Starting phenix.real_space_refine on Sat Jan 20 08:18:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/01_2024/8dmb_27533.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/01_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_27533/01_2024/8dmb_27533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/01_2024/8dmb_27533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/01_2024/8dmb_27533.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmb_27533/01_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-1.21-5211/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: 7.41, per 1000 atoms: 0.52 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: 13.06 Conformation dependent library (CDL) restraints added in 787.9 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: 7.94 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: 6.22 Time building geometry restraints manager: 13.25 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: 6309 35.61 - 71.23: 672 71.23 - 106.84: 142 106.84 - 142.46: 1 142.46 - 178.07: 2 Dihedral angle restraints: 7126 sinusoidal: 6023 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 7123 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: 0.270 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: 0.160 Extract box with map and model: 2.020 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 55.340 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.320 ------------------------------------------------------------------------------- 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 : 22.764 178.072 5125 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 : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.9213 time to fit residues: 43.6798 Evaluate side-chains 30 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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: 10.0000 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9239 Z= 0.211 Angle : 0.612 6.383 13808 Z= 0.335 Chirality : 0.038 0.182 1722 Planarity : 0.006 0.051 751 Dihedral : 23.563 178.996 4463 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 2.25 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: 0.88 (0.48), residues: 324 helix: 1.15 (0.50), residues: 98 sheet: 0.48 (0.53), residues: 100 loop : 0.41 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP P 343 HIS 0.003 0.001 HIS P 165 PHE 0.011 0.001 PHE P 135 TYR 0.011 0.002 TYR P 127 ARG 0.005 0.001 ARG P 145 *********************** 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 30 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.745 Fit side-chains REVERT: P 269 ASP cc_start: 0.6958 (t0) cc_final: 0.6746 (t70) outliers start: 3 outliers final: 2 residues processed: 29 average time/residue: 0.7654 time to fit residues: 26.9434 Evaluate side-chains 28 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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: 0.9980 chunk 16 optimal weight: 9.9990 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: 5.9990 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9239 Z= 0.283 Angle : 0.626 6.155 13808 Z= 0.342 Chirality : 0.039 0.216 1722 Planarity : 0.007 0.051 751 Dihedral : 23.706 179.420 4461 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.11 % Allowed : 8.15 % Favored : 90.74 % 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: 0.57 (0.47), residues: 324 helix: 1.19 (0.49), residues: 98 sheet: 0.09 (0.52), residues: 105 loop : 0.18 (0.59), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 289 HIS 0.007 0.002 HIS P 242 PHE 0.015 0.002 PHE P 135 TYR 0.013 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 28 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.748 Fit side-chains REVERT: P 323 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8244 (ttm170) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.7711 time to fit residues: 25.1960 Evaluate side-chains 27 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 24 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9239 Z= 0.202 Angle : 0.554 4.523 13808 Z= 0.303 Chirality : 0.035 0.179 1722 Planarity : 0.005 0.036 751 Dihedral : 23.613 178.410 4461 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.74 % Allowed : 10.00 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.47), residues: 324 helix: 1.76 (0.50), residues: 98 sheet: 0.14 (0.52), residues: 100 loop : 0.27 (0.58), 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 242 PHE 0.008 0.001 PHE P 135 TYR 0.009 0.001 TYR P 127 ARG 0.006 0.000 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 25 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: P 19 MET cc_start: 0.8809 (tpt) cc_final: 0.8568 (tpt) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.8018 time to fit residues: 23.5039 Evaluate side-chains 25 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 71 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 10.0000 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: 0.3980 chunk 50 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- 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: 0.8174 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9239 Z= 0.257 Angle : 0.582 5.010 13808 Z= 0.317 Chirality : 0.037 0.175 1722 Planarity : 0.006 0.041 751 Dihedral : 23.691 179.177 4461 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: 0.79 (0.46), residues: 324 helix: 1.59 (0.49), residues: 98 sheet: 0.15 (0.52), residues: 100 loop : 0.14 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP P 343 HIS 0.004 0.002 HIS P 165 PHE 0.014 0.001 PHE P 135 TYR 0.010 0.002 TYR P 127 ARG 0.007 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 27 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.702 Fit side-chains REVERT: P 47 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8671 (mt) REVERT: P 323 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8190 (ttm170) outliers start: 4 outliers final: 2 residues processed: 26 average time/residue: 0.8307 time to fit residues: 26.0774 Evaluate side-chains 27 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 4.9990 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: 3.9990 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.8195 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9239 Z= 0.316 Angle : 0.616 5.105 13808 Z= 0.330 Chirality : 0.039 0.177 1722 Planarity : 0.006 0.051 751 Dihedral : 23.774 177.417 4461 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.85 % Allowed : 10.00 % Favored : 88.15 % 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: 1.29 (0.49), residues: 98 sheet: 0.05 (0.52), residues: 100 loop : -0.25 (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 0.013 0.001 PHE P 135 TYR 0.012 0.002 TYR P 127 ARG 0.008 0.001 ARG P 79 *********************** 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 30 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: P 47 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8685 (mt) REVERT: P 323 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8224 (ttm170) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.9142 time to fit residues: 31.0995 Evaluate side-chains 28 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 3.9990 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: 2.9990 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9239 Z= 0.300 Angle : 0.595 5.033 13808 Z= 0.322 Chirality : 0.038 0.180 1722 Planarity : 0.006 0.040 751 Dihedral : 23.680 177.664 4461 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.22 % Allowed : 11.11 % 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: 0.30 (0.46), residues: 324 helix: 1.40 (0.50), residues: 98 sheet: -0.00 (0.51), residues: 105 loop : -0.49 (0.55), 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 0.011 0.002 TYR P 46 ARG 0.007 0.001 ARG P 79 *********************** 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 29 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.805 Fit side-chains REVERT: P 47 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8679 (mt) REVERT: P 323 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8246 (ttm170) outliers start: 6 outliers final: 3 residues processed: 27 average time/residue: 0.8796 time to fit residues: 28.0306 Evaluate side-chains 27 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 226 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 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 : 0.005 0.044 9239 Z= 0.315 Angle : 0.609 4.988 13808 Z= 0.328 Chirality : 0.039 0.177 1722 Planarity : 0.007 0.057 751 Dihedral : 23.687 177.659 4461 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.96 % Allowed : 10.37 % 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: 0.19 (0.46), residues: 324 helix: 1.30 (0.50), residues: 98 sheet: -0.08 (0.51), residues: 105 loop : -0.53 (0.55), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP P 343 HIS 0.004 0.002 HIS P 165 PHE 0.013 0.001 PHE P 135 TYR 0.011 0.002 TYR P 46 ARG 0.009 0.001 ARG P 80 *********************** 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 32 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 24 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: P 47 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8694 (mt) REVERT: P 226 HIS cc_start: 0.5445 (OUTLIER) cc_final: 0.4952 (m170) REVERT: P 323 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8261 (ttm170) outliers start: 8 outliers final: 4 residues processed: 31 average time/residue: 0.9557 time to fit residues: 35.4959 Evaluate side-chains 31 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 226 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 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: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 226 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 9239 Z= 0.452 Angle : 0.689 5.607 13808 Z= 0.364 Chirality : 0.043 0.198 1722 Planarity : 0.008 0.067 751 Dihedral : 23.749 177.175 4461 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.59 % Allowed : 11.11 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline------------------------------------------------------------------------------- Optimize residue side-chains **************************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 54, in __init__ sys.stdout.flush() IOError: [Errno 28] No space left on device