Starting phenix.real_space_refine on Wed Nov 13 23:43:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol7_16953/11_2024/8ol7_16953.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol7_16953/11_2024/8ol7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol7_16953/11_2024/8ol7_16953.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol7_16953/11_2024/8ol7_16953.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol7_16953/11_2024/8ol7_16953.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol7_16953/11_2024/8ol7_16953.cif" } resolution = 3.0 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= 0.006 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-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2320 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.48, per 1000 atoms: 0.64 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: 0.59 Conformation dependent library (CDL) restraints added in 297.7 milliseconds 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: 0.40 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: 0.59 Time building geometry restraints manager: 0.68 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: 0.00 Found NCS groups: ncs_group { reference = 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' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.010 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.090 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:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.990 ------------------------------------------------------------------------------- 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= 0.386 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (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 HIS 0.006 0.003 HIS B 14 PHE 0.005 0.002 PHE I 19 TYR 0.006 0.002 TYR F 10 *********************** 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 : 0.307 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: 1.0486 time to fit residues: 42.2173 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 : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2360 Z= 0.232 Angle : 0.650 7.610 3160 Z= 0.346 Chirality : 0.060 0.139 350 Planarity : 0.002 0.006 400 Dihedral : 4.691 18.278 320 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.43 % Allowed : 10.00 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.44), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 14 PHE 0.007 0.002 PHE A 20 TYR 0.009 0.001 TYR E 10 *********************** 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 24 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.239 Fit side-chains REVERT: E 28 LYS cc_start: 0.7900 (mttt) cc_final: 0.7647 (mttm) REVERT: F 28 LYS cc_start: 0.8095 (mttt) cc_final: 0.7824 (mttp) outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 1.5279 time to fit residues: 35.9536 Evaluate side-chains 22 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 0.0970 chunk 27 optimal weight: 0.0010 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2360 Z= 0.118 Angle : 0.531 8.262 3160 Z= 0.276 Chirality : 0.057 0.126 350 Planarity : 0.001 0.007 400 Dihedral : 4.010 16.676 320 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.45), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 13 PHE 0.003 0.001 PHE F 19 TYR 0.009 0.001 TYR E 10 *********************** 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 23 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.208 Fit side-chains REVERT: E 28 LYS cc_start: 0.7891 (mttt) cc_final: 0.7651 (mttp) REVERT: F 28 LYS cc_start: 0.7966 (mttt) cc_final: 0.7684 (mttp) outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 1.6728 time to fit residues: 37.5654 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 : 0.274 ------------------------------------------------------------------------------- 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 3 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.028 2360 Z= 0.460 Angle : 0.704 7.356 3160 Z= 0.396 Chirality : 0.062 0.148 350 Planarity : 0.003 0.008 400 Dihedral : 5.521 18.070 320 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.30 % Allowed : 13.04 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.44), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 14 PHE 0.010 0.003 PHE I 19 TYR 0.010 0.002 TYR D 10 *********************** 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 25 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.297 Fit side-chains REVERT: E 28 LYS cc_start: 0.7972 (mttt) cc_final: 0.7712 (mttm) REVERT: F 28 LYS cc_start: 0.8082 (mttt) cc_final: 0.7787 (mttm) REVERT: H 28 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7682 (mttm) outliers start: 3 outliers final: 1 residues processed: 22 average time/residue: 1.8672 time to fit residues: 41.9629 Evaluate side-chains 20 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 21 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2360 Z= 0.155 Angle : 0.537 7.848 3160 Z= 0.291 Chirality : 0.058 0.129 350 Planarity : 0.002 0.008 400 Dihedral : 4.398 19.321 320 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.43 % Allowed : 14.35 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.45), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 13 PHE 0.004 0.001 PHE F 19 TYR 0.007 0.001 TYR E 10 *********************** 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 22 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 21 time to evaluate : 0.263 Fit side-chains REVERT: H 28 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7629 (mttm) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 1.8127 time to fit residues: 38.9032 Evaluate side-chains 20 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4232 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= 0.448 Angle : 0.688 7.026 3160 Z= 0.388 Chirality : 0.062 0.144 350 Planarity : 0.003 0.008 400 Dihedral : 5.317 16.898 320 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.44), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 13 PHE 0.010 0.003 PHE I 19 TYR 0.009 0.002 TYR C 10 *********************** 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 20 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.279 Fit side-chains REVERT: E 35 MET cc_start: 0.7484 (ttm) cc_final: 0.7284 (ttp) REVERT: H 28 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7725 (mttm) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 1.9379 time to fit residues: 39.5943 Evaluate side-chains 18 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2360 Z= 0.258 Angle : 0.596 7.061 3160 Z= 0.331 Chirality : 0.059 0.140 350 Planarity : 0.002 0.007 400 Dihedral : 4.843 17.869 320 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.43 % Allowed : 15.22 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.45), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 13 PHE 0.008 0.002 PHE I 19 TYR 0.006 0.001 TYR E 10 *********************** 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 21 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.198 Fit side-chains REVERT: H 28 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7715 (mttp) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 1.6503 time to fit residues: 33.6919 Evaluate side-chains 20 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 2 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2360 Z= 0.410 Angle : 0.682 6.745 3160 Z= 0.383 Chirality : 0.062 0.143 350 Planarity : 0.002 0.008 400 Dihedral : 5.303 17.034 320 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.87 % Allowed : 14.78 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (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 HIS 0.007 0.003 HIS E 13 PHE 0.010 0.003 PHE F 19 TYR 0.008 0.002 TYR D 10 *********************** 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 22 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.261 Fit side-chains REVERT: H 28 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7741 (mttm) outliers start: 2 outliers final: 1 residues processed: 20 average time/residue: 1.8710 time to fit residues: 38.2040 Evaluate side-chains 19 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.0000 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2360 Z= 0.152 Angle : 0.527 6.803 3160 Z= 0.289 Chirality : 0.057 0.129 350 Planarity : 0.002 0.006 400 Dihedral : 4.507 19.641 320 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 15.22 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.44), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 14 PHE 0.003 0.001 PHE D 19 TYR 0.008 0.001 TYR E 10 *********************** 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 20 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.259 Fit side-chains REVERT: H 28 LYS cc_start: 0.8169 (ttmm) cc_final: 0.7722 (mttm) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 1.7369 time to fit residues: 35.6101 Evaluate side-chains 20 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2360 Z= 0.353 Angle : 0.650 6.626 3160 Z= 0.365 Chirality : 0.061 0.140 350 Planarity : 0.002 0.007 400 Dihedral : 5.043 17.194 320 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.43 % Allowed : 14.78 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.44), 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 HIS 0.006 0.003 HIS H 13 PHE 0.009 0.003 PHE D 19 TYR 0.007 0.002 TYR D 10 ********************** 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 : 0.234 Fit side-chains REVERT: H 28 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7768 (mttm) outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 1.9203 time to fit residues: 43.0233 Evaluate side-chains 19 residues out of total 230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 27 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.113723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.094062 restraints weight = 3154.440| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.84 r_work: 0.3777 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2360 Z= 0.248 Angle : 0.591 6.668 3160 Z= 0.330 Chirality : 0.059 0.138 350 Planarity : 0.002 0.007 400 Dihedral : 4.899 17.875 320 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.43 % Allowed : 14.78 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.44), residues: 300 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 14 PHE 0.007 0.002 PHE C 19 TYR 0.006 0.001 TYR E 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1303.66 seconds wall clock time: 24 minutes 17.13 seconds (1457.13 seconds total)