to fit residues: 11.8397 Evaluate side-chains 17 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 HIS A 299 HIS C 299 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.184145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.169026 restraints weight = 4362.851| |-----------------------------------------------------------------------------| r_work (start): 0.4694 rms_B_bonded: 2.39 r_work: 0.4616 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4533 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.4533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 1200 Z= 0.245 Angle : 0.705 5.602 1608 Z= 0.358 Chirality : 0.053 0.134 195 Planarity : 0.003 0.021 201 Dihedral : 6.170 21.458 162 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.57), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 TYR 0.014 0.004 TYR C 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.207 Fit side-chains REVERT: B 321 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7527 (mtmm) REVERT: A 321 LYS cc_start: 0.8590 (mttt) cc_final: 0.8257 (mttm) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.3793 time to fit residues: 9.1293 Evaluate side-chains 17 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 10 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.4852 r_free = 0.4852 target = 0.191281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.176070 restraints weight = 4550.775| |-----------------------------------------------------------------------------| r_work (start): 0.4752 rms_B_bonded: 2.47 r_work: 0.4675 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4590 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.4590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 1200 Z= 0.132 Angle : 0.550 4.597 1608 Z= 0.278 Chirality : 0.054 0.135 195 Planarity : 0.003 0.021 201 Dihedral : 5.186 17.356 162 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 15.97 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.59), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 299 TYR 0.009 0.003 TYR C 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: B 321 LYS cc_start: 0.8162 (mtmt) cc_final: 0.7587 (mttp) REVERT: A 291 CYS cc_start: 0.8398 (t) cc_final: 0.7864 (m) REVERT: A 321 LYS cc_start: 0.8580 (mttt) cc_final: 0.8230 (mttm) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.3978 time to fit residues: 9.1469 Evaluate side-chains 16 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4706 r_free = 0.4706 target = 0.183585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.168288 restraints weight = 4472.141| |-----------------------------------------------------------------------------| r_work (start): 0.4728 rms_B_bonded: 2.27 r_work: 0.4667 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4592 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1200 Z= 0.168 Angle : 0.551 4.473 1608 Z= 0.278 Chirality : 0.052 0.130 195 Planarity : 0.003 0.028 201 Dihedral : 5.085 16.700 162 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.69 % Allowed : 16.67 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.61), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 299 TYR 0.006 0.001 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: B 321 LYS cc_start: 0.8348 (mtmt) cc_final: 0.7866 (mttp) REVERT: A 291 CYS cc_start: 0.8256 (t) cc_final: 0.7871 (m) REVERT: A 321 LYS cc_start: 0.8599 (mttt) cc_final: 0.8296 (mttm) REVERT: C 311 LYS cc_start: 0.8907 (mttt) cc_final: 0.8608 (mttp) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.4252 time to fit residues: 9.2753 Evaluate side-chains 19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 300 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.4685 r_free = 0.4685 target = 0.179321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.164240 restraints weight = 4525.481| |-----------------------------------------------------------------------------| r_work (start): 0.4708 rms_B_bonded: 2.28 r_work: 0.4647 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4568 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 1200 Z= 0.167 Angle : 0.537 4.642 1608 Z= 0.271 Chirality : 0.052 0.134 195 Planarity : 0.003 0.027 201 Dihedral : 5.005 15.528 162 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.69 % Allowed : 16.67 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.61), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 299 TYR 0.007 0.002 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7681 (mttm) REVERT: B 321 LYS cc_start: 0.8356 (mtmt) cc_final: 0.7937 (mttp) REVERT: A 321 LYS cc_start: 0.8622 (mttt) cc_final: 0.8337 (mttm) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.4782 time to fit residues: 10.2854 Evaluate side-chains 20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.4794 r_free = 0.4794 target = 0.178834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.163919 restraints weight = 4567.466| |-----------------------------------------------------------------------------| r_work (start): 0.4694 rms_B_bonded: 2.19 r_work: 0.4630 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4550 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 1200 Z= 0.197 Angle : 0.552 4.756 1608 Z= 0.279 Chirality : 0.052 0.135 195 Planarity : 0.004 0.030 201 Dihedral : 5.010 15.350 162 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.69 % Allowed : 18.06 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.61), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 299 TYR 0.007 0.002 TYR C 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: B 317 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7609 (mttm) REVERT: B 321 LYS cc_start: 0.8316 (mtmt) cc_final: 0.7869 (mttp) REVERT: A 321 LYS cc_start: 0.8616 (mttt) cc_final: 0.8318 (mttm) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.4835 time to fit residues: 9.4626 Evaluate side-chains 19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 300 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 0.0170 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 overall best weight: 1.1222 ------------------------------------------------------------------------------- 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 = 0.4831 r_free = 0.4831 target = 0.181985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.166987 restraints weight = 4581.576| |-----------------------------------------------------------------------------| r_work (start): 0.4730 rms_B_bonded: 2.24 r_work: 0.4666 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.4582 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1200 Z= 0.139 Angle : 0.527 4.587 1608 Z= 0.261 Chirality : 0.052 0.132 195 Planarity : 0.004 0.031 201 Dihedral : 4.731 14.618 162 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.39 % Allowed : 18.06 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.62), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 299 TYR 0.006 0.002 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: B 321 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7881 (mttp) REVERT: A 317 LYS cc_start: 0.8556 (tttt) cc_final: 0.8298 (tttm) REVERT: A 321 LYS cc_start: 0.8613 (mttt) cc_final: 0.8311 (mttm) outliers start: 2 outliers final: 1 residues processed: 19 average time/residue: 0.4551 time to fit residues: 9.4166 Evaluate side-chains 18 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 300 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 0.0970 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.4698 r_free = 0.4698 target = 0.162244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.146570 restraints weight = 4849.385| |-----------------------------------------------------------------------------| r_work (start): 0.4578 rms_B_bonded: 2.46 r_work: 0.4520 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4434 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 1200 Z= 0.132 Angle : 0.519 4.381 1608 Z= 0.257 Chirality : 0.052 0.131 195 Planarity : 0.003 0.030 201 Dihedral : 4.630 14.674 162 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 19.44 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.62), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 299 TYR 0.006 0.002 TYR C 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.199 Fit side-chains REVERT: B 321 LYS cc_start: 0.8269 (mtmt) cc_final: 0.7817 (mttp) REVERT: A 317 LYS cc_start: 0.8512 (tttt) cc_final: 0.8237 (tttm) REVERT: A 321 LYS cc_start: 0.8563 (mttt) cc_final: 0.8247 (mttm) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.4721 time to fit residues: 9.2494 Evaluate side-chains 18 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4714 r_free = 0.4714 target = 0.165061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.148450 restraints weight = 4637.718| |-----------------------------------------------------------------------------| r_work (start): 0.4598 rms_B_bonded: 2.41 r_work: 0.4539 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4458 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 1200 Z= 0.131 Angle : 0.512 4.659 1608 Z= 0.254 Chirality : 0.052 0.131 195 Planarity : 0.004 0.030 201 Dihedral : 4.567 14.797 162 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.69 % Allowed : 18.75 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.63), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 299 TYR 0.006 0.001 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.196 Fit side-chains REVERT: B 321 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7769 (mttp) REVERT: A 317 LYS cc_start: 0.8484 (tttt) cc_final: 0.8237 (tttm) REVERT: A 321 LYS cc_start: 0.8554 (mttt) cc_final: 0.8231 (mttm) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.4089 time to fit residues: 8.0598 Evaluate side-chains 18 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.0670 chunk 5 optimal weight: 0.8980 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 = 0.4766 r_free = 0.4766 target = 0.186892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.172083 restraints weight = 4416.887| |-----------------------------------------------------------------------------| r_work (start): 0.4777 rms_B_bonded: 2.27 r_work: 0.4718 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4636 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 1200 Z= 0.118 Angle : 0.513 4.364 1608 Z= 0.253 Chirality : 0.052 0.130 195 Planarity : 0.004 0.031 201 Dihedral : 4.521 16.399 162 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.69 % Allowed : 20.14 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.63), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 299 TYR 0.006 0.001 TYR B 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.215 Fit side-chains REVERT: B 321 LYS cc_start: 0.8326 (mtmt) cc_final: 0.7873 (mttp) REVERT: A 317 LYS cc_start: 0.8487 (tttt) cc_final: 0.8256 (tttm) REVERT: A 321 LYS cc_start: 0.8584 (mttt) cc_final: 0.8279 (mttm) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.4925 time to fit residues: 9.0953 Evaluate side-chains 16 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.4830 r_free = 0.4830 target = 0.181261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.166451 restraints weight = 4542.339| |-----------------------------------------------------------------------------| r_work (start): 0.4724 rms_B_bonded: 2.24 r_work: 0.4665 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4583 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 1200 Z= 0.155 Angle : 0.524 4.466 1608 Z= 0.262 Chirality : 0.052 0.135 195 Planarity : 0.004 0.030 201 Dihedral : 4.633 17.004 162 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.69 % Allowed : 20.14 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.64), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 299 TYR 0.005 0.001 TYR B 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2674.60 seconds wall clock time: 46 minutes 6.52 seconds (2766.52 seconds total)