Starting phenix.real_space_refine on Fri May 9 15:40:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jb0_61303/05_2025/9jb0_61303.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jb0_61303/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jb0_61303/05_2025/9jb0_61303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jb0_61303/05_2025/9jb0_61303.map" model { file = "/net/cci-nas-00/data/ceres_data/9jb0_61303/05_2025/9jb0_61303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jb0_61303/05_2025/9jb0_61303.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3012 Number of models: 1 Model: "" Number of chains: 2 Chain: "AA" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 121 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "AA" 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: A, C, B, E, D, BB, F, CC, DD, EE, FF Time building chain proxies: 1.28, per 1000 atoms: 0.42 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: 0.68 Conformation dependent library (CDL) restraints added in 305.2 milliseconds 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: 0.56 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: 0.78 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: 0.03 Found NCS groups: ncs_group { reference = chain 'AA' selection = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'BB' selection = chain 'F' selection = chain 'CC' selection = chain 'DD' selection = chain 'EE' selection = chain 'FF' } 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: 0.680 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.510 Find NCS groups from input model: 0.070 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:9.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (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 HIS 0.006 0.003 HISDD 13 PHE 0.008 0.002 PHEFF 20 TYR 0.003 0.001 TYRBB 10 Details of bonding type rmsd link_TRANS : bond 0.00200 ( 12) link_TRANS : angle 0.15072 ( 36) covalent geometry : bond 0.00371 ( 3048) covalent geometry : angle 0.39689 ( 4080) *********************** 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 : 0.273 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: 1.4239 time to fit residues: 41.0202 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 : 0.286 ------------------------------------------------------------------------------- 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 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.134153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.090123 restraints weight = 3170.101| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.87 r_work: 0.3196 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.0573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3060 Z= 0.154 Angle : 0.375 2.577 4116 Z= 0.223 Chirality : 0.056 0.129 468 Planarity : 0.001 0.005 516 Dihedral : 4.520 12.939 433 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.43 % Allowed : 41.67 % Favored : 55.90 % 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: -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 HIS 0.005 0.002 HIS E 13 PHE 0.009 0.002 PHE D 20 TYR 0.004 0.001 TYREE 10 Details of bonding type rmsd link_TRANS : bond 0.00161 ( 12) link_TRANS : angle 0.13781 ( 36) covalent geometry : bond 0.00345 ( 3048) covalent geometry : angle 0.37658 ( 4080) *********************** 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 37 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.319 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8601 (mttp) cc_final: 0.8382 (mttt) REVERT: DD 35 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7842 (tpt) REVERT: EE 28 LYS cc_start: 0.8690 (mttp) cc_final: 0.8388 (mttt) REVERT: D 28 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8182 (mtmm) outliers start: 7 outliers final: 1 residues processed: 32 average time/residue: 1.3280 time to fit residues: 43.7878 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 : 0.323 ------------------------------------------------------------------------------- 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 18 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.131639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.087696 restraints weight = 3148.678| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.84 r_work: 0.3166 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3060 Z= 0.212 Angle : 0.418 2.874 4116 Z= 0.245 Chirality : 0.057 0.127 468 Planarity : 0.002 0.006 516 Dihedral : 4.801 14.504 432 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.12 % Allowed : 39.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.11 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HISBB 13 PHE 0.012 0.003 PHE E 20 TYR 0.004 0.001 TYR E 10 Details of bonding type rmsd link_TRANS : bond 0.00230 ( 12) link_TRANS : angle 0.14278 ( 36) covalent geometry : bond 0.00486 ( 3048) covalent geometry : angle 0.41946 ( 4080) *********************** 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 39 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.296 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8582 (mttp) cc_final: 0.8366 (mttt) REVERT: DD 35 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7798 (tpt) REVERT: EE 28 LYS cc_start: 0.8696 (mttp) cc_final: 0.8372 (mttt) REVERT: D 28 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8019 (mtmm) outliers start: 9 outliers final: 2 residues processed: 32 average time/residue: 1.2574 time to fit residues: 41.4314 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 : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DD residue 35 MET 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 20 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 0.0370 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.3662 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.130069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.086492 restraints weight = 3264.935| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.86 r_work: 0.3147 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3060 Z= 0.256 Angle : 0.460 3.257 4116 Z= 0.266 Chirality : 0.058 0.130 468 Planarity : 0.002 0.007 516 Dihedral : 5.122 19.020 432 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.43), 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 HIS 0.006 0.003 HIS E 13 PHE 0.014 0.003 PHE E 20 TYR 0.005 0.001 TYR E 10 Details of bonding type rmsd link_TRANS : bond 0.00275 ( 12) link_TRANS : angle 0.17195 ( 36) covalent geometry : bond 0.00588 ( 3048) covalent geometry : angle 0.46165 ( 4080) *********************** 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 36 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.313 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8647 (mttp) cc_final: 0.8428 (mttt) REVERT: DD 35 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7866 (tpt) REVERT: EE 28 LYS cc_start: 0.8784 (mttp) cc_final: 0.8455 (mttt) REVERT: D 28 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8073 (mtmm) outliers start: 4 outliers final: 2 residues processed: 33 average time/residue: 1.2710 time to fit residues: 43.2514 Evaluate side-chains 36 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DD residue 35 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.132125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.088816 restraints weight = 3209.111| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.84 r_work: 0.3193 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3060 Z= 0.168 Angle : 0.405 2.630 4116 Z= 0.236 Chirality : 0.057 0.126 468 Planarity : 0.002 0.005 516 Dihedral : 4.937 18.340 432 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.39 % Allowed : 41.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.43), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.14 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 13 PHE 0.010 0.002 PHE D 20 TYR 0.003 0.001 TYR E 10 Details of bonding type rmsd link_TRANS : bond 0.00189 ( 12) link_TRANS : angle 0.13933 ( 36) covalent geometry : bond 0.00382 ( 3048) covalent geometry : angle 0.40609 ( 4080) *********************** 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 35 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.298 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8604 (mttp) cc_final: 0.8383 (mttt) REVERT: DD 35 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.7797 (tpt) REVERT: EE 28 LYS cc_start: 0.8760 (mttp) cc_final: 0.8433 (mttt) REVERT: D 28 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8094 (mtmm) outliers start: 4 outliers final: 0 residues processed: 31 average time/residue: 1.3535 time to fit residues: 43.2283 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 : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain DD residue 35 MET Chi-restraints excluded: chain D residue 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 0.0770 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.130658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.087597 restraints weight = 3294.871| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.84 r_work: 0.3173 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3060 Z= 0.212 Angle : 0.438 2.949 4116 Z= 0.254 Chirality : 0.057 0.128 468 Planarity : 0.002 0.006 516 Dihedral : 5.048 19.708 432 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.08 % Allowed : 40.97 % Favored : 56.94 % 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: -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 HIS 0.006 0.002 HIS E 13 PHE 0.012 0.003 PHE E 20 TYR 0.003 0.001 TYR E 10 Details of bonding type rmsd link_TRANS : bond 0.00227 ( 12) link_TRANS : angle 0.14865 ( 36) covalent geometry : bond 0.00485 ( 3048) covalent geometry : angle 0.43949 ( 4080) *********************** 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 37 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.321 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8594 (mttp) cc_final: 0.8378 (mttt) REVERT: EE 28 LYS cc_start: 0.8731 (mttp) cc_final: 0.8408 (mttt) REVERT: D 28 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8043 (mtmm) outliers start: 6 outliers final: 2 residues processed: 32 average time/residue: 1.3049 time to fit residues: 43.0227 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 : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.127473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.085851 restraints weight = 3250.247| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.78 r_work: 0.3146 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1230 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= 0.262 Angle : 0.480 3.321 4116 Z= 0.276 Chirality : 0.058 0.130 468 Planarity : 0.002 0.007 516 Dihedral : 5.313 22.023 432 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.43), 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 HIS 0.006 0.003 HIS E 13 PHE 0.014 0.003 PHE E 20 TYR 0.004 0.001 TYR E 10 Details of bonding type rmsd link_TRANS : bond 0.00278 ( 12) link_TRANS : angle 0.16710 ( 36) covalent geometry : bond 0.00604 ( 3048) covalent geometry : angle 0.48202 ( 4080) *********************** 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 35 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.280 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8604 (mttp) cc_final: 0.8372 (mttt) REVERT: DD 35 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.7831 (tpt) REVERT: EE 28 LYS cc_start: 0.8740 (mttp) cc_final: 0.8428 (mttt) REVERT: D 28 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8090 (mtmm) outliers start: 4 outliers final: 1 residues processed: 32 average time/residue: 1.3086 time to fit residues: 43.0983 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 : 0.321 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.128285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.086884 restraints weight = 3242.150| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.77 r_work: 0.3170 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3060 Z= 0.230 Angle : 0.467 3.368 4116 Z= 0.267 Chirality : 0.058 0.128 468 Planarity : 0.002 0.006 516 Dihedral : 5.320 22.637 432 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.69 % Allowed : 41.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.43), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.29 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 13 PHE 0.013 0.003 PHE E 20 TYR 0.003 0.001 TYR E 10 Details of bonding type rmsd link_TRANS : bond 0.00245 ( 12) link_TRANS : angle 0.16231 ( 36) covalent geometry : bond 0.00530 ( 3048) covalent geometry : angle 0.46862 ( 4080) *********************** 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 32 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.294 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8631 (mttp) cc_final: 0.8404 (mttt) REVERT: EE 28 LYS cc_start: 0.8756 (mttp) cc_final: 0.8447 (mttt) REVERT: D 28 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8090 (mtmm) outliers start: 2 outliers final: 0 residues processed: 30 average time/residue: 1.4592 time to fit residues: 45.0169 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 : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.129679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.088915 restraints weight = 3264.512| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.75 r_work: 0.3202 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 0.027 3060 Z= 0.175 Angle : 0.439 4.577 4116 Z= 0.250 Chirality : 0.057 0.127 468 Planarity : 0.002 0.006 516 Dihedral : 5.164 21.450 432 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.69 % Allowed : 41.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.43), 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 HIS 0.005 0.002 HIS E 13 PHE 0.011 0.002 PHE D 20 TYR 0.003 0.001 TYR E 10 Details of bonding type rmsd link_TRANS : bond 0.00190 ( 12) link_TRANS : angle 0.14185 ( 36) covalent geometry : bond 0.00402 ( 3048) covalent geometry : angle 0.44099 ( 4080) *********************** 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 32 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.424 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8653 (mttp) cc_final: 0.8428 (mttt) REVERT: EE 28 LYS cc_start: 0.8768 (mttp) cc_final: 0.8460 (mttt) REVERT: D 28 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8133 (mtmm) outliers start: 2 outliers final: 1 residues processed: 30 average time/residue: 1.4847 time to fit residues: 45.9021 Evaluate side-chains 32 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CC residue 35 MET Chi-restraints excluded: chain D residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.129405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.088791 restraints weight = 3201.433| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.74 r_work: 0.3199 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3060 Z= 0.183 Angle : 0.439 3.707 4116 Z= 0.251 Chirality : 0.057 0.128 468 Planarity : 0.002 0.006 516 Dihedral : 5.080 20.991 432 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.39 % Allowed : 41.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.44), 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 HIS 0.005 0.002 HIS E 13 PHE 0.011 0.002 PHE D 20 TYR 0.003 0.001 TYR E 10 Details of bonding type rmsd link_TRANS : bond 0.00193 ( 12) link_TRANS : angle 0.14039 ( 36) covalent geometry : bond 0.00421 ( 3048) covalent geometry : angle 0.44060 ( 4080) ********************** 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 34 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.306 Fit side-chains REVERT: DD 28 LYS cc_start: 0.8630 (mttp) cc_final: 0.8402 (mttt) REVERT: EE 28 LYS cc_start: 0.8744 (mttp) cc_final: 0.8433 (mttt) REVERT: D 28 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8124 (mtmm) outliers start: 4 outliers final: 1 residues processed: 30 average time/residue: 1.4058 time to fit residues: 43.3852 Evaluate side-chains 32 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CC residue 35 MET Chi-restraints excluded: chain D residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.0000 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.134509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.092588 restraints weight = 3175.841| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.80 r_work: 0.3263 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3060 Z= 0.115 Angle : 0.391 3.917 4116 Z= 0.224 Chirality : 0.056 0.125 468 Planarity : 0.001 0.005 516 Dihedral : 4.789 18.251 432 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.39 % Allowed : 41.67 % Favored : 56.94 % 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: -0.22 (0.44), residues: 348 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.16 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 13 PHE 0.006 0.002 PHE D 20 TYR 0.002 0.001 TYR E 10 Details of bonding type rmsd link_TRANS : bond 0.00126 ( 12) link_TRANS : angle 0.10837 ( 36) covalent geometry : bond 0.00261 ( 3048) covalent geometry : angle 0.39243 ( 4080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2360.47 seconds wall clock time: 41 minutes 24.37 seconds (2484.37 seconds total)