Starting phenix.real_space_refine on Fri May 9 13:58:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z67_39794/05_2025/8z67_39794_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z67_39794/05_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_39794/05_2025/8z67_39794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z67_39794/05_2025/8z67_39794.map" model { file = "/net/cci-nas-00/data/ceres_data/8z67_39794/05_2025/8z67_39794_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z67_39794/05_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-5687/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: 2.10, per 1000 atoms: 0.91 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: 0.59 Conformation dependent library (CDL) restraints added in 291.9 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: 0.22 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: 0.63 Time building geometry restraints manager: 0.71 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: 0.250 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.040 Process input model: 10.850 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.910 ------------------------------------------------------------------------------- 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 : 0.224 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: 0.2348 time to fit residues: 8.0094 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 : 0.246 ------------------------------------------------------------------------------- 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: 0.3142 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 : 0.248 Fit side-chains REVERT: R 181 MET cc_start: 0.7524 (tpt) cc_final: 0.7039 (tpt) REVERT: R 269 HIS cc_start: 0.7921 (OUTLIER) cc_final: 0.7584 (m-70) outliers start: 5 outliers final: 2 residues processed: 31 average time/residue: 0.2444 time to fit residues: 8.5852 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 : 0.228 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 = 0.120790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111439 restraints weight = 2854.905| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.36 r_work: 0.3176 rms_B_bonded: 1.72 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 6.678 3254 Z= 0.279 Chirality : 0.041 0.200 372 Planarity : 0.004 0.033 401 Dihedral : 3.882 14.622 322 Min Nonbonded Distance : 2.621 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 0.005 0.001 HIS R 165 PHE 0.013 0.002 PHE R 169 TYR 0.014 0.001 TYR R 102 ARG 0.001 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 176) hydrogen bonds : angle 4.34542 ( 522) SS BOND : bond 0.00234 ( 1) SS BOND : angle 1.30728 ( 2) covalent geometry : bond 0.00318 ( 2376) covalent geometry : angle 0.52923 ( 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 : 0.423 Fit side-chains REVERT: R 39 LEU cc_start: 0.7651 (tp) cc_final: 0.7400 (tt) REVERT: R 181 MET cc_start: 0.7509 (tpt) cc_final: 0.7073 (tpt) REVERT: R 247 ARG cc_start: 0.6500 (mtm110) cc_final: 0.6138 (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: 0.2523 time to fit residues: 8.5644 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 : 0.245 ------------------------------------------------------------------------------- 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: 0.5980 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 chunk 14 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.120511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111224 restraints weight = 2851.742| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.37 r_work: 0.3264 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2377 Z= 0.150 Angle : 0.535 6.633 3254 Z= 0.282 Chirality : 0.042 0.223 372 Planarity : 0.004 0.032 401 Dihedral : 3.922 18.655 322 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.71 % Allowed : 11.97 % Favored : 86.32 % 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: 1.60 (0.50), residues: 295 helix: 1.89 (0.33), residues: 237 sheet: None (None), residues: 0 loop : -2.61 (0.77), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 40 HIS 0.004 0.001 HIS R 17 PHE 0.012 0.002 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 0.03842 ( 176) hydrogen bonds : angle 4.28121 ( 522) SS BOND : bond 0.00269 ( 1) SS BOND : angle 1.16877 ( 2) covalent geometry : bond 0.00354 ( 2376) covalent geometry : angle 0.53474 ( 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 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.265 Fit side-chains REVERT: R 39 LEU cc_start: 0.7681 (tp) cc_final: 0.7426 (tt) REVERT: R 181 MET cc_start: 0.7492 (tpt) cc_final: 0.7057 (tpt) REVERT: R 247 ARG cc_start: 0.6548 (mtm110) cc_final: 0.6185 (mtp-110) REVERT: R 269 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7688 (m-70) outliers start: 4 outliers final: 2 residues processed: 29 average time/residue: 0.2498 time to fit residues: 8.1786 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 : 0.241 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 0.0980 chunk 14 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.118281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108631 restraints weight = 2948.930| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.44 r_work: 0.3282 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1610 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= 0.135 Angle : 0.518 6.630 3254 Z= 0.272 Chirality : 0.042 0.254 372 Planarity : 0.003 0.032 401 Dihedral : 3.841 18.598 322 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.83 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: 1.74 (0.50), residues: 295 helix: 2.00 (0.34), residues: 237 sheet: None (None), residues: 0 loop : -2.56 (0.78), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 115 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 176) hydrogen bonds : angle 4.20371 ( 522) SS BOND : bond 0.00263 ( 1) SS BOND : angle 1.11601 ( 2) covalent geometry : bond 0.00310 ( 2376) covalent geometry : angle 0.51752 ( 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: 4 poor density : 28 time to evaluate : 0.229 Fit side-chains REVERT: R 39 LEU cc_start: 0.7656 (tp) cc_final: 0.7414 (tt) REVERT: R 181 MET cc_start: 0.7470 (tpt) cc_final: 0.7075 (tpt) REVERT: R 247 ARG cc_start: 0.6513 (mtm110) cc_final: 0.6150 (mtp-110) outliers start: 4 outliers final: 2 residues processed: 29 average time/residue: 0.2627 time to fit residues: 8.6365 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 : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 166 THR 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: 0.5980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.119821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110447 restraints weight = 2860.821| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.39 r_work: 0.3181 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1661 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= 0.142 Angle : 0.519 6.607 3254 Z= 0.273 Chirality : 0.042 0.238 372 Planarity : 0.003 0.032 401 Dihedral : 3.794 18.301 322 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.85 % Allowed : 11.97 % Favored : 87.18 % 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: 1.71 (0.50), residues: 295 helix: 1.98 (0.33), residues: 237 sheet: None (None), residues: 0 loop : -2.62 (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 0.03768 ( 176) hydrogen bonds : angle 4.19816 ( 522) SS BOND : bond 0.00229 ( 1) SS BOND : angle 1.12651 ( 2) covalent geometry : bond 0.00334 ( 2376) covalent geometry : angle 0.51881 ( 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 32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.233 Fit side-chains REVERT: R 39 LEU cc_start: 0.7640 (tp) cc_final: 0.7418 (tt) REVERT: R 181 MET cc_start: 0.7435 (tpt) cc_final: 0.7078 (tpt) REVERT: R 247 ARG cc_start: 0.6538 (mtm110) cc_final: 0.6162 (mtp-110) outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 0.2539 time to fit residues: 8.5834 Evaluate side-chains 29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 166 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 1 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.121039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111562 restraints weight = 2927.842| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.41 r_work: 0.3198 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1726 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= 0.145 Angle : 0.518 6.589 3254 Z= 0.273 Chirality : 0.042 0.248 372 Planarity : 0.003 0.032 401 Dihedral : 3.781 18.144 322 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.28 % Allowed : 13.25 % Favored : 85.47 % 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: 1.97 (0.34), residues: 237 sheet: None (None), residues: 0 loop : -2.64 (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 97 TYR 0.011 0.001 TYR R 102 ARG 0.001 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 176) hydrogen bonds : angle 4.19246 ( 522) SS BOND : bond 0.00258 ( 1) SS BOND : angle 1.07850 ( 2) covalent geometry : bond 0.00342 ( 2376) covalent geometry : angle 0.51758 ( 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 : 0.259 Fit side-chains REVERT: R 39 LEU cc_start: 0.7645 (tp) cc_final: 0.7433 (tt) REVERT: R 181 MET cc_start: 0.7412 (tpt) cc_final: 0.7038 (tpt) REVERT: R 247 ARG cc_start: 0.6556 (mtm110) cc_final: 0.6180 (mtp-110) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.2757 time to fit residues: 8.3582 Evaluate side-chains 28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 166 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.115762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105797 restraints weight = 3080.319| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.59 r_work: 0.3248 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1744 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= 0.155 Angle : 0.530 6.577 3254 Z= 0.279 Chirality : 0.044 0.264 372 Planarity : 0.004 0.032 401 Dihedral : 3.810 18.022 322 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.85 % Allowed : 14.10 % Favored : 85.04 % 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: 1.61 (0.50), residues: 295 helix: 1.91 (0.33), residues: 238 sheet: None (None), residues: 0 loop : -2.73 (0.79), residues: 57 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 0.03835 ( 176) hydrogen bonds : angle 4.21028 ( 522) SS BOND : bond 0.00272 ( 1) SS BOND : angle 1.08713 ( 2) covalent geometry : bond 0.00371 ( 2376) covalent geometry : angle 0.52991 ( 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 26 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.228 Fit side-chains REVERT: R 39 LEU cc_start: 0.7513 (tp) cc_final: 0.7304 (tt) REVERT: R 181 MET cc_start: 0.7350 (tpt) cc_final: 0.6895 (tpt) REVERT: R 247 ARG cc_start: 0.6498 (mtm110) cc_final: 0.6138 (mtp-110) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.2556 time to fit residues: 6.9593 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 : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 166 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.118657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109024 restraints weight = 2860.141| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.46 r_work: 0.3172 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1789 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= 0.138 Angle : 0.516 6.586 3254 Z= 0.272 Chirality : 0.043 0.290 372 Planarity : 0.003 0.031 401 Dihedral : 3.745 17.413 322 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: 1.76 (0.50), residues: 295 helix: 2.00 (0.34), residues: 237 sheet: None (None), residues: 0 loop : -2.54 (0.79), residues: 58 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 0.002 PHE R 169 TYR 0.012 0.001 TYR R 102 ARG 0.001 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 176) hydrogen bonds : angle 4.16862 ( 522) SS BOND : bond 0.00231 ( 1) SS BOND : angle 1.02332 ( 2) covalent geometry : bond 0.00323 ( 2376) covalent geometry : angle 0.51571 ( 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 : 0.257 Fit side-chains REVERT: R 39 LEU cc_start: 0.7581 (tp) cc_final: 0.7376 (tt) REVERT: R 181 MET cc_start: 0.7356 (tpt) cc_final: 0.6898 (tpt) REVERT: R 247 ARG cc_start: 0.6516 (mtm110) cc_final: 0.6153 (mtp-110) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.2567 time to fit residues: 7.0296 Evaluate side-chains 24 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.116314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106848 restraints weight = 2939.948| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.43 r_work: 0.3254 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1801 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= 0.146 Angle : 0.524 6.587 3254 Z= 0.275 Chirality : 0.043 0.305 372 Planarity : 0.004 0.032 401 Dihedral : 3.773 16.564 322 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.43 % Allowed : 15.38 % 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: 1.65 (0.50), residues: 295 helix: 1.92 (0.33), residues: 238 sheet: None (None), residues: 0 loop : -2.64 (0.77), residues: 57 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 0.010 0.002 PHE R 97 TYR 0.013 0.001 TYR R 102 ARG 0.001 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 176) hydrogen bonds : angle 4.17496 ( 522) SS BOND : bond 0.00250 ( 1) SS BOND : angle 0.91698 ( 2) covalent geometry : bond 0.00343 ( 2376) covalent geometry : angle 0.52344 ( 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 25 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.228 Fit side-chains REVERT: R 181 MET cc_start: 0.7421 (tpt) cc_final: 0.6926 (tpt) REVERT: R 247 ARG cc_start: 0.6595 (mtm110) cc_final: 0.6223 (mtp-110) outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.2807 time to fit residues: 7.5335 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 : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.115263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.105241 restraints weight = 2967.280| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.58 r_work: 0.3246 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2377 Z= 0.169 Angle : 0.545 6.581 3254 Z= 0.287 Chirality : 0.045 0.315 372 Planarity : 0.004 0.032 401 Dihedral : 3.865 17.198 322 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.28 % Allowed : 15.38 % 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: 1.54 (0.50), residues: 295 helix: 1.85 (0.33), residues: 238 sheet: None (None), residues: 0 loop : -2.70 (0.76), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 40 HIS 0.006 0.001 HIS R 17 PHE 0.012 0.002 PHE R 97 TYR 0.012 0.002 TYR R 76 ARG 0.001 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 176) hydrogen bonds : angle 4.25213 ( 522) SS BOND : bond 0.00267 ( 1) SS BOND : angle 0.91712 ( 2) covalent geometry : bond 0.00408 ( 2376) covalent geometry : angle 0.54512 ( 3252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1552.73 seconds wall clock time: 27 minutes 44.75 seconds (1664.75 seconds total)