Starting phenix.real_space_refine on Wed Nov 13 23:06:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3t_38898/11_2024/8y3t_38898.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3t_38898/11_2024/8y3t_38898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3t_38898/11_2024/8y3t_38898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3t_38898/11_2024/8y3t_38898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3t_38898/11_2024/8y3t_38898.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y3t_38898/11_2024/8y3t_38898.cif" } resolution = 2.61 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= 0.004 sd= 0.091 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 6 5.16 5 C 1126 2.51 5 N 308 2.21 5 O 350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 1790 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 895 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 2.04, per 1000 atoms: 1.14 Number of scatterers: 1790 At special positions: 0 Unit cell: (62.7, 47.5, 60.8, 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 6 16.00 O 350 8.00 N 308 7.00 C 1126 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: 0.41 Conformation dependent library (CDL) restraints added in 258.0 milliseconds 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 448 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 21.0% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 97 through 112 removed outlier: 3.525A pdb=" N LEU A 112 " --> pdb=" O MET A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 Processing helix chain 'B' and resid 97 through 112 removed outlier: 3.525A pdb=" N LEU B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 5.457A pdb=" N VAL A 8 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 20 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU A 31 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 25 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ARG A 83 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ARG B 83 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE B 25 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU B 31 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL B 20 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL B 8 " --> pdb=" O VAL B 20 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 270 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: 0.48 Time building geometry restraints manager: 0.49 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: 590 1.34 - 1.45: 278 1.45 - 1.57: 942 1.57 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 1820 Sorted by residual: bond pdb=" CB THR A 45 " pdb=" CG2 THR A 45 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" CB THR B 45 " pdb=" CG2 THR B 45 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 bond pdb=" CB ARG A 56 " pdb=" CG ARG A 56 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" CB ARG B 56 " pdb=" CG ARG B 56 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" C VAL B 20 " pdb=" N ALA B 21 " ideal model delta sigma weight residual 1.331 1.313 0.018 1.59e-02 3.96e+03 1.32e+00 ... (remaining 1815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 2260 1.17 - 2.34: 182 2.34 - 3.50: 24 3.50 - 4.67: 6 4.67 - 5.84: 4 Bond angle restraints: 2476 Sorted by residual: angle pdb=" N ASN A 55 " pdb=" CA ASN A 55 " pdb=" C ASN A 55 " ideal model delta sigma weight residual 109.24 112.99 -3.75 1.67e+00 3.59e-01 5.04e+00 angle pdb=" N ASN B 55 " pdb=" CA ASN B 55 " pdb=" C ASN B 55 " ideal model delta sigma weight residual 109.24 112.94 -3.70 1.67e+00 3.59e-01 4.92e+00 angle pdb=" C ALA A 124 " pdb=" N ASN A 125 " pdb=" CA ASN A 125 " ideal model delta sigma weight residual 121.54 125.69 -4.15 1.91e+00 2.74e-01 4.72e+00 angle pdb=" C ALA B 124 " pdb=" N ASN B 125 " pdb=" CA ASN B 125 " ideal model delta sigma weight residual 121.54 125.69 -4.15 1.91e+00 2.74e-01 4.72e+00 angle pdb=" N PRO B 117 " pdb=" CA PRO B 117 " pdb=" C PRO B 117 " ideal model delta sigma weight residual 112.47 116.08 -3.61 2.06e+00 2.36e-01 3.08e+00 ... (remaining 2471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 1016 16.84 - 33.68: 64 33.68 - 50.52: 10 50.52 - 67.36: 2 67.36 - 84.20: 2 Dihedral angle restraints: 1094 sinusoidal: 404 harmonic: 690 Sorted by residual: dihedral pdb=" CA ASN B 55 " pdb=" C ASN B 55 " pdb=" N ARG B 56 " pdb=" CA ARG B 56 " ideal model delta harmonic sigma weight residual 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASN A 55 " pdb=" C ASN A 55 " pdb=" N ARG A 56 " pdb=" CA ARG A 56 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA LYS B 113 " pdb=" C LYS B 113 " pdb=" N ASP B 114 " pdb=" CA ASP B 114 " ideal model delta harmonic sigma weight residual -180.00 -156.91 -23.09 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 1091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 162 0.034 - 0.069: 82 0.069 - 0.103: 30 0.103 - 0.137: 10 0.137 - 0.171: 6 Chirality restraints: 290 Sorted by residual: chirality pdb=" CA ILE A 128 " pdb=" N ILE A 128 " pdb=" C ILE A 128 " pdb=" CB ILE A 128 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CA ILE B 128 " pdb=" N ILE B 128 " pdb=" C ILE B 128 " pdb=" CB ILE B 128 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CB THR A 45 " pdb=" CA THR A 45 " pdb=" OG1 THR A 45 " pdb=" CG2 THR A 45 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 287 not shown) Planarity restraints: 320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 4 " -0.014 2.00e-02 2.50e+03 1.14e-02 2.27e+00 pdb=" CG PHE B 4 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE B 4 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 4 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 4 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 4 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 4 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 4 " -0.014 2.00e-02 2.50e+03 1.14e-02 2.26e+00 pdb=" CG PHE A 4 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 4 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 4 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 4 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 4 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 4 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 116 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A 117 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.020 5.00e-02 4.00e+02 ... (remaining 317 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 280 2.76 - 3.30: 1705 3.30 - 3.83: 3045 3.83 - 4.37: 3731 4.37 - 4.90: 6444 Nonbonded interactions: 15205 Sorted by model distance: nonbonded pdb=" O GLY A 110 " pdb=" ND2 ASN A 116 " model vdw 2.231 3.120 nonbonded pdb=" O GLY B 110 " pdb=" ND2 ASN B 116 " model vdw 2.231 3.120 nonbonded pdb=" NH2 ARG A 56 " pdb=" OD1 ASN B 125 " model vdw 2.328 3.120 nonbonded pdb=" OD1 ASN A 125 " pdb=" NH2 ARG B 56 " model vdw 2.380 3.120 nonbonded pdb=" O ALA B 41 " pdb=" NH2 ARG B 83 " model vdw 2.407 3.120 ... (remaining 15200 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.070 Find NCS groups from input model: 0.050 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:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.008 0.053 1820 Z= 0.521 Angle : 0.716 5.839 2476 Z= 0.397 Chirality : 0.051 0.171 290 Planarity : 0.004 0.036 320 Dihedral : 12.615 84.198 646 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.54), residues: 230 helix: 0.37 (0.67), residues: 52 sheet: 0.45 (0.58), residues: 78 loop : -0.03 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP A 32 PHE 0.025 0.003 PHE A 4 TYR 0.008 0.002 TYR A 129 ARG 0.005 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.337 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 1.6449 time to fit residues: 81.7775 Evaluate side-chains 43 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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: 0.7718 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1820 Z= 0.213 Angle : 0.540 5.493 2476 Z= 0.292 Chirality : 0.046 0.148 290 Planarity : 0.005 0.035 320 Dihedral : 5.271 26.374 252 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.58 % Allowed : 10.31 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.55), residues: 230 helix: 1.38 (0.68), residues: 52 sheet: 0.26 (0.57), residues: 78 loop : 0.31 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 32 PHE 0.015 0.002 PHE B 4 TYR 0.009 0.001 TYR A 42 ARG 0.002 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.183 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 52 average time/residue: 1.6096 time to fit residues: 84.7720 Evaluate side-chains 52 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 0.0470 chunk 20 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.3882 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1820 Z= 0.188 Angle : 0.505 5.447 2476 Z= 0.271 Chirality : 0.045 0.145 290 Planarity : 0.004 0.036 320 Dihedral : 4.888 24.486 252 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.12 % Allowed : 11.34 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.56), residues: 230 helix: 1.75 (0.71), residues: 52 sheet: 0.34 (0.54), residues: 88 loop : 0.43 (0.69), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 32 PHE 0.012 0.002 PHE B 4 TYR 0.008 0.001 TYR A 42 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.242 Fit side-chains REVERT: B 103 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8227 (tm) outliers start: 8 outliers final: 3 residues processed: 54 average time/residue: 1.5853 time to fit residues: 86.7674 Evaluate side-chains 54 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7671 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1820 Z= 0.160 Angle : 0.490 5.373 2476 Z= 0.262 Chirality : 0.045 0.141 290 Planarity : 0.004 0.037 320 Dihedral : 4.639 23.123 252 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.61 % Allowed : 13.92 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.56), residues: 230 helix: 1.94 (0.73), residues: 52 sheet: 0.44 (0.54), residues: 88 loop : 0.49 (0.69), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 32 PHE 0.009 0.001 PHE A 4 TYR 0.007 0.001 TYR B 58 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.216 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 55 average time/residue: 1.3540 time to fit residues: 75.4875 Evaluate side-chains 55 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.0040 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1820 Z= 0.147 Angle : 0.476 5.356 2476 Z= 0.253 Chirality : 0.044 0.141 290 Planarity : 0.004 0.037 320 Dihedral : 4.495 22.618 252 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 2.58 % Allowed : 15.98 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.55), residues: 230 helix: 2.01 (0.74), residues: 52 sheet: 0.29 (0.55), residues: 78 loop : 0.67 (0.63), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 32 PHE 0.008 0.001 PHE B 4 TYR 0.008 0.001 TYR B 42 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.205 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 54 average time/residue: 1.5434 time to fit residues: 84.5736 Evaluate side-chains 54 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 5 optimal weight: 0.0980 chunk 21 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 2 optimal weight: 0.0060 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1820 Z= 0.128 Angle : 0.466 5.310 2476 Z= 0.247 Chirality : 0.044 0.141 290 Planarity : 0.004 0.036 320 Dihedral : 4.309 21.728 252 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 3.61 % Allowed : 17.53 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.55), residues: 230 helix: 2.07 (0.75), residues: 52 sheet: 0.39 (0.55), residues: 78 loop : 0.72 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 32 PHE 0.007 0.001 PHE B 4 TYR 0.008 0.001 TYR A 58 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.209 Fit side-chains REVERT: A 25 PHE cc_start: 0.8197 (t80) cc_final: 0.7909 (t80) outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 1.5617 time to fit residues: 87.1138 Evaluate side-chains 56 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 45 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.0470 chunk 13 optimal weight: 0.0670 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1820 Z= 0.114 Angle : 0.457 5.270 2476 Z= 0.241 Chirality : 0.044 0.141 290 Planarity : 0.004 0.036 320 Dihedral : 4.001 19.479 252 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.03 % Allowed : 20.10 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.55), residues: 230 helix: 2.11 (0.77), residues: 52 sheet: 0.27 (0.56), residues: 74 loop : 0.79 (0.62), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 32 PHE 0.007 0.001 PHE A 4 TYR 0.007 0.001 TYR B 58 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.203 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 1.4828 time to fit residues: 87.1582 Evaluate side-chains 54 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 1 optimal weight: 0.0970 chunk 16 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 1820 Z= 0.123 Angle : 0.473 5.292 2476 Z= 0.247 Chirality : 0.044 0.139 290 Planarity : 0.004 0.037 320 Dihedral : 4.040 19.518 252 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.03 % Allowed : 21.65 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.55), residues: 230 helix: 2.05 (0.76), residues: 52 sheet: 0.38 (0.56), residues: 74 loop : 0.75 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 32 PHE 0.008 0.002 PHE B 25 TYR 0.007 0.001 TYR B 58 ARG 0.003 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.205 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 1.5315 time to fit residues: 82.2777 Evaluate side-chains 51 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 0.2980 chunk 17 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1820 Z= 0.174 Angle : 0.501 5.396 2476 Z= 0.261 Chirality : 0.044 0.140 290 Planarity : 0.004 0.035 320 Dihedral : 4.369 21.907 252 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.03 % Allowed : 21.65 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.56), residues: 230 helix: 1.86 (0.75), residues: 52 sheet: 0.81 (0.54), residues: 88 loop : 0.50 (0.66), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 32 PHE 0.007 0.002 PHE B 4 TYR 0.008 0.001 TYR B 58 ARG 0.002 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.201 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 1.6560 time to fit residues: 88.9413 Evaluate side-chains 54 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 16 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.1180 ------------------------------------------------------------------------------- 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: 0.7642 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1820 Z= 0.162 Angle : 0.495 5.354 2476 Z= 0.258 Chirality : 0.044 0.140 290 Planarity : 0.004 0.034 320 Dihedral : 4.364 21.917 252 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.03 % Allowed : 22.68 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.56), residues: 230 helix: 1.80 (0.74), residues: 52 sheet: 0.79 (0.54), residues: 88 loop : 0.55 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 32 PHE 0.007 0.002 PHE B 25 TYR 0.008 0.001 TYR A 58 ARG 0.002 0.000 ARG A 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.164 Fit side-chains REVERT: B 49 ARG cc_start: 0.7102 (ptt-90) cc_final: 0.6836 (ptt90) outliers start: 2 outliers final: 2 residues processed: 51 average time/residue: 1.5863 time to fit residues: 81.9467 Evaluate side-chains 53 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 14 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.0970 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 21 optimal weight: 0.2980 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.158590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138386 restraints weight = 1859.472| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.80 r_work: 0.3542 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 1820 Z= 0.134 Angle : 0.481 5.305 2476 Z= 0.251 Chirality : 0.044 0.141 290 Planarity : 0.004 0.035 320 Dihedral : 4.184 20.860 252 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 1.55 % Allowed : 21.65 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.55), residues: 230 helix: 1.93 (0.76), residues: 52 sheet: 0.58 (0.58), residues: 74 loop : 0.76 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 32 PHE 0.007 0.002 PHE B 25 TYR 0.007 0.001 TYR B 58 ARG 0.002 0.000 ARG A 56 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1716.33 seconds wall clock time: 35 minutes 6.07 seconds (2106.07 seconds total)