Starting phenix.real_space_refine on Wed Sep 17 03:19:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jb0_61303/09_2025/9jb0_61303.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jb0_61303/09_2025/9jb0_61303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jb0_61303/09_2025/9jb0_61303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jb0_61303/09_2025/9jb0_61303.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jb0_61303/09_2025/9jb0_61303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jb0_61303/09_2025/9jb0_61303.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1956 2.51 5 N 504 2.21 5 O 540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3012 Number of models: 1 Model: "" Number of chains: 2 Chain: "CC" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "CC" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 130 Classifications: {'peptide': 20} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 19} Restraints were copied for chains: BB, DD, EE, FF, AA, A, B, C, D, E, F Time building chain proxies: 0.52, per 1000 atoms: 0.17 Number of scatterers: 3012 At special positions: 0 Unit cell: (70.55, 73.87, 45.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 540 8.00 N 504 7.00 C 1956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " DAS A 23 " - " GLU A 22 " " DAS B 23 " - " GLU B 22 " " DAS C 23 " - " GLU C 22 " " DAS D 23 " - " GLU D 22 " " DAS E 23 " - " GLU E 22 " " DAS F 23 " - " GLU F 22 " " DASAA 23 " - " GLUAA 22 " " DASBB 23 " - " GLUBB 22 " " DASCC 23 " - " GLUCC 22 " " DASDD 23 " - " GLUDD 22 " " DASEE 23 " - " GLUEE 22 " " DASFF 23 " - " GLUFF 22 " Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 79.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DASCC 23 " pdb=" CB DASBB 23 " pdb=" CB DASDD 23 " pdb=" CB DASEE 23 " pdb=" CB DASFF 23 " pdb=" CB DASAA 23 " pdb=" CB DAS A 23 " pdb=" CB DAS B 23 " pdb=" CB DAS C 23 " pdb=" CB DAS D 23 " pdb=" CB DAS E 23 " pdb=" CB DAS F 23 " Number of C-beta restraints generated: 648 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 972 1.34 - 1.45: 413 1.45 - 1.57: 1639 1.57 - 1.68: 0 1.68 - 1.79: 24 Bond restraints: 3048 Sorted by residual: bond pdb=" C GLYBB 37 " pdb=" N GLYBB 38 " ideal model delta sigma weight residual 1.331 1.323 0.008 1.46e-02 4.69e+03 2.77e-01 bond pdb=" C GLY F 37 " pdb=" N GLY F 38 " ideal model delta sigma weight residual 1.331 1.323 0.008 1.46e-02 4.69e+03 2.75e-01 bond pdb=" C GLYDD 37 " pdb=" N GLYDD 38 " ideal model delta sigma weight residual 1.331 1.323 0.007 1.46e-02 4.69e+03 2.56e-01 bond pdb=" C GLYEE 37 " pdb=" N GLYEE 38 " ideal model delta sigma weight residual 1.331 1.323 0.007 1.46e-02 4.69e+03 2.40e-01 bond pdb=" C GLY A 37 " pdb=" N GLY A 38 " ideal model delta sigma weight residual 1.331 1.323 0.007 1.46e-02 4.69e+03 2.33e-01 ... (remaining 3043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.43: 3296 0.43 - 0.86: 590 0.86 - 1.29: 122 1.29 - 1.72: 48 1.72 - 2.15: 24 Bond angle restraints: 4080 Sorted by residual: angle pdb=" C VALCC 12 " pdb=" N HISCC 13 " pdb=" CA HISCC 13 " ideal model delta sigma weight residual 121.75 119.69 2.06 1.73e+00 3.34e-01 1.41e+00 angle pdb=" C VALFF 12 " pdb=" N HISFF 13 " pdb=" CA HISFF 13 " ideal model delta sigma weight residual 121.75 119.71 2.04 1.73e+00 3.34e-01 1.40e+00 angle pdb=" C VAL C 12 " pdb=" N HIS C 13 " pdb=" CA HIS C 13 " ideal model delta sigma weight residual 121.75 119.72 2.03 1.73e+00 3.34e-01 1.37e+00 angle pdb=" C VALDD 12 " pdb=" N HISDD 13 " pdb=" CA HISDD 13 " ideal model delta sigma weight residual 121.75 119.73 2.02 1.73e+00 3.34e-01 1.36e+00 angle pdb=" C VALBB 12 " pdb=" N HISBB 13 " pdb=" CA HISBB 13 " ideal model delta sigma weight residual 121.75 119.74 2.01 1.73e+00 3.34e-01 1.35e+00 ... (remaining 4075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.77: 1344 11.77 - 23.54: 192 23.54 - 35.31: 72 35.31 - 47.08: 40 47.08 - 58.85: 56 Dihedral angle restraints: 1704 sinusoidal: 648 harmonic: 1056 Sorted by residual: dihedral pdb=" CG LYSBB 28 " pdb=" CD LYSBB 28 " pdb=" CE LYSBB 28 " pdb=" NZ LYSBB 28 " ideal model delta sinusoidal sigma weight residual 60.00 1.15 58.85 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CG LYSFF 28 " pdb=" CD LYSFF 28 " pdb=" CE LYSFF 28 " pdb=" NZ LYSFF 28 " ideal model delta sinusoidal sigma weight residual 60.00 1.16 58.84 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CG LYS E 28 " pdb=" CD LYS E 28 " pdb=" CE LYS E 28 " pdb=" NZ LYS E 28 " ideal model delta sinusoidal sigma weight residual 60.00 1.16 58.84 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 1701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 182 0.024 - 0.049: 142 0.049 - 0.073: 48 0.073 - 0.097: 23 0.097 - 0.122: 73 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA VALFF 12 " pdb=" N VALFF 12 " pdb=" C VALFF 12 " pdb=" CB VALFF 12 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA VALBB 12 " pdb=" N VALBB 12 " pdb=" C VALBB 12 " pdb=" CB VALBB 12 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA VALAA 12 " pdb=" N VALAA 12 " pdb=" C VALAA 12 " pdb=" CB VALAA 12 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.55e-01 ... (remaining 465 not shown) Planarity restraints: 528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 13 " 0.005 2.00e-02 2.50e+03 5.26e-03 4.15e-01 pdb=" CG HIS E 13 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS E 13 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 13 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS E 13 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS E 13 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 13 " 0.005 2.00e-02 2.50e+03 5.21e-03 4.07e-01 pdb=" CG HIS C 13 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS C 13 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS C 13 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 13 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS C 13 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HISBB 13 " 0.005 2.00e-02 2.50e+03 5.14e-03 3.97e-01 pdb=" CG HISBB 13 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HISBB 13 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HISBB 13 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HISBB 13 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HISBB 13 " 0.001 2.00e-02 2.50e+03 ... (remaining 525 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.08: 2079 3.08 - 3.53: 2833 3.53 - 3.99: 5012 3.99 - 4.44: 5978 4.44 - 4.90: 10410 Nonbonded interactions: 26312 Sorted by model distance: nonbonded pdb=" CG LYS A 28 " pdb=" NZ LYS A 28 " model vdw 2.623 2.816 nonbonded pdb=" CG LYS B 28 " pdb=" NZ LYS B 28 " model vdw 2.624 2.816 nonbonded pdb=" CG LYSDD 28 " pdb=" NZ LYSDD 28 " model vdw 2.624 2.816 nonbonded pdb=" CG LYS C 28 " pdb=" NZ LYS C 28 " model vdw 2.624 2.816 nonbonded pdb=" CG LYSCC 28 " pdb=" NZ LYSCC 28 " model vdw 2.624 2.816 ... (remaining 26307 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: 0.02 Found NCS groups: ncs_group { reference = chain 'CC' selection = chain 'BB' selection = chain 'DD' selection = chain 'EE' selection = chain 'FF' selection = chain 'AA' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.820 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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 : 0.004 0.017 3060 Z= 0.169 Angle : 0.395 2.149 4116 Z= 0.232 Chirality : 0.055 0.122 468 Planarity : 0.002 0.005 516 Dihedral : 18.888 58.848 1020 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.69 % Allowed : 40.97 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.09 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYRBB 10 PHE 0.008 0.002 PHEFF 20 HIS 0.006 0.003 HISDD 13 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 3048) covalent geometry : angle 0.39689 ( 4080) link_TRANS : bond 0.00200 ( 12) link_TRANS : angle 0.15072 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.106 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8704 (mttp) cc_final: 0.8455 (mttt) REVERT: EE 28 LYS cc_start: 0.8737 (mttp) cc_final: 0.8521 (mttm) REVERT: FF 28 LYS cc_start: 0.8966 (mttp) cc_final: 0.8694 (mttm) REVERT: E 28 LYS cc_start: 0.8763 (mttp) cc_final: 0.8483 (mttm) outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 0.7419 time to fit residues: 21.2687 Evaluate side-chains 27 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.0030 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.0000 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.139325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.095408 restraints weight = 3158.397| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.89 r_work: 0.3283 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 3060 Z= 0.080 Angle : 0.327 1.840 4116 Z= 0.196 Chirality : 0.055 0.121 468 Planarity : 0.001 0.004 516 Dihedral : 4.169 11.669 433 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.08 % Allowed : 44.44 % Favored : 53.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.07 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYREE 10 PHE 0.004 0.001 PHE A 20 HIS 0.004 0.002 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00165 ( 3048) covalent geometry : angle 0.32879 ( 4080) link_TRANS : bond 0.00086 ( 12) link_TRANS : angle 0.10430 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.114 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8506 (mttp) cc_final: 0.8280 (mttt) REVERT: DD 35 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.7711 (tpt) REVERT: EE 28 LYS cc_start: 0.8537 (mttp) cc_final: 0.8208 (mttt) REVERT: AA 35 MET cc_start: 0.8048 (tpt) cc_final: 0.7830 (tpp) REVERT: D 28 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8057 (mtmm) outliers start: 6 outliers final: 1 residues processed: 31 average time/residue: 0.6674 time to fit residues: 21.2279 Evaluate side-chains 32 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DD residue 35 MET Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain D residue 28 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.122860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.081501 restraints weight = 3370.635| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.78 r_work: 0.3067 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.072 3060 Z= 0.565 Angle : 0.698 4.571 4116 Z= 0.393 Chirality : 0.064 0.145 468 Planarity : 0.004 0.011 516 Dihedral : 5.785 24.853 432 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.82 % Allowed : 37.15 % Favored : 59.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.43), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.33 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR E 10 PHE 0.025 0.005 PHE E 20 HIS 0.010 0.004 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.01302 ( 3048) covalent geometry : angle 0.70066 ( 4080) link_TRANS : bond 0.00600 ( 12) link_TRANS : angle 0.29546 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.117 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8600 (mttp) cc_final: 0.8390 (mttt) REVERT: DD 35 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.7751 (tpt) REVERT: EE 28 LYS cc_start: 0.8756 (mttp) cc_final: 0.8438 (mttt) REVERT: D 28 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8066 (mtmm) outliers start: 11 outliers final: 3 residues processed: 34 average time/residue: 0.6300 time to fit residues: 22.0362 Evaluate side-chains 37 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DD residue 35 MET Chi-restraints excluded: chain EE residue 26 SER Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain D residue 28 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.132629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.089794 restraints weight = 3232.569| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.82 r_work: 0.3210 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3060 Z= 0.141 Angle : 0.406 3.214 4116 Z= 0.232 Chirality : 0.057 0.124 468 Planarity : 0.002 0.006 516 Dihedral : 5.149 21.795 432 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.04 % Allowed : 40.97 % Favored : 57.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.43), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.24 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYRBB 10 PHE 0.010 0.002 PHE D 20 HIS 0.005 0.002 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3048) covalent geometry : angle 0.40791 ( 4080) link_TRANS : bond 0.00162 ( 12) link_TRANS : angle 0.15904 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.111 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8597 (mttp) cc_final: 0.8376 (mttt) REVERT: DD 35 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.7785 (tpt) REVERT: EE 28 LYS cc_start: 0.8764 (mttp) cc_final: 0.8438 (mttt) REVERT: D 28 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8074 (mtmm) outliers start: 3 outliers final: 0 residues processed: 31 average time/residue: 0.7305 time to fit residues: 23.1948 Evaluate side-chains 33 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DD residue 35 MET Chi-restraints excluded: chain D residue 28 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.126501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.084517 restraints weight = 3259.044| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.81 r_work: 0.3119 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 3060 Z= 0.315 Angle : 0.531 3.598 4116 Z= 0.301 Chirality : 0.059 0.133 468 Planarity : 0.002 0.007 516 Dihedral : 5.535 24.370 432 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.74 % Allowed : 39.93 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.43), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.39 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR E 10 PHE 0.016 0.004 PHE E 20 HIS 0.007 0.003 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00731 ( 3048) covalent geometry : angle 0.53265 ( 4080) link_TRANS : bond 0.00331 ( 12) link_TRANS : angle 0.20055 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.113 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8620 (mttp) cc_final: 0.8396 (mttt) REVERT: DD 35 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.7846 (tpt) REVERT: EE 28 LYS cc_start: 0.8746 (mttp) cc_final: 0.8435 (mttt) REVERT: D 28 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8081 (mtmm) outliers start: 5 outliers final: 1 residues processed: 32 average time/residue: 0.6722 time to fit residues: 22.0679 Evaluate side-chains 34 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DD residue 35 MET Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain D residue 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.0770 chunk 12 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 overall best weight: 0.2896 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.137047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.095153 restraints weight = 3207.810| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.83 r_work: 0.3287 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 3060 Z= 0.089 Angle : 0.379 4.216 4116 Z= 0.216 Chirality : 0.056 0.118 468 Planarity : 0.001 0.005 516 Dihedral : 4.833 18.396 432 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.39 % Allowed : 39.58 % Favored : 59.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.18 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYRCC 10 PHE 0.007 0.002 PHEEE 20 HIS 0.003 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00190 ( 3048) covalent geometry : angle 0.38045 ( 4080) link_TRANS : bond 0.00115 ( 12) link_TRANS : angle 0.13141 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.110 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8624 (mttp) cc_final: 0.8403 (mttt) REVERT: EE 28 LYS cc_start: 0.8765 (mttp) cc_final: 0.8443 (mttt) outliers start: 4 outliers final: 0 residues processed: 31 average time/residue: 0.6854 time to fit residues: 21.7822 Evaluate side-chains 29 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 15 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.132953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.090343 restraints weight = 3257.272| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.84 r_work: 0.3217 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3060 Z= 0.163 Angle : 0.419 3.613 4116 Z= 0.240 Chirality : 0.057 0.126 468 Planarity : 0.002 0.005 516 Dihedral : 4.844 17.605 432 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.39 % Allowed : 40.28 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.19 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR E 10 PHE 0.009 0.002 PHE D 20 HIS 0.005 0.002 HISDD 13 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 3048) covalent geometry : angle 0.42039 ( 4080) link_TRANS : bond 0.00168 ( 12) link_TRANS : angle 0.12194 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.116 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8606 (mttp) cc_final: 0.8379 (mttt) REVERT: EE 28 LYS cc_start: 0.8727 (mttp) cc_final: 0.8416 (mttt) outliers start: 4 outliers final: 1 residues processed: 30 average time/residue: 0.7198 time to fit residues: 22.1465 Evaluate side-chains 31 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.127970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.086584 restraints weight = 3319.507| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.81 r_work: 0.3166 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3060 Z= 0.245 Angle : 0.486 3.758 4116 Z= 0.278 Chirality : 0.058 0.129 468 Planarity : 0.002 0.006 516 Dihedral : 5.204 20.128 432 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.39 % Allowed : 40.97 % Favored : 57.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.28 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR E 10 PHE 0.013 0.003 PHE E 20 HIS 0.006 0.003 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 3048) covalent geometry : angle 0.48768 ( 4080) link_TRANS : bond 0.00250 ( 12) link_TRANS : angle 0.16894 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.114 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8642 (mttp) cc_final: 0.8413 (mttt) REVERT: EE 28 LYS cc_start: 0.8749 (mttp) cc_final: 0.8448 (mttt) outliers start: 4 outliers final: 1 residues processed: 31 average time/residue: 0.6475 time to fit residues: 20.5955 Evaluate side-chains 31 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CC residue 35 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.129367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.088332 restraints weight = 3329.013| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.79 r_work: 0.3193 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3060 Z= 0.191 Angle : 0.448 4.155 4116 Z= 0.255 Chirality : 0.057 0.128 468 Planarity : 0.002 0.006 516 Dihedral : 5.099 20.128 432 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.04 % Allowed : 41.32 % Favored : 57.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.43), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.28 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR E 10 PHE 0.011 0.002 PHE E 20 HIS 0.005 0.002 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 3048) covalent geometry : angle 0.44956 ( 4080) link_TRANS : bond 0.00203 ( 12) link_TRANS : angle 0.14575 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.118 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8656 (mttp) cc_final: 0.8429 (mttt) REVERT: EE 28 LYS cc_start: 0.8745 (mttp) cc_final: 0.8440 (mttt) outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 0.7044 time to fit residues: 21.6274 Evaluate side-chains 31 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CC residue 35 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.130556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089979 restraints weight = 3256.304| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.77 r_work: 0.3217 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3060 Z= 0.162 Angle : 0.427 4.149 4116 Z= 0.244 Chirality : 0.057 0.126 468 Planarity : 0.002 0.005 516 Dihedral : 4.977 19.265 432 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.04 % Allowed : 41.67 % Favored : 57.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.25 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR E 10 PHE 0.009 0.002 PHE D 20 HIS 0.005 0.002 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 3048) covalent geometry : angle 0.42841 ( 4080) link_TRANS : bond 0.00172 ( 12) link_TRANS : angle 0.13046 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 696 Ramachandran restraints generated. 348 Oldfield, 0 Emsley, 348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.085 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8633 (mttp) cc_final: 0.8414 (mttt) REVERT: EE 28 LYS cc_start: 0.8742 (mttp) cc_final: 0.8433 (mttt) outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 0.7097 time to fit residues: 21.7838 Evaluate side-chains 31 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CC residue 35 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.0020 chunk 6 optimal weight: 1.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.129355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.088443 restraints weight = 3262.468| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.77 r_work: 0.3202 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3060 Z= 0.191 Angle : 0.444 4.513 4116 Z= 0.254 Chirality : 0.057 0.128 468 Planarity : 0.002 0.006 516 Dihedral : 5.003 20.505 432 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.69 % Allowed : 42.01 % Favored : 57.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.27 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR E 10 PHE 0.011 0.002 PHE E 20 HIS 0.005 0.002 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 3048) covalent geometry : angle 0.44529 ( 4080) link_TRANS : bond 0.00200 ( 12) link_TRANS : angle 0.14593 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1241.83 seconds wall clock time: 21 minutes 57.28 seconds (1317.28 seconds total)