Starting phenix.real_space_refine on Sat Apr 26 16:16:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z67_39794/04_2025/8z67_39794_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z67_39794/04_2025/8z67_39794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z67_39794/04_2025/8z67_39794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z67_39794/04_2025/8z67_39794.map" model { file = "/net/cci-nas-00/data/ceres_data/8z67_39794/04_2025/8z67_39794_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z67_39794/04_2025/8z67_39794_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 1527 2.51 5 N 380 2.21 5 O 383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2304 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2304 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 284} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 9, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 77 Time building chain proxies: 2.03, per 1000 atoms: 0.88 Number of scatterers: 2304 At special positions: 0 Unit cell: (74.692, 58.912, 62.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 383 8.00 N 380 7.00 C 1527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 283.8 milliseconds 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 1 sheets defined 81.8% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'R' and resid 18 through 48 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 51 through 79 removed outlier: 3.593A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 120 removed outlier: 3.695A pdb=" N CYS R 90 " --> pdb=" O GLY R 86 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 129 Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.528A pdb=" N HIS R 155 " --> pdb=" O PRO R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 188 Processing helix chain 'R' and resid 190 through 210 Processing helix chain 'R' and resid 215 through 254 Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 259 through 264 Processing helix chain 'R' and resid 264 through 275 Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 304 Processing sheet with id=AA1, first strand: chain 'R' and resid 158 through 160 removed outlier: 3.769A pdb=" N PHE R 159 " --> pdb=" O PHE R 167 " (cutoff:3.500A) 176 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.61 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 342 1.29 - 1.42: 718 1.42 - 1.55: 1295 1.55 - 1.68: 3 1.68 - 1.82: 18 Bond restraints: 2376 Sorted by residual: bond pdb=" CA ASP R 12 " pdb=" C ASP R 12 " ideal model delta sigma weight residual 1.531 1.389 0.142 1.15e-02 7.56e+03 1.53e+02 bond pdb=" CA ASN R 82 " pdb=" C ASN R 82 " ideal model delta sigma weight residual 1.522 1.426 0.096 1.18e-02 7.18e+03 6.67e+01 bond pdb=" C HIS R 17 " pdb=" O HIS R 17 " ideal model delta sigma weight residual 1.237 1.153 0.084 1.33e-02 5.65e+03 3.97e+01 bond pdb=" N SER R 13 " pdb=" CA SER R 13 " ideal model delta sigma weight residual 1.462 1.378 0.084 1.35e-02 5.49e+03 3.86e+01 bond pdb=" N ASN R 82 " pdb=" CA ASN R 82 " ideal model delta sigma weight residual 1.460 1.388 0.072 1.17e-02 7.31e+03 3.77e+01 ... (remaining 2371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 3204 3.94 - 7.89: 41 7.89 - 11.83: 5 11.83 - 15.78: 1 15.78 - 19.72: 1 Bond angle restraints: 3252 Sorted by residual: angle pdb=" N ILE R 84 " pdb=" CA ILE R 84 " pdb=" C ILE R 84 " ideal model delta sigma weight residual 111.77 125.02 -13.25 1.04e+00 9.25e-01 1.62e+02 angle pdb=" N GLY R 88 " pdb=" CA GLY R 88 " pdb=" C GLY R 88 " ideal model delta sigma weight residual 112.77 123.90 -11.13 1.28e+00 6.10e-01 7.56e+01 angle pdb=" N HIS R 85 " pdb=" CA HIS R 85 " pdb=" C HIS R 85 " ideal model delta sigma weight residual 111.24 100.16 11.08 1.29e+00 6.01e-01 7.38e+01 angle pdb=" N GLY R 259 " pdb=" CA GLY R 259 " pdb=" C GLY R 259 " ideal model delta sigma weight residual 113.18 93.46 19.72 2.37e+00 1.78e-01 6.92e+01 angle pdb=" C PRO R 87 " pdb=" N GLY R 88 " pdb=" CA GLY R 88 " ideal model delta sigma weight residual 120.00 127.97 -7.97 1.10e+00 8.26e-01 5.25e+01 ... (remaining 3247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.57: 1189 14.57 - 29.14: 121 29.14 - 43.71: 37 43.71 - 58.28: 3 58.28 - 72.85: 4 Dihedral angle restraints: 1354 sinusoidal: 479 harmonic: 875 Sorted by residual: dihedral pdb=" N ILE R 84 " pdb=" C ILE R 84 " pdb=" CA ILE R 84 " pdb=" CB ILE R 84 " ideal model delta harmonic sigma weight residual 123.40 137.69 -14.29 0 2.50e+00 1.60e-01 3.27e+01 dihedral pdb=" C ILE R 84 " pdb=" N ILE R 84 " pdb=" CA ILE R 84 " pdb=" CB ILE R 84 " ideal model delta harmonic sigma weight residual -122.00 -135.56 13.56 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" C HIS R 17 " pdb=" N HIS R 17 " pdb=" CA HIS R 17 " pdb=" CB HIS R 17 " ideal model delta harmonic sigma weight residual -122.60 -132.37 9.77 0 2.50e+00 1.60e-01 1.53e+01 ... (remaining 1351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 347 0.120 - 0.239: 19 0.239 - 0.359: 4 0.359 - 0.479: 1 0.479 - 0.599: 1 Chirality restraints: 372 Sorted by residual: chirality pdb=" CA ILE R 84 " pdb=" N ILE R 84 " pdb=" C ILE R 84 " pdb=" CB ILE R 84 " both_signs ideal model delta sigma weight residual False 2.43 1.83 0.60 2.00e-01 2.50e+01 8.96e+00 chirality pdb=" CB VAL R 297 " pdb=" CA VAL R 297 " pdb=" CG1 VAL R 297 " pdb=" CG2 VAL R 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA HIS R 17 " pdb=" N HIS R 17 " pdb=" C HIS R 17 " pdb=" CB HIS R 17 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 369 not shown) Planarity restraints: 401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY R 253 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C GLY R 253 " -0.064 2.00e-02 2.50e+03 pdb=" O GLY R 253 " 0.024 2.00e-02 2.50e+03 pdb=" N ARG R 254 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS R 79 " 0.033 2.00e-02 2.50e+03 2.44e-02 8.92e+00 pdb=" CG HIS R 79 " -0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS R 79 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 HIS R 79 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS R 79 " 0.020 2.00e-02 2.50e+03 pdb=" NE2 HIS R 79 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS R 10 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C HIS R 10 " 0.043 2.00e-02 2.50e+03 pdb=" O HIS R 10 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL R 11 " -0.014 2.00e-02 2.50e+03 ... (remaining 398 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 4 2.35 - 2.98: 1164 2.98 - 3.62: 3779 3.62 - 4.26: 5255 4.26 - 4.90: 9168 Nonbonded interactions: 19370 Sorted by model distance: nonbonded pdb=" CB SER R 13 " pdb=" OD1 ASP R 16 " model vdw 1.708 3.440 nonbonded pdb=" CB SER R 13 " pdb=" CG ASP R 16 " model vdw 2.037 3.670 nonbonded pdb=" N GLY R 259 " pdb=" N PHE R 260 " model vdw 2.166 2.560 nonbonded pdb=" O LEU R 272 " pdb=" OG1 THR R 275 " model vdw 2.325 3.040 nonbonded pdb=" CB SER R 13 " pdb=" OD2 ASP R 16 " model vdw 2.355 3.440 ... (remaining 19365 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.770 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 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 : 0.011 0.142 2377 Z= 0.762 Angle : 1.101 19.722 3254 Z= 0.672 Chirality : 0.075 0.599 372 Planarity : 0.006 0.037 401 Dihedral : 13.562 72.849 787 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.71 % Allowed : 4.27 % Favored : 94.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 8.33 % 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 (0.50), residues: 295 helix: 1.47 (0.34), residues: 235 sheet: None (None), residues: 0 loop : -2.86 (0.71), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 256 HIS 0.025 0.003 HIS R 17 PHE 0.033 0.002 PHE R 169 TYR 0.015 0.002 TYR R 102 ARG 0.002 0.000 ARG R 247 Details of bonding type rmsd hydrogen bonds : bond 0.10979 ( 176) hydrogen bonds : angle 5.46506 ( 522) SS BOND : bond 0.00204 ( 1) SS BOND : angle 2.92451 ( 2) covalent geometry : bond 0.01088 ( 2376) covalent geometry : angle 1.09868 ( 3252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.250 Fit side-chains REVERT: R 181 MET cc_start: 0.6336 (tpt) cc_final: 0.5852 (tpt) outliers start: 4 outliers final: 2 residues processed: 30 average time/residue: 0.2403 time to fit residues: 8.2597 Evaluate side-chains 26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110499 restraints weight = 2931.004| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.24 r_work: 0.3262 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2377 Z= 0.169 Angle : 0.567 6.684 3254 Z= 0.297 Chirality : 0.042 0.143 372 Planarity : 0.004 0.034 401 Dihedral : 4.337 17.544 326 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.14 % Allowed : 8.55 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.49), residues: 295 helix: 1.78 (0.33), residues: 233 sheet: None (None), residues: 0 loop : -2.78 (0.73), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 256 HIS 0.005 0.001 HIS R 17 PHE 0.023 0.002 PHE R 169 TYR 0.015 0.002 TYR R 102 ARG 0.002 0.000 ARG R 185 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 176) hydrogen bonds : angle 4.49357 ( 522) SS BOND : bond 0.00372 ( 1) SS BOND : angle 1.54592 ( 2) covalent geometry : bond 0.00400 ( 2376) covalent geometry : angle 0.56574 ( 3252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.229 Fit side-chains REVERT: R 181 MET cc_start: 0.7524 (tpt) cc_final: 0.7039 (tpt) REVERT: R 269 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.7583 (m-70) outliers start: 5 outliers final: 2 residues processed: 31 average time/residue: 0.2457 time to fit residues: 8.6176 Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 269 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.0470 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.0870 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 165 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111453 restraints weight = 2856.087| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.36 r_work: 0.3175 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2377 Z= 0.138 Angle : 0.530 6.668 3254 Z= 0.279 Chirality : 0.041 0.202 372 Planarity : 0.004 0.033 401 Dihedral : 3.882 14.564 322 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.71 % Allowed : 11.54 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.50), residues: 295 helix: 2.08 (0.34), residues: 231 sheet: None (None), residues: 0 loop : -2.67 (0.73), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 256 HIS 0.004 0.001 HIS R 17 PHE 0.013 0.002 PHE R 169 TYR 0.014 0.001 TYR R 102 ARG 0.001 0.000 ARG R 185 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 176) hydrogen bonds : angle 4.34477 ( 522) SS BOND : bond 0.00242 ( 1) SS BOND : angle 1.30000 ( 2) covalent geometry : bond 0.00317 ( 2376) covalent geometry : angle 0.52937 ( 3252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.235 Fit side-chains REVERT: R 39 LEU cc_start: 0.7654 (tp) cc_final: 0.7401 (tt) REVERT: R 181 MET cc_start: 0.7511 (tpt) cc_final: 0.7076 (tpt) REVERT: R 247 ARG cc_start: 0.6496 (mtm110) cc_final: 0.6134 (mtp-110) REVERT: R 269 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7501 (m-70) outliers start: 4 outliers final: 1 residues processed: 30 average time/residue: 0.2626 time to fit residues: 8.8911 Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 269 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 14 optimal weight: 0.0570 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.110212 restraints weight = 2879.389| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.40 r_work: 0.3282 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2377 Z= 0.134 Angle : 0.522 6.662 3254 Z= 0.275 Chirality : 0.041 0.220 372 Planarity : 0.003 0.032 401 Dihedral : 3.869 18.214 322 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.28 % Allowed : 11.97 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.50), residues: 295 helix: 1.96 (0.34), residues: 237 sheet: None (None), residues: 0 loop : -2.61 (0.77), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 40 HIS 0.004 0.001 HIS R 17 PHE 0.011 0.001 PHE R 169 TYR 0.013 0.001 TYR R 102 ARG 0.001 0.000 ARG R 185 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 176) hydrogen bonds : angle 4.23390 ( 522) SS BOND : bond 0.00277 ( 1) SS BOND : angle 1.21324 ( 2) covalent geometry : bond 0.00307 ( 2376) covalent geometry : angle 0.52142 ( 3252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.250 Fit side-chains REVERT: R 39 LEU cc_start: 0.7686 (tp) cc_final: 0.7424 (tt) REVERT: R 181 MET cc_start: 0.7508 (tpt) cc_final: 0.7065 (tpt) REVERT: R 247 ARG cc_start: 0.6537 (mtm110) cc_final: 0.6164 (mtp-110) REVERT: R 269 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7728 (m-70) outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 0.2624 time to fit residues: 8.5847 Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 269 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 0.6980 chunk 14 optimal weight: 0.0970 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.0010 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.0870 overall best weight: 0.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.107518 restraints weight = 3017.667| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.60 r_work: 0.3268 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2377 Z= 0.123 Angle : 0.506 6.683 3254 Z= 0.265 Chirality : 0.041 0.257 372 Planarity : 0.003 0.032 401 Dihedral : 3.756 17.198 322 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.28 % Allowed : 12.82 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.50), residues: 295 helix: 2.07 (0.34), residues: 237 sheet: None (None), residues: 0 loop : -2.52 (0.78), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 40 HIS 0.004 0.001 HIS R 17 PHE 0.010 0.001 PHE R 93 TYR 0.012 0.001 TYR R 102 ARG 0.001 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 176) hydrogen bonds : angle 4.14995 ( 522) SS BOND : bond 0.00175 ( 1) SS BOND : angle 1.11806 ( 2) covalent geometry : bond 0.00276 ( 2376) covalent geometry : angle 0.50542 ( 3252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.257 Fit side-chains REVERT: R 39 LEU cc_start: 0.7504 (tp) cc_final: 0.7256 (tt) REVERT: R 181 MET cc_start: 0.7420 (tpt) cc_final: 0.7015 (tpt) REVERT: R 247 ARG cc_start: 0.6417 (mtm110) cc_final: 0.6046 (mtp-110) outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 0.2682 time to fit residues: 9.1085 Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.0170 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111492 restraints weight = 2846.139| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.38 r_work: 0.3218 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2377 Z= 0.139 Angle : 0.517 6.647 3254 Z= 0.271 Chirality : 0.042 0.236 372 Planarity : 0.003 0.032 401 Dihedral : 3.729 16.573 322 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.85 % Allowed : 12.39 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.50), residues: 295 helix: 2.03 (0.33), residues: 237 sheet: None (None), residues: 0 loop : -2.60 (0.78), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 40 HIS 0.005 0.001 HIS R 17 PHE 0.011 0.002 PHE R 93 TYR 0.012 0.001 TYR R 102 ARG 0.001 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 176) hydrogen bonds : angle 4.15900 ( 522) SS BOND : bond 0.00243 ( 1) SS BOND : angle 1.15022 ( 2) covalent geometry : bond 0.00326 ( 2376) covalent geometry : angle 0.51591 ( 3252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.264 Fit side-chains REVERT: R 39 LEU cc_start: 0.7643 (tp) cc_final: 0.7424 (tt) REVERT: R 181 MET cc_start: 0.7396 (tpt) cc_final: 0.7025 (tpt) REVERT: R 247 ARG cc_start: 0.6547 (mtm110) cc_final: 0.6174 (mtp-110) outliers start: 2 outliers final: 1 residues processed: 29 average time/residue: 0.2627 time to fit residues: 8.6297 Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 1 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.0050 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.116291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106288 restraints weight = 3056.260| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.57 r_work: 0.3261 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2377 Z= 0.142 Angle : 0.516 6.608 3254 Z= 0.271 Chirality : 0.042 0.242 372 Planarity : 0.003 0.032 401 Dihedral : 3.701 16.444 322 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.28 % Allowed : 12.82 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.50), residues: 295 helix: 2.03 (0.33), residues: 237 sheet: None (None), residues: 0 loop : -2.60 (0.78), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 40 HIS 0.005 0.001 HIS R 17 PHE 0.010 0.002 PHE R 93 TYR 0.012 0.001 TYR R 102 ARG 0.001 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 176) hydrogen bonds : angle 4.16097 ( 522) SS BOND : bond 0.00266 ( 1) SS BOND : angle 1.05748 ( 2) covalent geometry : bond 0.00334 ( 2376) covalent geometry : angle 0.51576 ( 3252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.210 Fit side-chains REVERT: R 39 LEU cc_start: 0.7561 (tp) cc_final: 0.7329 (tt) REVERT: R 181 MET cc_start: 0.7396 (tpt) cc_final: 0.6931 (tpt) REVERT: R 247 ARG cc_start: 0.6509 (mtm110) cc_final: 0.6140 (mtp-110) outliers start: 3 outliers final: 3 residues processed: 27 average time/residue: 0.2830 time to fit residues: 8.6142 Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 174 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 0.0020 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107617 restraints weight = 2995.364| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.44 r_work: 0.3240 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2377 Z= 0.152 Angle : 0.523 6.594 3254 Z= 0.275 Chirality : 0.043 0.258 372 Planarity : 0.004 0.032 401 Dihedral : 3.742 15.800 322 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.71 % Allowed : 12.39 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.50), residues: 295 helix: 1.97 (0.33), residues: 237 sheet: None (None), residues: 0 loop : -2.60 (0.78), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 40 HIS 0.005 0.001 HIS R 17 PHE 0.011 0.002 PHE R 97 TYR 0.012 0.001 TYR R 102 ARG 0.001 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 176) hydrogen bonds : angle 4.18761 ( 522) SS BOND : bond 0.00262 ( 1) SS BOND : angle 1.03496 ( 2) covalent geometry : bond 0.00364 ( 2376) covalent geometry : angle 0.52272 ( 3252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.219 Fit side-chains REVERT: R 39 LEU cc_start: 0.7645 (tp) cc_final: 0.7434 (tt) REVERT: R 181 MET cc_start: 0.7396 (tpt) cc_final: 0.6929 (tpt) REVERT: R 247 ARG cc_start: 0.6582 (mtm110) cc_final: 0.6210 (mtp-110) outliers start: 4 outliers final: 2 residues processed: 26 average time/residue: 0.2751 time to fit residues: 8.0251 Evaluate side-chains 26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 174 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 0.0010 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 10 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112717 restraints weight = 2821.028| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.36 r_work: 0.3200 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2377 Z= 0.126 Angle : 0.505 6.616 3254 Z= 0.265 Chirality : 0.042 0.288 372 Planarity : 0.003 0.032 401 Dihedral : 3.600 13.304 322 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.85 % Allowed : 14.96 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.51), residues: 295 helix: 1.99 (0.34), residues: 243 sheet: None (None), residues: 0 loop : -2.42 (0.85), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 40 HIS 0.004 0.001 HIS R 241 PHE 0.010 0.001 PHE R 169 TYR 0.013 0.001 TYR R 102 ARG 0.001 0.000 ARG R 185 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 176) hydrogen bonds : angle 4.09081 ( 522) SS BOND : bond 0.00245 ( 1) SS BOND : angle 1.01516 ( 2) covalent geometry : bond 0.00287 ( 2376) covalent geometry : angle 0.50493 ( 3252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.255 Fit side-chains REVERT: R 181 MET cc_start: 0.7404 (tpt) cc_final: 0.6947 (tpt) REVERT: R 247 ARG cc_start: 0.6542 (mtm110) cc_final: 0.6176 (mtp-110) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.3084 time to fit residues: 8.3493 Evaluate side-chains 26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 174 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.0370 chunk 1 optimal weight: 0.5980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.111902 restraints weight = 2877.366| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.40 r_work: 0.3204 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2377 Z= 0.126 Angle : 0.511 6.627 3254 Z= 0.268 Chirality : 0.042 0.294 372 Planarity : 0.003 0.032 401 Dihedral : 3.586 12.284 322 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.85 % Allowed : 15.38 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.51), residues: 295 helix: 1.99 (0.34), residues: 243 sheet: None (None), residues: 0 loop : -2.39 (0.84), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 40 HIS 0.004 0.001 HIS R 17 PHE 0.010 0.001 PHE R 169 TYR 0.013 0.001 TYR R 102 ARG 0.001 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 176) hydrogen bonds : angle 4.07225 ( 522) SS BOND : bond 0.00229 ( 1) SS BOND : angle 0.97282 ( 2) covalent geometry : bond 0.00287 ( 2376) covalent geometry : angle 0.51011 ( 3252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 590 Ramachandran restraints generated. 295 Oldfield, 0 Emsley, 295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.232 Fit side-chains REVERT: R 181 MET cc_start: 0.7383 (tpt) cc_final: 0.6919 (tpt) REVERT: R 247 ARG cc_start: 0.6542 (mtm110) cc_final: 0.6180 (mtp-110) outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.2826 time to fit residues: 7.9201 Evaluate side-chains 25 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 174 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105578 restraints weight = 2953.864| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.54 r_work: 0.3228 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2377 Z= 0.181 Angle : 0.560 6.606 3254 Z= 0.294 Chirality : 0.045 0.294 372 Planarity : 0.004 0.032 401 Dihedral : 3.799 14.445 322 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.43 % Allowed : 16.24 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.50), residues: 295 helix: 1.86 (0.33), residues: 238 sheet: None (None), residues: 0 loop : -2.65 (0.76), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 40 HIS 0.006 0.001 HIS R 17 PHE 0.013 0.002 PHE R 97 TYR 0.013 0.002 TYR R 76 ARG 0.001 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 176) hydrogen bonds : angle 4.26423 ( 522) SS BOND : bond 0.00269 ( 1) SS BOND : angle 0.86565 ( 2) covalent geometry : bond 0.00439 ( 2376) covalent geometry : angle 0.55940 ( 3252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1628.98 seconds wall clock time: 28 minutes 40.58 seconds (1720.58 seconds total)