Starting phenix.real_space_refine on Fri Feb 16 02:52:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/02_2024/8dmb_27533.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/02_2024/8dmb_27533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/02_2024/8dmb_27533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/02_2024/8dmb_27533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/02_2024/8dmb_27533.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/02_2024/8dmb_27533.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 274 5.49 5 Mg 2 5.21 5 S 9 5.16 5 C 4303 2.51 5 N 1586 2.21 5 O 2323 1.98 5 H 5728 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14225 Number of models: 1 Model: "" Number of chains: 5 Chain: "P" Number of atoms: 5376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5376 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 20, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "W" Number of atoms: 7634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 7634 Classifications: {'RNA': 237} Modifications used: {'3*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 14, 'rna3p_pur': 109, 'rna3p_pyr': 103} Link IDs: {'rna2p': 25, 'rna3p': 211} Chain breaks: 4 Chain: "X" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 893 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "Y" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 320 Classifications: {'DNA': 10} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 9} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.62, per 1000 atoms: 0.54 Number of scatterers: 14225 At special positions: 0 Unit cell: (108.68, 128.128, 102.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 9 16.00 P 274 15.00 Mg 2 11.99 O 2323 8.00 N 1586 7.00 C 4303 6.00 H 5728 1.00 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: 13.20 Conformation dependent library (CDL) restraints added in 806.1 milliseconds 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 604 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 3 sheets defined 34.5% alpha, 21.3% beta 108 base pairs and 159 stacking pairs defined. Time for finding SS restraints: 7.46 Creating SS restraints... Processing helix chain 'P' and resid 22 through 32 Processing helix chain 'P' and resid 92 through 112 Processing helix chain 'P' and resid 130 through 151 removed outlier: 4.105A pdb=" N ILE P 150 " --> pdb=" O GLU P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 168 Processing helix chain 'P' and resid 171 through 179 removed outlier: 4.974A pdb=" N VAL P 177 " --> pdb=" O TYR P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 192 removed outlier: 3.668A pdb=" N LYS P 190 " --> pdb=" O ARG P 186 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU P 191 " --> pdb=" O GLU P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 210 Processing helix chain 'P' and resid 226 through 239 Processing helix chain 'P' and resid 267 through 271 removed outlier: 3.581A pdb=" N VAL P 271 " --> pdb=" O LYS P 268 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 10 through 11 removed outlier: 7.201A pdb=" N VAL P 11 " --> pdb=" O MET P 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 193 through 197 removed outlier: 3.640A pdb=" N LEU P 155 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU P 159 " --> pdb=" O VAL P 64 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER P 77 " --> pdb=" O VAL P 81 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL P 81 " --> pdb=" O SER P 77 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N PHE P 249 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG P 84 " --> pdb=" O PHE P 249 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N TRP P 251 " --> pdb=" O ARG P 84 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N MET P 86 " --> pdb=" O TRP P 251 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ARG P 253 " --> pdb=" O MET P 86 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N PHE P 88 " --> pdb=" O ARG P 253 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE P 248 " --> pdb=" O VAL P 346 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG P 252 " --> pdb=" O SER P 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 323 through 327 removed outlier: 6.074A pdb=" N GLY P 315 " --> pdb=" O CYS P 304 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU P 291 " --> pdb=" O LEU P 334 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU P 334 " --> pdb=" O GLU P 291 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU P 293 " --> pdb=" O VAL P 332 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL P 332 " --> pdb=" O GLU P 293 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 330 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 285 hydrogen bonds 526 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 159 stacking parallelities Total time for adding SS restraints: 6.07 Time building geometry restraints manager: 13.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 5725 1.02 - 1.22: 5 1.22 - 1.41: 3882 1.41 - 1.61: 5326 1.61 - 1.81: 29 Bond restraints: 14967 Sorted by residual: bond pdb=" C ALA P 130 " pdb=" N PRO P 131 " ideal model delta sigma weight residual 1.334 1.373 -0.039 1.51e-02 4.39e+03 6.50e+00 bond pdb=" C3' DT Y 2 " pdb=" O3' DT Y 2 " ideal model delta sigma weight residual 1.422 1.498 -0.076 3.00e-02 1.11e+03 6.34e+00 bond pdb=" C TYR P 151 " pdb=" N PRO P 152 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.47e+00 bond pdb=" C1' DT Y 2 " pdb=" N1 DT Y 2 " ideal model delta sigma weight residual 1.490 1.552 -0.062 3.00e-02 1.11e+03 4.30e+00 bond pdb=" C4' U W 19 " pdb=" C3' U W 19 " ideal model delta sigma weight residual 1.521 1.491 0.030 1.50e-02 4.44e+03 3.97e+00 ... (remaining 14962 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.25: 1658 106.25 - 113.19: 14917 113.19 - 120.12: 5670 120.12 - 127.05: 3988 127.05 - 133.99: 639 Bond angle restraints: 26872 Sorted by residual: angle pdb=" O3' DT Y 2 " pdb=" C3' DT Y 2 " pdb=" C2' DT Y 2 " ideal model delta sigma weight residual 111.50 119.49 -7.99 1.50e+00 4.44e-01 2.84e+01 angle pdb=" C3' DT Y 2 " pdb=" O3' DT Y 2 " pdb=" P DG Y 3 " ideal model delta sigma weight residual 120.20 127.04 -6.84 1.50e+00 4.44e-01 2.08e+01 angle pdb=" C2' A W 11 " pdb=" C1' A W 11 " pdb=" N9 A W 11 " ideal model delta sigma weight residual 112.00 118.06 -6.06 1.50e+00 4.44e-01 1.63e+01 angle pdb=" C2' A W 251 " pdb=" C1' A W 251 " pdb=" N9 A W 251 " ideal model delta sigma weight residual 112.00 117.64 -5.64 1.50e+00 4.44e-01 1.41e+01 angle pdb=" C5' U W 19 " pdb=" C4' U W 19 " pdb=" O4' U W 19 " ideal model delta sigma weight residual 109.80 115.42 -5.62 1.50e+00 4.44e-01 1.40e+01 ... (remaining 26867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 6434 35.61 - 71.23: 784 71.23 - 106.84: 142 106.84 - 142.46: 1 142.46 - 178.07: 2 Dihedral angle restraints: 7363 sinusoidal: 6260 harmonic: 1103 Sorted by residual: dihedral pdb=" O4' U W 255 " pdb=" C1' U W 255 " pdb=" N1 U W 255 " pdb=" C2 U W 255 " ideal model delta sinusoidal sigma weight residual 232.00 53.93 178.07 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C W 146 " pdb=" C1' C W 146 " pdb=" N1 C W 146 " pdb=" C2 C W 146 " ideal model delta sinusoidal sigma weight residual -128.00 44.32 -172.32 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' C W 147 " pdb=" C1' C W 147 " pdb=" N1 C W 147 " pdb=" C2 C W 147 " ideal model delta sinusoidal sigma weight residual -160.00 -86.23 -73.77 1 1.50e+01 4.44e-03 3.07e+01 ... (remaining 7360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1316 0.052 - 0.104: 319 0.104 - 0.157: 70 0.157 - 0.209: 10 0.209 - 0.261: 7 Chirality restraints: 1722 Sorted by residual: chirality pdb=" C1' A W 11 " pdb=" O4' A W 11 " pdb=" C2' A W 11 " pdb=" N9 A W 11 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C1' A W 251 " pdb=" O4' A W 251 " pdb=" C2' A W 251 " pdb=" N9 A W 251 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C1' A W 189 " pdb=" O4' A W 189 " pdb=" C2' A W 189 " pdb=" N9 A W 189 " both_signs ideal model delta sigma weight residual False 2.46 2.21 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1719 not shown) Planarity restraints: 1284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG P 108 " 0.369 9.50e-02 1.11e+02 1.25e-01 2.38e+01 pdb=" NE ARG P 108 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG P 108 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG P 108 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG P 108 " -0.028 2.00e-02 2.50e+03 pdb="HH11 ARG P 108 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG P 108 " 0.024 2.00e-02 2.50e+03 pdb="HH21 ARG P 108 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG P 108 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 253 " 0.295 9.50e-02 1.11e+02 1.00e-01 1.75e+01 pdb=" NE ARG P 253 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG P 253 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG P 253 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG P 253 " -0.024 2.00e-02 2.50e+03 pdb="HH11 ARG P 253 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG P 253 " 0.025 2.00e-02 2.50e+03 pdb="HH21 ARG P 253 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG P 253 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN P 170 " 0.025 2.00e-02 2.50e+03 3.26e-02 1.59e+01 pdb=" CG ASN P 170 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN P 170 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN P 170 " -0.054 2.00e-02 2.50e+03 pdb="HD21 ASN P 170 " 0.000 2.00e-02 2.50e+03 pdb="HD22 ASN P 170 " 0.049 2.00e-02 2.50e+03 ... (remaining 1281 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 1437 2.26 - 2.85: 24223 2.85 - 3.43: 33487 3.43 - 4.02: 52883 4.02 - 4.60: 74867 Nonbonded interactions: 186897 Sorted by model distance: nonbonded pdb="HO2' A W 152 " pdb=" OP2 U W 154 " model vdw 1.677 1.850 nonbonded pdb="HO2' G W 72 " pdb=" O2 C W 98 " model vdw 1.688 1.850 nonbonded pdb=" HZ1 LYS P 142 " pdb=" OP1 G W 250 " model vdw 1.717 1.850 nonbonded pdb=" O ARG P 108 " pdb=" HG1 THR P 112 " model vdw 1.718 1.850 nonbonded pdb=" OD1 ASP P 91 " pdb=" HZ1 LYS P 136 " model vdw 1.728 1.850 ... (remaining 186892 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 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: 0.170 Extract box with map and model: 2.090 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 54.840 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 0.076 9239 Z= 0.292 Angle : 0.905 7.989 13808 Z= 0.533 Chirality : 0.051 0.261 1722 Planarity : 0.014 0.143 751 Dihedral : 23.251 178.072 5273 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.74 % Allowed : 3.70 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.46), residues: 324 helix: 0.05 (0.48), residues: 95 sheet: 0.92 (0.62), residues: 76 loop : 0.21 (0.51), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP P 251 HIS 0.003 0.002 HIS P 78 PHE 0.010 0.002 PHE P 135 TYR 0.018 0.004 TYR P 127 ARG 0.021 0.003 ARG P 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.9134 time to fit residues: 43.4330 Evaluate side-chains 30 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 226 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 226 HIS P 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9239 Z= 0.199 Angle : 0.603 6.301 13808 Z= 0.331 Chirality : 0.037 0.177 1722 Planarity : 0.006 0.053 751 Dihedral : 24.084 178.894 4611 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.11 % Allowed : 6.30 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.48), residues: 324 helix: 1.25 (0.51), residues: 98 sheet: 0.48 (0.53), residues: 100 loop : 0.44 (0.60), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 343 HIS 0.003 0.001 HIS P 165 PHE 0.010 0.001 PHE P 135 TYR 0.010 0.002 TYR P 127 ARG 0.005 0.001 ARG P 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.632 Fit side-chains REVERT: P 269 ASP cc_start: 0.6955 (t0) cc_final: 0.6743 (t70) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.7399 time to fit residues: 26.8043 Evaluate side-chains 28 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 71 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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: 0.8209 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 9239 Z= 0.393 Angle : 0.716 7.117 13808 Z= 0.384 Chirality : 0.044 0.234 1722 Planarity : 0.008 0.065 751 Dihedral : 24.387 178.605 4609 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.11 % Allowed : 8.89 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.46), residues: 324 helix: 0.85 (0.48), residues: 98 sheet: 0.11 (0.52), residues: 101 loop : -0.06 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 289 HIS 0.008 0.003 HIS P 165 PHE 0.019 0.002 PHE P 135 TYR 0.015 0.002 TYR P 127 ARG 0.005 0.001 ARG P 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.669 Fit side-chains REVERT: P 323 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8257 (ttm170) outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.7725 time to fit residues: 26.1260 Evaluate side-chains 26 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 323 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9239 Z= 0.284 Angle : 0.601 5.974 13808 Z= 0.325 Chirality : 0.038 0.186 1722 Planarity : 0.006 0.039 751 Dihedral : 24.265 179.406 4609 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.48 % Allowed : 10.00 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.46), residues: 324 helix: 1.40 (0.49), residues: 98 sheet: 0.07 (0.52), residues: 100 loop : -0.16 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP P 343 HIS 0.005 0.002 HIS P 165 PHE 0.011 0.001 PHE P 135 TYR 0.012 0.002 TYR P 127 ARG 0.006 0.001 ARG P 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.781 Fit side-chains REVERT: P 19 MET cc_start: 0.8860 (tpt) cc_final: 0.8612 (tpt) REVERT: P 47 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8663 (mt) outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.7143 time to fit residues: 23.6970 Evaluate side-chains 28 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 328 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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: 0.8189 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9239 Z= 0.297 Angle : 0.604 4.713 13808 Z= 0.326 Chirality : 0.038 0.169 1722 Planarity : 0.006 0.044 751 Dihedral : 24.235 178.805 4609 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.85 % Allowed : 10.37 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.46), residues: 324 helix: 1.36 (0.49), residues: 98 sheet: -0.06 (0.50), residues: 105 loop : -0.32 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP P 343 HIS 0.005 0.002 HIS P 165 PHE 0.013 0.001 PHE P 135 TYR 0.011 0.002 TYR P 127 ARG 0.011 0.001 ARG P 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.669 Fit side-chains REVERT: P 47 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8673 (mt) REVERT: P 323 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8245 (ttm170) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.8846 time to fit residues: 28.2931 Evaluate side-chains 27 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 323 ARG Chi-restraints excluded: chain P residue 328 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9239 Z= 0.266 Angle : 0.580 4.727 13808 Z= 0.314 Chirality : 0.037 0.169 1722 Planarity : 0.006 0.051 751 Dihedral : 24.174 178.711 4609 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.22 % Allowed : 10.74 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.46), residues: 324 helix: 1.43 (0.49), residues: 98 sheet: -0.05 (0.50), residues: 105 loop : -0.32 (0.57), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 343 HIS 0.004 0.001 HIS P 165 PHE 0.011 0.001 PHE P 135 TYR 0.010 0.002 TYR P 127 ARG 0.005 0.000 ARG P 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 22 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: P 47 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8659 (mt) REVERT: P 323 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8219 (ttm170) outliers start: 6 outliers final: 4 residues processed: 27 average time/residue: 0.9244 time to fit residues: 29.8436 Evaluate side-chains 28 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 22 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 310 THR Chi-restraints excluded: chain P residue 323 ARG Chi-restraints excluded: chain P residue 328 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.8209 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9239 Z= 0.346 Angle : 0.638 5.468 13808 Z= 0.342 Chirality : 0.040 0.188 1722 Planarity : 0.007 0.057 751 Dihedral : 24.273 177.078 4609 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.85 % Allowed : 11.48 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.46), residues: 324 helix: 1.20 (0.50), residues: 98 sheet: -0.13 (0.51), residues: 105 loop : -0.53 (0.56), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP P 343 HIS 0.005 0.002 HIS P 165 PHE 0.015 0.001 PHE P 135 TYR 0.012 0.002 TYR P 127 ARG 0.009 0.001 ARG P 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.686 Fit side-chains REVERT: P 47 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8668 (mt) REVERT: P 323 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8290 (ttm170) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.9645 time to fit residues: 28.2622 Evaluate side-chains 26 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 310 THR Chi-restraints excluded: chain P residue 323 ARG Chi-restraints excluded: chain P residue 328 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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: 0.8154 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9239 Z= 0.188 Angle : 0.542 4.579 13808 Z= 0.296 Chirality : 0.034 0.155 1722 Planarity : 0.005 0.057 751 Dihedral : 24.079 178.202 4609 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.85 % Allowed : 11.85 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.47), residues: 324 helix: 1.68 (0.51), residues: 98 sheet: 0.08 (0.52), residues: 100 loop : -0.25 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 343 HIS 0.002 0.001 HIS P 165 PHE 0.007 0.001 PHE P 135 TYR 0.008 0.001 TYR P 46 ARG 0.008 0.001 ARG P 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 47 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8661 (mt) REVERT: P 323 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8183 (ttm170) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 1.0156 time to fit residues: 31.8339 Evaluate side-chains 28 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 310 THR Chi-restraints excluded: chain P residue 323 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 9239 Z= 0.466 Angle : 0.701 5.747 13808 Z= 0.369 Chirality : 0.044 0.200 1722 Planarity : 0.008 0.067 751 Dihedral : 24.271 176.937 4609 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.22 % Allowed : 12.22 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.45), residues: 324 helix: 1.09 (0.49), residues: 98 sheet: -0.14 (0.51), residues: 105 loop : -0.83 (0.54), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP P 289 HIS 0.007 0.002 HIS P 165 PHE 0.017 0.002 PHE P 135 TYR 0.014 0.003 TYR P 46 ARG 0.008 0.001 ARG P 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 22 time to evaluate : 0.636 Fit side-chains REVERT: P 47 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8693 (mt) REVERT: P 323 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8314 (ttm170) outliers start: 6 outliers final: 3 residues processed: 27 average time/residue: 0.9744 time to fit residues: 30.9248 Evaluate side-chains 27 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 310 THR Chi-restraints excluded: chain P residue 323 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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: 0.8146 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9239 Z= 0.155 Angle : 0.535 4.594 13808 Z= 0.294 Chirality : 0.034 0.150 1722 Planarity : 0.006 0.066 751 Dihedral : 24.086 178.128 4609 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.48 % Allowed : 12.96 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.47), residues: 324 helix: 1.68 (0.51), residues: 98 sheet: 0.17 (0.52), residues: 100 loop : -0.36 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 343 HIS 0.002 0.001 HIS P 165 PHE 0.008 0.001 PHE P 135 TYR 0.008 0.001 TYR P 46 ARG 0.009 0.001 ARG P 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: P 47 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8662 (mt) REVERT: P 323 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8215 (ttm170) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.9700 time to fit residues: 30.4689 Evaluate side-chains 27 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 71 ASP Chi-restraints excluded: chain P residue 310 THR Chi-restraints excluded: chain P residue 323 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.142852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110659 restraints weight = 27474.286| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.27 r_work: 0.3045 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9239 Z= 0.271 Angle : 0.578 4.762 13808 Z= 0.313 Chirality : 0.037 0.170 1722 Planarity : 0.006 0.066 751 Dihedral : 24.103 177.609 4609 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.85 % Allowed : 12.59 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.46), residues: 324 helix: 1.56 (0.50), residues: 98 sheet: 0.06 (0.51), residues: 105 loop : -0.60 (0.56), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 343 HIS 0.004 0.001 HIS P 165 PHE 0.013 0.001 PHE P 135 TYR 0.010 0.002 TYR P 46 ARG 0.008 0.001 ARG P 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4007.30 seconds wall clock time: 71 minutes 32.21 seconds (4292.21 seconds total)