Starting phenix.real_space_refine on Thu Dec 7 15:48:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjp_4565/12_2023/6qjp_4565.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjp_4565/12_2023/6qjp_4565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjp_4565/12_2023/6qjp_4565.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjp_4565/12_2023/6qjp_4565.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjp_4565/12_2023/6qjp_4565.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjp_4565/12_2023/6qjp_4565.pdb" } resolution = 3.5 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= 0.001 sd= 0.012 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: 3 Type Number sf(0) Gaussians C 522 2.51 5 N 141 2.21 5 O 153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 816 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 272 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain breaks: 1 Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 272 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain breaks: 1 Chain: "B" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 272 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain breaks: 1 Time building chain proxies: 0.80, per 1000 atoms: 0.98 Number of scatterers: 816 At special positions: 0 Unit cell: (52.44, 69, 37.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 153 8.00 N 141 7.00 C 522 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 - 3.50 Amino acid : False - 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: 0.25 Conformation dependent library (CDL) restraints added in 145.1 milliseconds 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 204 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 3 sheets defined 0.0% alpha, 62.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 288 removed outlier: 6.132A pdb=" N GLN A 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN C 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LYS C 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS A 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ASP C 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU A 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N SER C 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 284 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL C 287 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN A 286 " --> pdb=" O VAL C 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.448A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 313 through 318 removed outlier: 6.011A pdb=" N ASP A 314 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS C 317 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER A 316 " --> pdb=" O LYS C 317 " (cutoff:3.500A) 22 hydrogen bonds defined for protein. 66 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: 0.17 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 132 1.29 - 1.35: 114 1.35 - 1.42: 33 1.42 - 1.48: 123 1.48 - 1.55: 414 Bond restraints: 816 Sorted by residual: bond pdb=" CG1 ILE B 278 " pdb=" CD1 ILE B 278 " ideal model delta sigma weight residual 1.513 1.435 0.078 3.90e-02 6.57e+02 3.98e+00 bond pdb=" CG1 ILE A 278 " pdb=" CD1 ILE A 278 " ideal model delta sigma weight residual 1.513 1.435 0.078 3.90e-02 6.57e+02 3.97e+00 bond pdb=" CG1 ILE C 278 " pdb=" CD1 ILE C 278 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.94e+00 bond pdb=" CA SER A 320 " pdb=" CB SER A 320 " ideal model delta sigma weight residual 1.535 1.510 0.025 1.90e-02 2.77e+03 1.70e+00 bond pdb=" CA SER C 320 " pdb=" CB SER C 320 " ideal model delta sigma weight residual 1.535 1.511 0.024 1.90e-02 2.77e+03 1.64e+00 ... (remaining 811 not shown) Histogram of bond angle deviations from ideal: 103.23 - 108.32: 49 108.32 - 113.41: 495 113.41 - 118.49: 163 118.49 - 123.58: 353 123.58 - 128.67: 26 Bond angle restraints: 1086 Sorted by residual: angle pdb=" C THR B 319 " pdb=" CA THR B 319 " pdb=" CB THR B 319 " ideal model delta sigma weight residual 110.30 103.23 7.07 1.98e+00 2.55e-01 1.28e+01 angle pdb=" C THR A 319 " pdb=" CA THR A 319 " pdb=" CB THR A 319 " ideal model delta sigma weight residual 110.30 103.25 7.05 1.98e+00 2.55e-01 1.27e+01 angle pdb=" C THR C 319 " pdb=" CA THR C 319 " pdb=" CB THR C 319 " ideal model delta sigma weight residual 110.30 103.25 7.05 1.98e+00 2.55e-01 1.27e+01 angle pdb=" CA TYR A 310 " pdb=" CB TYR A 310 " pdb=" CG TYR A 310 " ideal model delta sigma weight residual 113.90 118.52 -4.62 1.80e+00 3.09e-01 6.58e+00 angle pdb=" CA TYR C 310 " pdb=" CB TYR C 310 " pdb=" CG TYR C 310 " ideal model delta sigma weight residual 113.90 118.48 -4.58 1.80e+00 3.09e-01 6.48e+00 ... (remaining 1081 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 5.21: 339 5.21 - 10.41: 94 10.41 - 15.61: 65 15.61 - 20.80: 21 20.80 - 26.00: 9 Dihedral angle restraints: 528 sinusoidal: 222 harmonic: 306 Sorted by residual: dihedral pdb=" C THR B 319 " pdb=" N THR B 319 " pdb=" CA THR B 319 " pdb=" CB THR B 319 " ideal model delta harmonic sigma weight residual -122.00 -113.14 -8.86 0 2.50e+00 1.60e-01 1.25e+01 dihedral pdb=" C THR A 319 " pdb=" N THR A 319 " pdb=" CA THR A 319 " pdb=" CB THR A 319 " ideal model delta harmonic sigma weight residual -122.00 -113.19 -8.81 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" C THR C 319 " pdb=" N THR C 319 " pdb=" CA THR C 319 " pdb=" CB THR C 319 " ideal model delta harmonic sigma weight residual -122.00 -113.19 -8.81 0 2.50e+00 1.60e-01 1.24e+01 ... (remaining 525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 65 0.037 - 0.074: 46 0.074 - 0.111: 18 0.111 - 0.149: 9 0.149 - 0.186: 3 Chirality restraints: 141 Sorted by residual: chirality pdb=" CA THR B 319 " pdb=" N THR B 319 " pdb=" C THR B 319 " pdb=" CB THR B 319 " both_signs ideal model delta sigma weight residual False 2.53 2.71 -0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA THR C 319 " pdb=" N THR C 319 " pdb=" C THR C 319 " pdb=" CB THR C 319 " both_signs ideal model delta sigma weight residual False 2.53 2.71 -0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA THR A 319 " pdb=" N THR A 319 " pdb=" C THR A 319 " pdb=" CB THR A 319 " both_signs ideal model delta sigma weight residual False 2.53 2.71 -0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 138 not shown) Planarity restraints: 126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " -0.036 2.00e-02 2.50e+03 1.94e-02 7.52e+00 pdb=" CG TYR C 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " -0.036 2.00e-02 2.50e+03 1.94e-02 7.50e+00 pdb=" CG TYR B 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.036 2.00e-02 2.50e+03 1.93e-02 7.44e+00 pdb=" CG TYR A 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.012 2.00e-02 2.50e+03 ... (remaining 123 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.06: 452 3.06 - 3.52: 777 3.52 - 3.98: 1135 3.98 - 4.44: 989 4.44 - 4.90: 2318 Nonbonded interactions: 5671 Sorted by model distance: nonbonded pdb=" C THR B 319 " pdb=" OG1 THR B 319 " model vdw 2.605 2.616 nonbonded pdb=" C THR A 319 " pdb=" OG1 THR A 319 " model vdw 2.606 2.616 nonbonded pdb=" C THR C 319 " pdb=" OG1 THR C 319 " model vdw 2.606 2.616 nonbonded pdb=" N THR C 319 " pdb=" O THR C 319 " model vdw 2.646 2.496 nonbonded pdb=" N THR A 319 " pdb=" O THR A 319 " model vdw 2.646 2.496 ... (remaining 5666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 group one per residue 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.310 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.050 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 0.009 0.078 816 Z= 0.622 Angle : 1.011 7.071 1086 Z= 0.536 Chirality : 0.065 0.186 141 Planarity : 0.007 0.036 126 Dihedral : 9.521 26.002 324 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: -2.50 (0.78), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.60), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.036 0.015 TYR C 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.114 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1078 time to fit residues: 3.5038 Evaluate side-chains 14 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.116 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 overall best weight: 1.4488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 816 Z= 0.230 Angle : 0.632 4.538 1086 Z= 0.325 Chirality : 0.051 0.130 141 Planarity : 0.005 0.033 126 Dihedral : 6.526 17.901 102 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.94 % Allowed : 7.84 % Favored : 89.22 % 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: -2.44 (0.79), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.60), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.005 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.136 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 0.0599 time to fit residues: 1.6750 Evaluate side-chains 14 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.134 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0166 time to fit residues: 0.2211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 816 Z= 0.412 Angle : 0.792 6.578 1086 Z= 0.410 Chirality : 0.053 0.130 141 Planarity : 0.005 0.024 126 Dihedral : 7.226 19.660 102 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.96 % Allowed : 12.75 % Favored : 85.29 % 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: -3.14 (0.74), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.007 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.112 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.0542 time to fit residues: 1.2785 Evaluate side-chains 17 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.110 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0144 time to fit residues: 0.1732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 816 Z= 0.136 Angle : 0.590 4.991 1086 Z= 0.293 Chirality : 0.051 0.121 141 Planarity : 0.002 0.014 126 Dihedral : 6.324 17.270 102 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 13.73 % Favored : 86.27 % 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: -3.00 (0.73), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.004 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0519 time to fit residues: 1.1081 Evaluate side-chains 14 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.118 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.7488 ------------------------------------------------------------------------------- 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: 0.7465 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 816 Z= 0.250 Angle : 0.658 5.064 1086 Z= 0.336 Chirality : 0.051 0.124 141 Planarity : 0.003 0.012 126 Dihedral : 6.556 17.636 102 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.96 % Allowed : 11.76 % Favored : 86.27 % 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: -3.15 (0.73), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.55), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.006 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.116 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 16 average time/residue: 0.0535 time to fit residues: 1.1594 Evaluate side-chains 18 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.109 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0141 time to fit residues: 0.1920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.7520 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 816 Z= 0.305 Angle : 0.732 5.852 1086 Z= 0.369 Chirality : 0.051 0.124 141 Planarity : 0.003 0.012 126 Dihedral : 6.792 18.633 102 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % 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: -3.47 (0.73), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.55), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.007 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.115 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0558 time to fit residues: 1.1709 Evaluate side-chains 15 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.100 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.4738 ------------------------------------------------------------------------------- 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: 0.7480 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 816 Z= 0.218 Angle : 0.689 5.453 1086 Z= 0.344 Chirality : 0.051 0.121 141 Planarity : 0.002 0.010 126 Dihedral : 6.490 17.772 102 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % 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: -3.39 (0.72), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.55), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.005 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.100 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0515 time to fit residues: 1.1686 Evaluate side-chains 15 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.122 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.0370 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9833 ------------------------------------------------------------------------------- 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: 0.7423 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 816 Z= 0.159 Angle : 0.645 5.698 1086 Z= 0.316 Chirality : 0.051 0.122 141 Planarity : 0.002 0.011 126 Dihedral : 6.168 16.666 102 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % 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: -3.22 (0.72), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.55), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.004 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.109 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0520 time to fit residues: 1.1746 Evaluate side-chains 15 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 1.7408 ------------------------------------------------------------------------------- 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: 0.7501 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 816 Z= 0.239 Angle : 0.677 5.088 1086 Z= 0.344 Chirality : 0.051 0.123 141 Planarity : 0.003 0.012 126 Dihedral : 6.349 17.291 102 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.98 % Allowed : 14.71 % Favored : 84.31 % 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: -3.35 (0.73), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.006 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.112 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.0557 time to fit residues: 1.1903 Evaluate side-chains 17 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.119 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0155 time to fit residues: 0.1841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 816 Z= 0.398 Angle : 0.836 6.458 1086 Z= 0.422 Chirality : 0.053 0.126 141 Planarity : 0.003 0.016 126 Dihedral : 6.985 18.783 102 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % 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: -3.65 (0.74), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.029 0.008 TYR A 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 186 Ramachandran restraints generated. 93 Oldfield, 0 Emsley, 93 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.110 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0546 time to fit residues: 1.2276 Evaluate side-chains 17 residues out of total 102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.110 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.7488 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.130331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.109884 restraints weight = 1294.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.113048 restraints weight = 625.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.115085 restraints weight = 409.935| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 816 Z= 0.247 Angle : 0.726 5.861 1086 Z= 0.360 Chirality : 0.051 0.122 141 Planarity : 0.003 0.013 126 Dihedral : 6.637 18.685 102 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % 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: -3.47 (0.73), residues: 93 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.006 TYR A 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 657.79 seconds wall clock time: 17 minutes 41.00 seconds (1061.00 seconds total)