Starting phenix.real_space_refine on Mon Feb 10 20:52:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkg_14041/02_2025/7qkg_14041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkg_14041/02_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_14041/02_2025/7qkg_14041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkg_14041/02_2025/7qkg_14041.map" model { file = "/net/cci-nas-00/data/ceres_data/7qkg_14041/02_2025/7qkg_14041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkg_14041/02_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-5592/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: 2.25, per 1000 atoms: 0.91 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: 0.52 Conformation dependent library (CDL) restraints added in 148.5 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: 0.67 Time building geometry restraints manager: 0.64 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: 1.420 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.490 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.650 ------------------------------------------------------------------------------- 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 : 0.214 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: 0.4398 time to fit residues: 12.3844 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 : 0.241 ------------------------------------------------------------------------------- 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: 4.9990 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 = 33)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.169027 restraints weight = 4362.851| |-----------------------------------------------------------------------------| r_work (start): 0.4694 rms_B_bonded: 2.39 r_work: 0.4616 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.4536 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 0.215 Fit side-chains REVERT: B 321 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7530 (mtmm) REVERT: A 321 LYS cc_start: 0.8588 (mttt) cc_final: 0.8255 (mttm) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.3775 time to fit residues: 9.0894 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 : 0.160 ------------------------------------------------------------------------------- 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: 4.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4781 r_free = 0.4781 target = 0.183034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.168329 restraints weight = 4711.250| |-----------------------------------------------------------------------------| r_work (start): 0.4676 rms_B_bonded: 2.36 r_work: 0.4606 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4521 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4021 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= 0.189 Angle : 0.589 5.042 1608 Z= 0.302 Chirality : 0.054 0.135 195 Planarity : 0.003 0.026 201 Dihedral : 5.510 18.782 162 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % 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: -2.07 (0.59), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 299 TYR 0.010 0.003 TYR B 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 19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: B 321 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7709 (mttp) REVERT: A 321 LYS cc_start: 0.8593 (mttt) cc_final: 0.8251 (mttm) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.4473 time to fit residues: 9.2971 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 : 0.209 ------------------------------------------------------------------------------- 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: 3.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.180765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.166096 restraints weight = 4760.093| |-----------------------------------------------------------------------------| r_work (start): 0.4659 rms_B_bonded: 2.35 r_work: 0.4594 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.4512 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4292 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= 0.203 Angle : 0.579 5.162 1608 Z= 0.292 Chirality : 0.053 0.134 195 Planarity : 0.004 0.032 201 Dihedral : 5.301 17.656 162 Min Nonbonded Distance : 2.627 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: -2.05 (0.60), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.46), 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 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 20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: B 321 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7738 (mttp) REVERT: A 321 LYS cc_start: 0.8603 (mttt) cc_final: 0.8297 (mttm) REVERT: C 311 LYS cc_start: 0.8868 (mttt) cc_final: 0.8525 (mttp) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.4363 time to fit residues: 9.0356 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 : 0.225 ------------------------------------------------------------------------------- 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: 5.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.4758 r_free = 0.4758 target = 0.177104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.162137 restraints weight = 4616.486| |-----------------------------------------------------------------------------| r_work (start): 0.4664 rms_B_bonded: 2.18 r_work: 0.4599 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4519 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 1200 Z= 0.199 Angle : 0.554 5.131 1608 Z= 0.282 Chirality : 0.053 0.135 195 Planarity : 0.004 0.031 201 Dihedral : 5.151 16.386 162 Min Nonbonded Distance : 2.631 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: -1.93 (0.62), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 299 TYR 0.008 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 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 Fit side-chains REVERT: B 317 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7637 (mttm) REVERT: B 321 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7774 (mttp) REVERT: A 321 LYS cc_start: 0.8605 (mttt) cc_final: 0.8302 (mttm) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.4555 time to fit residues: 9.3971 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 ------------------------------------------------------------------------------- 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: 0.9990 chunk 7 optimal weight: 0.0050 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 = 0.4824 r_free = 0.4824 target = 0.182209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.167325 restraints weight = 4519.731| |-----------------------------------------------------------------------------| r_work (start): 0.4729 rms_B_bonded: 2.28 r_work: 0.4669 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4589 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 1200 Z= 0.111 Angle : 0.506 4.462 1608 Z= 0.253 Chirality : 0.052 0.130 195 Planarity : 0.004 0.032 201 Dihedral : 4.664 14.416 162 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 18.06 % Favored : 81.94 % 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 B 299 TYR 0.005 0.001 TYR B 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 18 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.184 Fit side-chains REVERT: B 321 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7803 (mttp) REVERT: A 317 LYS cc_start: 0.8551 (tttt) cc_final: 0.8290 (tttm) REVERT: A 321 LYS cc_start: 0.8581 (mttt) cc_final: 0.8271 (mttm) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.4021 time to fit residues: 7.9726 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 : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 0.1980 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.4602 r_free = 0.4602 target = 0.155067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.139943 restraints weight = 5029.846| |-----------------------------------------------------------------------------| r_work (start): 0.4484 rms_B_bonded: 2.38 r_work: 0.4429 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4345 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 1200 Z= 0.211 Angle : 0.550 4.843 1608 Z= 0.279 Chirality : 0.052 0.137 195 Planarity : 0.004 0.031 201 Dihedral : 4.893 14.488 162 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % 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: -1.71 (0.62), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.47), 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 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: 1 poor density : 19 time to evaluate : 0.217 Fit side-chains REVERT: B 317 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7542 (mttm) REVERT: B 321 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7861 (mttp) REVERT: A 317 LYS cc_start: 0.8561 (tttt) cc_final: 0.8302 (tttm) REVERT: A 321 LYS cc_start: 0.8588 (mttt) cc_final: 0.8281 (mttm) outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.4597 time to fit residues: 9.4897 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 7 optimal weight: 0.0040 chunk 14 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.4697 r_free = 0.4697 target = 0.162697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.146817 restraints weight = 4807.008| |-----------------------------------------------------------------------------| r_work (start): 0.4588 rms_B_bonded: 2.45 r_work: 0.4535 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4454 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4959 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= 0.105 Angle : 0.492 4.247 1608 Z= 0.246 Chirality : 0.052 0.134 195 Planarity : 0.004 0.030 201 Dihedral : 4.482 13.909 162 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 1.22 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: -1.47 (0.62), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.47), 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 *********************** 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: 1 poor density : 17 time to evaluate : 0.211 Fit side-chains REVERT: B 321 LYS cc_start: 0.8276 (mtmt) cc_final: 0.7815 (mttp) REVERT: A 317 LYS cc_start: 0.8501 (tttt) cc_final: 0.8244 (tttm) REVERT: A 321 LYS cc_start: 0.8557 (mttt) cc_final: 0.8262 (mttm) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.4232 time to fit residues: 7.9194 Evaluate side-chains 17 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.0870 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- 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 = 0.4644 r_free = 0.4644 target = 0.159009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.142913 restraints weight = 4757.485| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 2.40 r_work: 0.4457 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4370 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4967 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= 0.164 Angle : 0.517 4.616 1608 Z= 0.262 Chirality : 0.052 0.135 195 Planarity : 0.004 0.032 201 Dihedral : 4.651 13.795 162 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.69 % Allowed : 19.44 % Favored : 79.86 % 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: -1.50 (0.62), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 299 TYR 0.005 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 : 0.213 Fit side-chains REVERT: B 321 LYS cc_start: 0.8287 (mtmt) cc_final: 0.7822 (mttp) REVERT: A 317 LYS cc_start: 0.8524 (tttt) cc_final: 0.8276 (tttm) REVERT: A 321 LYS cc_start: 0.8588 (mttt) cc_final: 0.8279 (mttm) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.4035 time to fit residues: 7.9901 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 : 0.203 ------------------------------------------------------------------------------- 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: 4.9990 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4673 r_free = 0.4673 target = 0.160622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.144883 restraints weight = 4821.203| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 2.44 r_work: 0.4495 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4408 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 1200 Z= 0.120 Angle : 0.490 4.382 1608 Z= 0.246 Chirality : 0.052 0.134 195 Planarity : 0.004 0.033 201 Dihedral : 4.460 14.154 162 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.69 % Allowed : 19.44 % Favored : 79.86 % 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: -1.42 (0.63), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 299 TYR 0.005 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 : 0.195 Fit side-chains REVERT: B 321 LYS cc_start: 0.8280 (mtmt) cc_final: 0.7818 (mttp) REVERT: A 317 LYS cc_start: 0.8520 (tttt) cc_final: 0.8282 (tttm) REVERT: A 321 LYS cc_start: 0.8556 (mttt) cc_final: 0.8257 (mttm) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.4359 time to fit residues: 8.1669 Evaluate side-chains 17 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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: 3.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4672 r_free = 0.4672 target = 0.160530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.144867 restraints weight = 4875.588| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 2.47 r_work: 0.4500 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4413 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 1200 Z= 0.116 Angle : 0.490 4.379 1608 Z= 0.246 Chirality : 0.053 0.137 195 Planarity : 0.004 0.032 201 Dihedral : 4.397 14.072 162 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % 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: -1.34 (0.64), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 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: 2594.42 seconds wall clock time: 46 minutes 9.25 seconds (2769.25 seconds total)