Starting phenix.real_space_refine on Fri Aug 22 12:39:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ol7_16953/08_2025/8ol7_16953.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ol7_16953/08_2025/8ol7_16953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ol7_16953/08_2025/8ol7_16953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ol7_16953/08_2025/8ol7_16953.map" model { file = "/net/cci-nas-00/data/ceres_data/8ol7_16953/08_2025/8ol7_16953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ol7_16953/08_2025/8ol7_16953.cif" } resolution = 3.0 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= 0.006 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 10 5.16 5 C 1510 2.51 5 N 400 2.21 5 O 400 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2320 Number of models: 1 Model: "" Number of chains: 1 Chain: "J" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 232 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Restraints were copied for chains: A, B, C, D, E, F, G, H, I Time building chain proxies: 0.71, per 1000 atoms: 0.31 Number of scatterers: 2320 At special positions: 0 Unit cell: (58.984, 71.912, 39.592, 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 10 16.00 O 400 8.00 N 400 7.00 C 1510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 142.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 500 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'J' and resid 10 through 13 removed outlier: 5.852A pdb=" N GLU J 11 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 16 through 18 removed outlier: 5.743A pdb=" N LEU F 17 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 24 through 25 removed outlier: 6.613A pdb=" N VAL F 24 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL D 24 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 30 through 36 removed outlier: 7.052A pdb=" N ILE J 31 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE H 32 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY J 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU H 34 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET F 35 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL H 36 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU F 34 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET D 35 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL F 36 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU D 34 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET B 35 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL D 36 " --> pdb=" O MET B 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA6, first strand: chain 'A' and resid 16 through 17 Processing sheet with id=AA7, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.613A pdb=" N VAL A 24 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C 24 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL E 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL G 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.651A pdb=" N LEU C 34 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET A 35 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL C 36 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU E 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET C 35 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL E 36 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU G 34 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET E 35 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL G 36 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU I 34 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET G 35 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL I 36 " --> pdb=" O MET G 35 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.36 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 750 1.34 - 1.45: 414 1.45 - 1.57: 1176 1.57 - 1.68: 0 1.68 - 1.80: 20 Bond restraints: 2360 Sorted by residual: bond pdb=" C HIS B 13 " pdb=" O HIS B 13 " ideal model delta sigma weight residual 1.234 1.224 0.009 1.25e-02 6.40e+03 5.54e-01 bond pdb=" C HIS D 13 " pdb=" O HIS D 13 " ideal model delta sigma weight residual 1.234 1.224 0.009 1.25e-02 6.40e+03 5.40e-01 bond pdb=" C HIS J 13 " pdb=" O HIS J 13 " ideal model delta sigma weight residual 1.234 1.224 0.009 1.25e-02 6.40e+03 5.39e-01 bond pdb=" C HIS C 13 " pdb=" O HIS C 13 " ideal model delta sigma weight residual 1.234 1.224 0.009 1.25e-02 6.40e+03 5.32e-01 bond pdb=" CB PHE D 20 " pdb=" CG PHE D 20 " ideal model delta sigma weight residual 1.502 1.485 0.017 2.30e-02 1.89e+03 5.25e-01 ... (remaining 2355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 2980 1.35 - 2.69: 120 2.69 - 4.04: 40 4.04 - 5.39: 10 5.39 - 6.74: 10 Bond angle restraints: 3160 Sorted by residual: angle pdb=" C VAL I 18 " pdb=" N PHE I 19 " pdb=" CA PHE I 19 " ideal model delta sigma weight residual 122.53 117.93 4.60 1.92e+00 2.71e-01 5.73e+00 angle pdb=" C VAL G 18 " pdb=" N PHE G 19 " pdb=" CA PHE G 19 " ideal model delta sigma weight residual 122.53 117.94 4.59 1.92e+00 2.71e-01 5.73e+00 angle pdb=" C VAL F 18 " pdb=" N PHE F 19 " pdb=" CA PHE F 19 " ideal model delta sigma weight residual 122.53 117.94 4.59 1.92e+00 2.71e-01 5.71e+00 angle pdb=" C VAL B 18 " pdb=" N PHE B 19 " pdb=" CA PHE B 19 " ideal model delta sigma weight residual 122.53 117.96 4.57 1.92e+00 2.71e-01 5.68e+00 angle pdb=" C VAL D 18 " pdb=" N PHE D 19 " pdb=" CA PHE D 19 " ideal model delta sigma weight residual 122.53 117.96 4.57 1.92e+00 2.71e-01 5.66e+00 ... (remaining 3155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.50: 1020 8.50 - 16.99: 140 16.99 - 25.48: 50 25.48 - 33.97: 50 33.97 - 42.47: 20 Dihedral angle restraints: 1280 sinusoidal: 460 harmonic: 820 Sorted by residual: dihedral pdb=" CA LEU F 34 " pdb=" CB LEU F 34 " pdb=" CG LEU F 34 " pdb=" CD1 LEU F 34 " ideal model delta sinusoidal sigma weight residual 180.00 137.89 42.11 3 1.50e+01 4.44e-03 7.55e+00 dihedral pdb=" CA LEU H 34 " pdb=" CB LEU H 34 " pdb=" CG LEU H 34 " pdb=" CD1 LEU H 34 " ideal model delta sinusoidal sigma weight residual 180.00 137.90 42.10 3 1.50e+01 4.44e-03 7.55e+00 dihedral pdb=" CA LEU J 34 " pdb=" CB LEU J 34 " pdb=" CG LEU J 34 " pdb=" CD1 LEU J 34 " ideal model delta sinusoidal sigma weight residual 180.00 137.91 42.09 3 1.50e+01 4.44e-03 7.55e+00 ... (remaining 1277 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.031: 119 0.031 - 0.062: 131 0.062 - 0.093: 35 0.093 - 0.124: 50 0.124 - 0.154: 15 Chirality restraints: 350 Sorted by residual: chirality pdb=" CA HIS H 14 " pdb=" N HIS H 14 " pdb=" C HIS H 14 " pdb=" CB HIS H 14 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA HIS D 14 " pdb=" N HIS D 14 " pdb=" C HIS D 14 " pdb=" CB HIS D 14 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA HIS G 14 " pdb=" N HIS G 14 " pdb=" C HIS G 14 " pdb=" CB HIS G 14 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.80e-01 ... (remaining 347 not shown) Planarity restraints: 400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS I 13 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C HIS I 13 " 0.022 2.00e-02 2.50e+03 pdb=" O HIS I 13 " -0.008 2.00e-02 2.50e+03 pdb=" N HIS I 14 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 13 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.57e+00 pdb=" C HIS D 13 " -0.022 2.00e-02 2.50e+03 pdb=" O HIS D 13 " 0.008 2.00e-02 2.50e+03 pdb=" N HIS D 14 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 13 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.56e+00 pdb=" C HIS H 13 " -0.022 2.00e-02 2.50e+03 pdb=" O HIS H 13 " 0.008 2.00e-02 2.50e+03 pdb=" N HIS H 14 " 0.007 2.00e-02 2.50e+03 ... (remaining 397 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.08: 1410 3.08 - 3.53: 2268 3.53 - 3.99: 3595 3.99 - 4.44: 4509 4.44 - 4.90: 8113 Nonbonded interactions: 19895 Sorted by model distance: nonbonded pdb=" OD1 ASP G 23 " pdb=" N ASP I 23 " model vdw 2.619 3.120 nonbonded pdb=" OD1 ASP E 23 " pdb=" N ASP G 23 " model vdw 2.619 3.120 nonbonded pdb=" OD1 ASP B 23 " pdb=" N ASP D 23 " model vdw 2.619 3.120 nonbonded pdb=" OD1 ASP A 23 " pdb=" N ASP C 23 " model vdw 2.619 3.120 nonbonded pdb=" OD1 ASP D 23 " pdb=" N ASP F 23 " model vdw 2.619 3.120 ... (remaining 19890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'J' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 2.090 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: 0.000 Set scattering table: 0.010 Process input model: 5.070 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.006 0.021 2360 Z= 0.262 Angle : 0.811 6.735 3160 Z= 0.430 Chirality : 0.066 0.154 350 Planarity : 0.003 0.013 400 Dihedral : 13.037 42.467 780 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % 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: -2.92 (0.45), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR F 10 PHE 0.005 0.002 PHE I 19 HIS 0.006 0.003 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 2360) covalent geometry : angle 0.81110 ( 3160) hydrogen bonds : bond 0.19480 ( 54) hydrogen bonds : angle 9.20483 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.092 Fit side-chains REVERT: E 28 LYS cc_start: 0.7623 (mttt) cc_final: 0.7393 (mttm) REVERT: F 28 LYS cc_start: 0.7349 (mttt) cc_final: 0.7134 (mttm) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.4975 time to fit residues: 19.9255 Evaluate side-chains 26 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.115246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.094194 restraints weight = 3161.861| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.72 r_work: 0.3853 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2360 Z= 0.291 Angle : 0.752 7.651 3160 Z= 0.411 Chirality : 0.064 0.153 350 Planarity : 0.003 0.008 400 Dihedral : 5.522 19.047 320 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.43 % Allowed : 13.04 % Favored : 86.52 % 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: -2.61 (0.43), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR J 10 PHE 0.010 0.002 PHE I 19 HIS 0.007 0.003 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00626 ( 2360) covalent geometry : angle 0.75232 ( 3160) hydrogen bonds : bond 0.04579 ( 54) hydrogen bonds : angle 5.95388 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.092 Fit side-chains REVERT: A 28 LYS cc_start: 0.7890 (mttt) cc_final: 0.7621 (mttp) REVERT: B 28 LYS cc_start: 0.8012 (mttt) cc_final: 0.7702 (mttp) REVERT: E 28 LYS cc_start: 0.7006 (mttt) cc_final: 0.6739 (mttp) REVERT: F 28 LYS cc_start: 0.7359 (mttt) cc_final: 0.7035 (mttp) REVERT: H 28 LYS cc_start: 0.7009 (mttt) cc_final: 0.6654 (mttp) REVERT: I 26 SER cc_start: 0.7828 (m) cc_final: 0.7598 (t) outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 0.8541 time to fit residues: 25.2253 Evaluate side-chains 24 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 10.0000 chunk 28 optimal weight: 0.1980 chunk 19 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- 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 = 0.4290 r_free = 0.4290 target = 0.119987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.098988 restraints weight = 3146.890| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.77 r_work: 0.3928 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2360 Z= 0.124 Angle : 0.594 8.074 3160 Z= 0.313 Chirality : 0.058 0.134 350 Planarity : 0.002 0.008 400 Dihedral : 4.546 19.010 320 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.43 % Allowed : 13.04 % Favored : 86.52 % 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: -2.41 (0.44), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR E 10 PHE 0.004 0.001 PHE F 19 HIS 0.004 0.002 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 2360) covalent geometry : angle 0.59396 ( 3160) hydrogen bonds : bond 0.03196 ( 54) hydrogen bonds : angle 5.43200 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.105 Fit side-chains REVERT: A 28 LYS cc_start: 0.7917 (mttt) cc_final: 0.7634 (mttp) REVERT: B 28 LYS cc_start: 0.7914 (mttt) cc_final: 0.7584 (mttp) REVERT: E 28 LYS cc_start: 0.6983 (mttt) cc_final: 0.6697 (mttp) REVERT: F 28 LYS cc_start: 0.7256 (mttt) cc_final: 0.6899 (mttm) REVERT: H 28 LYS cc_start: 0.6921 (mttt) cc_final: 0.6582 (mttm) REVERT: I 26 SER cc_start: 0.7844 (m) cc_final: 0.7599 (t) outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.8083 time to fit residues: 19.7730 Evaluate side-chains 25 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 15 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.110762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.090670 restraints weight = 3204.046| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.71 r_work: 0.3758 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 2360 Z= 0.309 Angle : 0.721 7.464 3160 Z= 0.400 Chirality : 0.063 0.146 350 Planarity : 0.003 0.008 400 Dihedral : 5.521 17.432 320 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.87 % Allowed : 13.04 % Favored : 86.09 % 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: -2.57 (0.43), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR D 10 PHE 0.010 0.003 PHE J 19 HIS 0.006 0.003 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00678 ( 2360) covalent geometry : angle 0.72071 ( 3160) hydrogen bonds : bond 0.03949 ( 54) hydrogen bonds : angle 5.61344 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.095 Fit side-chains REVERT: A 28 LYS cc_start: 0.7976 (mttt) cc_final: 0.7735 (mttp) REVERT: B 28 LYS cc_start: 0.7968 (mttt) cc_final: 0.7626 (mttp) REVERT: E 28 LYS cc_start: 0.7085 (mttt) cc_final: 0.6764 (mttp) REVERT: F 28 LYS cc_start: 0.7288 (mttt) cc_final: 0.6929 (mttp) REVERT: H 28 LYS cc_start: 0.7240 (mttt) cc_final: 0.6907 (mttp) REVERT: I 28 LYS cc_start: 0.7582 (ttmm) cc_final: 0.7020 (mttm) outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 0.9344 time to fit residues: 20.9119 Evaluate side-chains 21 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.0570 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.115131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.094382 restraints weight = 3135.339| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.74 r_work: 0.3786 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2360 Z= 0.157 Angle : 0.605 7.648 3160 Z= 0.329 Chirality : 0.059 0.137 350 Planarity : 0.002 0.007 400 Dihedral : 4.812 18.806 320 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.43 % Allowed : 13.04 % Favored : 86.52 % 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: -2.47 (0.43), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR E 10 PHE 0.006 0.002 PHE J 19 HIS 0.004 0.002 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2360) covalent geometry : angle 0.60510 ( 3160) hydrogen bonds : bond 0.03252 ( 54) hydrogen bonds : angle 5.44697 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.093 Fit side-chains REVERT: A 28 LYS cc_start: 0.7949 (mttt) cc_final: 0.7680 (mttp) REVERT: B 28 LYS cc_start: 0.7928 (mttt) cc_final: 0.7639 (mttp) REVERT: E 28 LYS cc_start: 0.6999 (mttt) cc_final: 0.6686 (mttp) REVERT: F 28 LYS cc_start: 0.7265 (mttt) cc_final: 0.6920 (mttp) REVERT: H 28 LYS cc_start: 0.7216 (mttt) cc_final: 0.6906 (mttp) REVERT: I 28 LYS cc_start: 0.7548 (ttmm) cc_final: 0.7010 (mttm) outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.8680 time to fit residues: 19.4824 Evaluate side-chains 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.109225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.088952 restraints weight = 3173.613| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.75 r_work: 0.3727 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2360 Z= 0.254 Angle : 0.672 7.243 3160 Z= 0.374 Chirality : 0.061 0.143 350 Planarity : 0.002 0.007 400 Dihedral : 5.237 17.440 320 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.43 % Allowed : 13.04 % Favored : 86.52 % 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: -2.62 (0.43), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 10 PHE 0.009 0.003 PHE J 19 HIS 0.006 0.003 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 2360) covalent geometry : angle 0.67206 ( 3160) hydrogen bonds : bond 0.03723 ( 54) hydrogen bonds : angle 5.47255 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.054 Fit side-chains REVERT: A 28 LYS cc_start: 0.7963 (mttt) cc_final: 0.7679 (mttp) REVERT: B 28 LYS cc_start: 0.7880 (mttt) cc_final: 0.7597 (mttp) REVERT: E 28 LYS cc_start: 0.7158 (mttt) cc_final: 0.6852 (mttp) REVERT: F 28 LYS cc_start: 0.7251 (mttt) cc_final: 0.6910 (mttp) REVERT: H 28 LYS cc_start: 0.7230 (mttt) cc_final: 0.6902 (mttm) REVERT: I 28 LYS cc_start: 0.7628 (ttmm) cc_final: 0.7118 (mttm) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.8948 time to fit residues: 22.7102 Evaluate side-chains 22 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.113559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.092747 restraints weight = 3208.199| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.80 r_work: 0.3761 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2360 Z= 0.216 Angle : 0.643 7.040 3160 Z= 0.355 Chirality : 0.060 0.146 350 Planarity : 0.002 0.007 400 Dihedral : 5.043 17.396 320 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.43 % Allowed : 13.48 % Favored : 86.09 % 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: -2.72 (0.43), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 10 PHE 0.008 0.002 PHE D 19 HIS 0.005 0.003 HIS E 13 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 2360) covalent geometry : angle 0.64317 ( 3160) hydrogen bonds : bond 0.03524 ( 54) hydrogen bonds : angle 5.40807 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.092 Fit side-chains REVERT: J 15 GLN cc_start: 0.8947 (mp10) cc_final: 0.8651 (mp10) REVERT: A 28 LYS cc_start: 0.7890 (mttt) cc_final: 0.7656 (mttp) REVERT: B 28 LYS cc_start: 0.7783 (mttt) cc_final: 0.7390 (mttp) REVERT: E 28 LYS cc_start: 0.7069 (mttt) cc_final: 0.6763 (mttp) REVERT: F 28 LYS cc_start: 0.7093 (mttt) cc_final: 0.6743 (mttp) REVERT: H 28 LYS cc_start: 0.7176 (mttt) cc_final: 0.6857 (mttm) REVERT: I 28 LYS cc_start: 0.7643 (ttmm) cc_final: 0.7117 (mttm) outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.9126 time to fit residues: 24.1071 Evaluate side-chains 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.113120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.092808 restraints weight = 3159.191| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.79 r_work: 0.3776 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2360 Z= 0.180 Angle : 0.612 6.873 3160 Z= 0.338 Chirality : 0.059 0.142 350 Planarity : 0.002 0.007 400 Dihedral : 4.923 18.884 320 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.43 % Allowed : 13.04 % Favored : 86.52 % 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: -2.79 (0.43), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR E 10 PHE 0.007 0.002 PHE J 19 HIS 0.004 0.002 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 2360) covalent geometry : angle 0.61224 ( 3160) hydrogen bonds : bond 0.03371 ( 54) hydrogen bonds : angle 5.33041 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.087 Fit side-chains REVERT: A 28 LYS cc_start: 0.7893 (mttt) cc_final: 0.7642 (mttp) REVERT: B 28 LYS cc_start: 0.7737 (mttt) cc_final: 0.7355 (mttp) REVERT: E 28 LYS cc_start: 0.7062 (mttt) cc_final: 0.6770 (mttp) REVERT: F 28 LYS cc_start: 0.7035 (mttt) cc_final: 0.6729 (mttp) REVERT: H 28 LYS cc_start: 0.7184 (mttt) cc_final: 0.6858 (mttm) REVERT: I 28 LYS cc_start: 0.7653 (ttmm) cc_final: 0.7145 (mttp) outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.8703 time to fit residues: 19.4951 Evaluate side-chains 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.111832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.092143 restraints weight = 3156.394| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.78 r_work: 0.3747 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2360 Z= 0.136 Angle : 0.572 6.719 3160 Z= 0.314 Chirality : 0.058 0.138 350 Planarity : 0.002 0.007 400 Dihedral : 4.681 18.773 320 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.43 % Allowed : 12.61 % Favored : 86.96 % 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: -2.78 (0.44), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR E 10 PHE 0.005 0.001 PHE D 19 HIS 0.004 0.002 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 2360) covalent geometry : angle 0.57179 ( 3160) hydrogen bonds : bond 0.03205 ( 54) hydrogen bonds : angle 5.27870 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.054 Fit side-chains REVERT: A 28 LYS cc_start: 0.7788 (mttt) cc_final: 0.7529 (mttp) REVERT: B 28 LYS cc_start: 0.7737 (mttt) cc_final: 0.7347 (mttp) REVERT: E 28 LYS cc_start: 0.7037 (mttt) cc_final: 0.6743 (mttp) REVERT: F 28 LYS cc_start: 0.7140 (mttt) cc_final: 0.6812 (mttp) REVERT: H 28 LYS cc_start: 0.7228 (mttt) cc_final: 0.6946 (mttm) REVERT: I 28 LYS cc_start: 0.7607 (ttmm) cc_final: 0.7095 (mttm) outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.7248 time to fit residues: 16.2067 Evaluate side-chains 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.110331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.090436 restraints weight = 3267.444| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.83 r_work: 0.3744 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2360 Z= 0.250 Angle : 0.666 6.605 3160 Z= 0.371 Chirality : 0.061 0.144 350 Planarity : 0.002 0.008 400 Dihedral : 5.112 16.645 320 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.43 % Allowed : 13.48 % Favored : 86.09 % 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: -2.85 (0.43), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR D 10 PHE 0.009 0.003 PHE B 20 HIS 0.005 0.003 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 2360) covalent geometry : angle 0.66601 ( 3160) hydrogen bonds : bond 0.03662 ( 54) hydrogen bonds : angle 5.40861 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.052 Fit side-chains REVERT: J 15 GLN cc_start: 0.8944 (mp10) cc_final: 0.8695 (mp10) REVERT: A 28 LYS cc_start: 0.7980 (mttt) cc_final: 0.7686 (mttp) REVERT: B 28 LYS cc_start: 0.7826 (mttt) cc_final: 0.7539 (mttp) REVERT: E 28 LYS cc_start: 0.7170 (mttt) cc_final: 0.6879 (mttp) REVERT: F 28 LYS cc_start: 0.7253 (mttt) cc_final: 0.6944 (mttp) REVERT: H 28 LYS cc_start: 0.7283 (mttt) cc_final: 0.6979 (mttm) REVERT: I 28 LYS cc_start: 0.7723 (ttmm) cc_final: 0.7224 (mttm) outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.5600 time to fit residues: 12.5313 Evaluate side-chains 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 = 0.113119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.093422 restraints weight = 3125.185| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.71 r_work: 0.3775 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2360 Z= 0.102 Angle : 0.538 6.639 3160 Z= 0.294 Chirality : 0.057 0.134 350 Planarity : 0.002 0.007 400 Dihedral : 4.520 19.048 320 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.43 % Allowed : 13.48 % Favored : 86.09 % 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: -2.84 (0.44), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR E 10 PHE 0.003 0.001 PHE D 19 HIS 0.003 0.002 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 2360) covalent geometry : angle 0.53813 ( 3160) hydrogen bonds : bond 0.03126 ( 54) hydrogen bonds : angle 5.21480 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 915.47 seconds wall clock time: 16 minutes 25.04 seconds (985.04 seconds total)