Starting phenix.real_space_refine (version: dev) on Thu Feb 16 22:52:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/02_2023/6mlu_9146.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/02_2023/6mlu_9146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/02_2023/6mlu_9146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/02_2023/6mlu_9146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/02_2023/6mlu_9146.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mlu_9146/02_2023/6mlu_9146.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 Process input model Symmetric amino acids flipped Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 2516 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1258 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Chain: "B" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1258 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 9, 'TRANS': 143} Time building chain proxies: 2.09, per 1000 atoms: 0.83 Number of scatterers: 2516 At special positions: 0 Unit cell: (72.05, 73.36, 58.95, 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 28 16.00 O 446 8.00 N 426 7.00 C 1616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 164 " distance=2.04 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: 1.10 Conformation dependent library (CDL) restraints added in 341.7 milliseconds 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 596 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 6 sheets defined 24.2% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 173 through 184 Processing helix chain 'A' and resid 184 through 190 Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 173 through 184 Processing helix chain 'B' and resid 184 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 93 removed outlier: 4.585A pdb=" N VAL A 232 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 231 " --> pdb=" O ASP A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 167 removed outlier: 7.097A pdb=" N LEU A 159 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP A 154 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 161 " --> pdb=" O MET A 152 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ARG A 153 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 167 removed outlier: 7.097A pdb=" N LEU A 159 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP A 154 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 161 " --> pdb=" O MET A 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 93 removed outlier: 4.583A pdb=" N VAL B 232 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 231 " --> pdb=" O ASP B 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 167 removed outlier: 7.097A pdb=" N LEU B 159 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP B 154 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 161 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ARG B 153 " --> pdb=" O THR B 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 167 removed outlier: 7.097A pdb=" N LEU B 159 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP B 154 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 161 " --> pdb=" O MET B 152 " (cutoff:3.500A) 108 hydrogen bonds defined for protein. 300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.59 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 796 1.34 - 1.46: 577 1.46 - 1.58: 1159 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 2580 Sorted by residual: bond pdb=" CA HIS A 110 " pdb=" CB HIS A 110 " ideal model delta sigma weight residual 1.530 1.564 -0.033 1.69e-02 3.50e+03 3.91e+00 bond pdb=" CA HIS B 110 " pdb=" CB HIS B 110 " ideal model delta sigma weight residual 1.530 1.564 -0.033 1.69e-02 3.50e+03 3.89e+00 bond pdb=" CA ARG A 88 " pdb=" C ARG A 88 " ideal model delta sigma weight residual 1.525 1.555 -0.030 2.10e-02 2.27e+03 2.02e+00 bond pdb=" CA ARG B 88 " pdb=" C ARG B 88 " ideal model delta sigma weight residual 1.525 1.554 -0.029 2.10e-02 2.27e+03 1.88e+00 bond pdb=" N HIS B 110 " pdb=" CA HIS B 110 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.45e+00 ... (remaining 2575 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.65: 81 105.65 - 112.73: 1335 112.73 - 119.81: 849 119.81 - 126.89: 1178 126.89 - 133.97: 51 Bond angle restraints: 3494 Sorted by residual: angle pdb=" C ALA A 109 " pdb=" N HIS A 110 " pdb=" CA HIS A 110 " ideal model delta sigma weight residual 121.54 131.86 -10.32 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C ALA B 109 " pdb=" N HIS B 110 " pdb=" CA HIS B 110 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 angle pdb=" C LEU B 98 " pdb=" N GLU B 99 " pdb=" CA GLU B 99 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 angle pdb=" C LEU A 98 " pdb=" N GLU A 99 " pdb=" CA GLU A 99 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C LEU B 208 " pdb=" N GLU B 209 " pdb=" CA GLU B 209 " ideal model delta sigma weight residual 121.54 128.30 -6.76 1.91e+00 2.74e-01 1.25e+01 ... (remaining 3489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.37: 1401 11.37 - 22.73: 135 22.73 - 34.09: 24 34.09 - 45.46: 12 45.46 - 56.82: 6 Dihedral angle restraints: 1578 sinusoidal: 664 harmonic: 914 Sorted by residual: dihedral pdb=" CA HIS B 110 " pdb=" C HIS B 110 " pdb=" N VAL B 111 " pdb=" CA VAL B 111 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA HIS A 110 " pdb=" C HIS A 110 " pdb=" N VAL A 111 " pdb=" CA VAL A 111 " ideal model delta harmonic sigma weight residual 180.00 156.82 23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA TRP A 192 " pdb=" C TRP A 192 " pdb=" N LYS A 193 " pdb=" CA LYS A 193 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 1575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 277 0.055 - 0.109: 74 0.109 - 0.164: 28 0.164 - 0.218: 7 0.218 - 0.273: 2 Chirality restraints: 388 Sorted by residual: chirality pdb=" CA HIS B 110 " pdb=" N HIS B 110 " pdb=" C HIS B 110 " pdb=" CB HIS B 110 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA HIS A 110 " pdb=" N HIS A 110 " pdb=" C HIS A 110 " pdb=" CB HIS A 110 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB THR B 100 " pdb=" CA THR B 100 " pdb=" OG1 THR B 100 " pdb=" CG2 THR B 100 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 385 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 209 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C GLU B 209 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU B 209 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU B 210 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 209 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C GLU A 209 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU A 209 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 210 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 109 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C ALA B 109 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA B 109 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS B 110 " 0.010 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.90: 921 2.90 - 3.40: 2472 3.40 - 3.90: 4091 3.90 - 4.40: 4488 4.40 - 4.90: 7629 Nonbonded interactions: 19601 Sorted by model distance: nonbonded pdb=" OD1 ASP A 154 " pdb=" N MET A 158 " model vdw 2.406 2.520 nonbonded pdb=" OD1 ASP B 154 " pdb=" N MET B 158 " model vdw 2.409 2.520 nonbonded pdb=" NH1 ARG B 206 " pdb=" O PHE B 240 " model vdw 2.415 2.520 nonbonded pdb=" NH1 ARG A 206 " pdb=" O PHE A 240 " model vdw 2.415 2.520 nonbonded pdb=" OH TYR A 230 " pdb=" N TYR B 171 " model vdw 2.432 2.520 ... (remaining 19596 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 1616 2.51 5 N 426 2.21 5 O 446 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.210 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: 3.740 Check model and map are aligned: 0.030 Process input model: 12.320 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.005 0.044 2580 Z= 0.345 Angle : 1.046 10.429 3494 Z= 0.564 Chirality : 0.064 0.273 388 Planarity : 0.007 0.036 440 Dihedral : 9.856 47.411 976 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer Outliers : 0.69 % 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: -4.38 (0.42), residues: 302 helix: -2.79 (0.45), residues: 74 sheet: -1.76 (0.57), residues: 86 loop : -3.75 (0.42), residues: 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 163 average time/residue: 0.2299 time to fit residues: 41.3418 Evaluate side-chains 115 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 0.0000 chunk 8 optimal weight: 0.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 197 GLN ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 2580 Z= 0.207 Angle : 0.809 7.143 3494 Z= 0.426 Chirality : 0.054 0.217 388 Planarity : 0.005 0.032 440 Dihedral : 6.165 23.067 336 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer Outliers : 6.60 % 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: -3.20 (0.46), residues: 302 helix: -0.55 (0.59), residues: 74 sheet: -1.66 (0.53), residues: 90 loop : -3.39 (0.48), residues: 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 137 average time/residue: 0.1886 time to fit residues: 29.1689 Evaluate side-chains 122 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0506 time to fit residues: 1.1379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN A 140 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 2580 Z= 0.279 Angle : 0.838 7.031 3494 Z= 0.440 Chirality : 0.056 0.270 388 Planarity : 0.005 0.026 440 Dihedral : 6.260 21.577 336 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 27.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer Outliers : 7.99 % 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: -2.99 (0.46), residues: 302 helix: 0.04 (0.59), residues: 74 sheet: -2.05 (0.47), residues: 94 loop : -3.11 (0.51), residues: 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 0.283 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 119 average time/residue: 0.1856 time to fit residues: 24.7988 Evaluate side-chains 116 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.275 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0290 time to fit residues: 1.1129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 overall best weight: 2.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 2580 Z= 0.250 Angle : 0.817 7.828 3494 Z= 0.423 Chirality : 0.054 0.285 388 Planarity : 0.004 0.028 440 Dihedral : 6.274 22.489 336 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 27.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer Outliers : 3.47 % 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: -2.94 (0.45), residues: 302 helix: 0.23 (0.57), residues: 74 sheet: -2.18 (0.47), residues: 96 loop : -3.04 (0.50), residues: 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 0.272 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 118 average time/residue: 0.1988 time to fit residues: 26.4934 Evaluate side-chains 119 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0371 time to fit residues: 0.8207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.6852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 2580 Z= 0.281 Angle : 0.847 8.602 3494 Z= 0.440 Chirality : 0.056 0.344 388 Planarity : 0.005 0.027 440 Dihedral : 6.344 22.098 336 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 31.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer Outliers : 6.25 % 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: -2.80 (0.46), residues: 302 helix: 0.48 (0.61), residues: 74 sheet: -1.81 (0.48), residues: 90 loop : -3.28 (0.48), residues: 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.303 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 122 average time/residue: 0.1935 time to fit residues: 26.6850 Evaluate side-chains 118 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 0.284 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0386 time to fit residues: 1.1173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 27 optimal weight: 0.0020 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 21 optimal weight: 7.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.7238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 2580 Z= 0.229 Angle : 0.869 9.519 3494 Z= 0.435 Chirality : 0.057 0.368 388 Planarity : 0.005 0.033 440 Dihedral : 6.242 22.788 336 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.91 % Favored : 87.09 % Rotamer Outliers : 2.43 % 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: -2.73 (0.46), residues: 302 helix: 0.50 (0.62), residues: 72 sheet: -1.61 (0.49), residues: 90 loop : -3.29 (0.49), residues: 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 116 average time/residue: 0.1900 time to fit residues: 24.9303 Evaluate side-chains 116 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0388 time to fit residues: 0.8397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 GLN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.7627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 2580 Z= 0.244 Angle : 0.925 10.663 3494 Z= 0.460 Chirality : 0.057 0.370 388 Planarity : 0.006 0.067 440 Dihedral : 6.332 22.386 336 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 27.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % Rotamer Outliers : 2.43 % 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: -2.45 (0.48), residues: 302 helix: 1.00 (0.63), residues: 72 sheet: -1.59 (0.50), residues: 94 loop : -3.19 (0.50), residues: 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 120 average time/residue: 0.2016 time to fit residues: 27.0592 Evaluate side-chains 115 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0508 time to fit residues: 0.8559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 0.0570 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.7875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 2580 Z= 0.282 Angle : 0.997 14.035 3494 Z= 0.483 Chirality : 0.059 0.381 388 Planarity : 0.006 0.056 440 Dihedral : 6.253 22.100 336 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.57 % Favored : 85.43 % Rotamer Outliers : 5.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.48), residues: 302 helix: 0.89 (0.63), residues: 72 sheet: -1.46 (0.51), residues: 90 loop : -3.42 (0.49), residues: 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 121 average time/residue: 0.1960 time to fit residues: 26.8058 Evaluate side-chains 125 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.308 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0310 time to fit residues: 0.9819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.8033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 2580 Z= 0.328 Angle : 1.062 13.759 3494 Z= 0.517 Chirality : 0.063 0.407 388 Planarity : 0.006 0.051 440 Dihedral : 6.480 22.366 336 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 33.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.48), residues: 302 helix: 1.09 (0.65), residues: 74 sheet: -1.37 (0.52), residues: 86 loop : -3.33 (0.47), residues: 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 0.271 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 118 average time/residue: 0.1960 time to fit residues: 26.1774 Evaluate side-chains 116 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.321 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0368 time to fit residues: 0.5333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN B 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.8295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 2580 Z= 0.284 Angle : 1.079 15.943 3494 Z= 0.514 Chirality : 0.063 0.405 388 Planarity : 0.007 0.046 440 Dihedral : 6.480 21.874 336 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 28.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.89 % Favored : 84.11 % Rotamer Outliers : 1.39 % 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: -2.47 (0.48), residues: 302 helix: 1.14 (0.64), residues: 72 sheet: -1.35 (0.51), residues: 90 loop : -3.49 (0.48), residues: 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 604 Ramachandran restraints generated. 302 Oldfield, 0 Emsley, 302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 0.334 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 123 average time/residue: 0.1939 time to fit residues: 26.8862 Evaluate side-chains 120 residues out of total 288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0357 time to fit residues: 0.4863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.121009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.098350 restraints weight = 7028.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.100934 restraints weight = 4072.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.102709 restraints weight = 2858.996| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.8369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 2580 Z= 0.310 Angle : 1.111 14.948 3494 Z= 0.533 Chirality : 0.063 0.409 388 Planarity : 0.008 0.063 440 Dihedral : 6.638 22.555 336 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 31.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.23 % Favored : 84.77 % Rotamer Outliers : 1.39 % 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: -2.33 (0.48), residues: 302 helix: 1.13 (0.64), residues: 72 sheet: -1.12 (0.53), residues: 86 loop : -3.38 (0.48), residues: 144 =============================================================================== Job complete usr+sys time: 1046.32 seconds wall clock time: 19 minutes 35.56 seconds (1175.56 seconds total)