Starting phenix.real_space_refine on Fri May 9 13:16:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dgi_46828/05_2025/9dgi_46828_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dgi_46828/05_2025/9dgi_46828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dgi_46828/05_2025/9dgi_46828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dgi_46828/05_2025/9dgi_46828.map" model { file = "/net/cci-nas-00/data/ceres_data/9dgi_46828/05_2025/9dgi_46828_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dgi_46828/05_2025/9dgi_46828_neut.cif" } resolution = 3.35 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= -0.002 sd= 0.047 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: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 1370 2.51 5 N 338 2.21 5 O 323 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2048 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2018 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'YVF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.59, per 1000 atoms: 1.26 Number of scatterers: 2048 At special positions: 0 Unit cell: (58.7949, 66.4638, 82.6537, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 F 3 9.00 O 323 8.00 N 338 7.00 C 1370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.51 Conformation dependent library (CDL) restraints added in 226.5 milliseconds 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 510 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 38.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 118 through 123 Processing helix chain 'R' and resid 128 through 135 removed outlier: 3.522A pdb=" N ASN R 134 " --> pdb=" O THR R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 140 Processing helix chain 'R' and resid 168 through 178 removed outlier: 3.826A pdb=" N ILE R 175 " --> pdb=" O VAL R 171 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP R 176 " --> pdb=" O TYR R 172 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 193 removed outlier: 3.702A pdb=" N LYS R 192 " --> pdb=" O VAL R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 198 removed outlier: 3.687A pdb=" N ALA R 198 " --> pdb=" O GLY R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 214 removed outlier: 3.660A pdb=" N ARG R 214 " --> pdb=" O THR R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 233 removed outlier: 3.537A pdb=" N ALA R 233 " --> pdb=" O ARG R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 242 removed outlier: 3.703A pdb=" N TRP R 241 " --> pdb=" O PHE R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 284 Processing helix chain 'R' and resid 296 through 311 removed outlier: 4.197A pdb=" N HIS R 302 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA R 305 " --> pdb=" O ALA R 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL R 306 " --> pdb=" O HIS R 302 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG R 307 " --> pdb=" O SER R 303 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET R 308 " --> pdb=" O HIS R 304 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE R 309 " --> pdb=" O ALA R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 366 removed outlier: 4.303A pdb=" N VAL R 364 " --> pdb=" O LEU R 360 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP R 366 " --> pdb=" O ILE R 362 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 388 removed outlier: 3.598A pdb=" N CYS R 386 " --> pdb=" O SER R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 397 31 hydrogen bonds defined for protein. 78 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: 0.37 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 286 1.31 - 1.44: 609 1.44 - 1.57: 1181 1.57 - 1.69: 2 1.69 - 1.82: 20 Bond restraints: 2098 Sorted by residual: bond pdb=" C05 YVF R 501 " pdb=" S09 YVF R 501 " ideal model delta sigma weight residual 1.722 1.611 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C12 YVF R 501 " pdb=" N11 YVF R 501 " ideal model delta sigma weight residual 1.345 1.454 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C06 YVF R 501 " pdb=" C07 YVF R 501 " ideal model delta sigma weight residual 1.420 1.521 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C08 YVF R 501 " pdb=" S09 YVF R 501 " ideal model delta sigma weight residual 1.710 1.615 0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C03 YVF R 501 " pdb=" O02 YVF R 501 " ideal model delta sigma weight residual 1.318 1.396 -0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 2093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 2715 2.86 - 5.71: 113 5.71 - 8.57: 28 8.57 - 11.43: 8 11.43 - 14.29: 1 Bond angle restraints: 2865 Sorted by residual: angle pdb=" N VAL R 249 " pdb=" CA VAL R 249 " pdb=" C VAL R 249 " ideal model delta sigma weight residual 113.43 103.97 9.46 1.09e+00 8.42e-01 7.53e+01 angle pdb=" N VAL R 291 " pdb=" CA VAL R 291 " pdb=" C VAL R 291 " ideal model delta sigma weight residual 112.29 105.80 6.49 9.40e-01 1.13e+00 4.77e+01 angle pdb=" N VAL R 351 " pdb=" CA VAL R 351 " pdb=" C VAL R 351 " ideal model delta sigma weight residual 113.10 106.44 6.66 9.70e-01 1.06e+00 4.71e+01 angle pdb=" N ILE R 218 " pdb=" CA ILE R 218 " pdb=" C ILE R 218 " ideal model delta sigma weight residual 113.53 107.73 5.80 9.80e-01 1.04e+00 3.51e+01 angle pdb=" N SER R 390 " pdb=" CA SER R 390 " pdb=" C SER R 390 " ideal model delta sigma weight residual 114.75 108.40 6.35 1.26e+00 6.30e-01 2.54e+01 ... (remaining 2860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 1139 15.70 - 31.40: 63 31.40 - 47.09: 18 47.09 - 62.79: 2 62.79 - 78.49: 6 Dihedral angle restraints: 1228 sinusoidal: 447 harmonic: 781 Sorted by residual: dihedral pdb=" CA VAL R 179 " pdb=" C VAL R 179 " pdb=" N PHE R 180 " pdb=" CA PHE R 180 " ideal model delta harmonic sigma weight residual -180.00 -134.23 -45.77 0 5.00e+00 4.00e-02 8.38e+01 dihedral pdb=" CA PHE R 180 " pdb=" C PHE R 180 " pdb=" N HIS R 181 " pdb=" CA HIS R 181 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA LEU R 288 " pdb=" C LEU R 288 " pdb=" N PHE R 289 " pdb=" CA PHE R 289 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 1225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 204 0.049 - 0.098: 102 0.098 - 0.146: 33 0.146 - 0.195: 8 0.195 - 0.244: 5 Chirality restraints: 352 Sorted by residual: chirality pdb=" CB ILE R 245 " pdb=" CA ILE R 245 " pdb=" CG1 ILE R 245 " pdb=" CG2 ILE R 245 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE R 354 " pdb=" CA ILE R 354 " pdb=" CG1 ILE R 354 " pdb=" CG2 ILE R 354 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE R 216 " pdb=" CA ILE R 216 " pdb=" CG1 ILE R 216 " pdb=" CG2 ILE R 216 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 349 not shown) Planarity restraints: 339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 250 " 0.056 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO R 251 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO R 251 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 251 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 357 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.40e+00 pdb=" N PRO R 358 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO R 358 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 358 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 230 " -0.042 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO R 231 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO R 231 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 231 " -0.035 5.00e-02 4.00e+02 ... (remaining 336 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 842 2.95 - 3.44: 1674 3.44 - 3.92: 2935 3.92 - 4.41: 3093 4.41 - 4.90: 5508 Nonbonded interactions: 14052 Sorted by model distance: nonbonded pdb=" N VAL R 249 " pdb=" N LEU R 250 " model vdw 2.462 2.560 nonbonded pdb=" ND1 HIS R 302 " pdb=" OD2 ASP R 338 " model vdw 2.488 3.120 nonbonded pdb=" O SER R 167 " pdb=" OG SER R 167 " model vdw 2.492 3.040 nonbonded pdb=" N VAL R 179 " pdb=" O VAL R 179 " model vdw 2.509 2.496 nonbonded pdb=" O SER R 401 " pdb=" NH1 ARG R 405 " model vdw 2.511 3.120 ... (remaining 14047 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: 1.350 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.480 Find NCS groups from input model: 0.010 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 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 : 0.008 0.111 2098 Z= 0.397 Angle : 1.475 14.287 2865 Z= 0.854 Chirality : 0.068 0.244 352 Planarity : 0.010 0.084 339 Dihedral : 13.491 78.487 718 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.12 % Favored : 89.49 % Rotamer: Outliers : 0.99 % Allowed : 3.94 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -8.28 (0.19), residues: 257 helix: -5.32 (0.09), residues: 186 sheet: None (None), residues: 0 loop : -5.15 (0.41), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP R 241 HIS 0.004 0.001 HIS R 178 PHE 0.020 0.002 PHE R 237 TYR 0.028 0.002 TYR R 294 ARG 0.006 0.001 ARG R 226 Details of bonding type rmsd hydrogen bonds : bond 0.35561 ( 31) hydrogen bonds : angle 10.18264 ( 78) covalent geometry : bond 0.00811 ( 2098) covalent geometry : angle 1.47518 ( 2865) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.237 Fit side-chains REVERT: R 126 LEU cc_start: 0.8646 (mp) cc_final: 0.8322 (tp) REVERT: R 191 PHE cc_start: 0.6109 (t80) cc_final: 0.4545 (m-10) REVERT: R 297 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7597 (mp) REVERT: R 343 LYS cc_start: 0.8012 (pttp) cc_final: 0.7803 (mttt) outliers start: 2 outliers final: 0 residues processed: 50 average time/residue: 0.1872 time to fit residues: 10.5021 Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 297 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.0070 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.0570 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.165767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.154058 restraints weight = 3613.782| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.91 r_work: 0.3788 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2098 Z= 0.109 Angle : 0.715 9.023 2865 Z= 0.368 Chirality : 0.044 0.176 352 Planarity : 0.007 0.077 339 Dihedral : 12.325 60.821 318 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.48 % Allowed : 9.36 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -7.59 (0.28), residues: 257 helix: -4.97 (0.17), residues: 178 sheet: None (None), residues: 0 loop : -4.58 (0.48), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 241 HIS 0.002 0.001 HIS R 178 PHE 0.016 0.001 PHE R 408 TYR 0.012 0.001 TYR R 294 ARG 0.006 0.001 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 31) hydrogen bonds : angle 5.76797 ( 78) covalent geometry : bond 0.00250 ( 2098) covalent geometry : angle 0.71452 ( 2865) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: R 126 LEU cc_start: 0.8686 (mp) cc_final: 0.8400 (tp) REVERT: R 343 LYS cc_start: 0.8126 (pttp) cc_final: 0.7812 (mttt) outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 0.1075 time to fit residues: 4.8723 Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 285 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.0670 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.163410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.151956 restraints weight = 3639.681| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.93 r_work: 0.3648 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2098 Z= 0.117 Angle : 0.672 7.426 2865 Z= 0.343 Chirality : 0.044 0.174 352 Planarity : 0.007 0.078 339 Dihedral : 10.208 56.183 316 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 3.94 % Allowed : 11.82 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -7.12 (0.33), residues: 257 helix: -4.76 (0.20), residues: 182 sheet: None (None), residues: 0 loop : -3.89 (0.58), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 241 HIS 0.002 0.001 HIS R 178 PHE 0.013 0.001 PHE R 408 TYR 0.011 0.001 TYR R 294 ARG 0.003 0.000 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.02665 ( 31) hydrogen bonds : angle 5.53634 ( 78) covalent geometry : bond 0.00287 ( 2098) covalent geometry : angle 0.67191 ( 2865) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.225 Fit side-chains REVERT: R 343 LYS cc_start: 0.8202 (pttp) cc_final: 0.7755 (mttt) outliers start: 8 outliers final: 6 residues processed: 35 average time/residue: 0.1284 time to fit residues: 5.4617 Evaluate side-chains 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 410 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.0770 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.165066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.153725 restraints weight = 3535.862| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.86 r_work: 0.3795 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 2098 Z= 0.094 Angle : 0.623 7.380 2865 Z= 0.316 Chirality : 0.043 0.154 352 Planarity : 0.007 0.077 339 Dihedral : 8.249 55.349 316 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.96 % Allowed : 13.79 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -6.66 (0.36), residues: 257 helix: -4.63 (0.21), residues: 179 sheet: None (None), residues: 0 loop : -3.19 (0.65), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 356 HIS 0.002 0.001 HIS R 181 PHE 0.010 0.001 PHE R 268 TYR 0.006 0.001 TYR R 294 ARG 0.004 0.001 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.01896 ( 31) hydrogen bonds : angle 5.33556 ( 78) covalent geometry : bond 0.00223 ( 2098) covalent geometry : angle 0.62350 ( 2865) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.219 Fit side-chains REVERT: R 343 LYS cc_start: 0.8093 (pttp) cc_final: 0.7875 (mttt) outliers start: 6 outliers final: 5 residues processed: 33 average time/residue: 0.1097 time to fit residues: 4.5180 Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 250 LEU Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 291 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.158108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146281 restraints weight = 3639.308| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.00 r_work: 0.3608 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2098 Z= 0.144 Angle : 0.661 7.408 2865 Z= 0.334 Chirality : 0.044 0.130 352 Planarity : 0.007 0.075 339 Dihedral : 8.400 54.087 316 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 6.40 % Allowed : 11.82 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -6.53 (0.37), residues: 257 helix: -4.56 (0.22), residues: 180 sheet: None (None), residues: 0 loop : -3.02 (0.68), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 241 HIS 0.003 0.001 HIS R 219 PHE 0.011 0.001 PHE R 177 TYR 0.010 0.001 TYR R 294 ARG 0.003 0.001 ARG R 409 Details of bonding type rmsd hydrogen bonds : bond 0.02431 ( 31) hydrogen bonds : angle 5.75319 ( 78) covalent geometry : bond 0.00351 ( 2098) covalent geometry : angle 0.66092 ( 2865) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.220 Fit side-chains REVERT: R 191 PHE cc_start: 0.5956 (t80) cc_final: 0.4234 (m-10) REVERT: R 297 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7255 (mp) REVERT: R 343 LYS cc_start: 0.8167 (pttp) cc_final: 0.7788 (mttt) REVERT: R 353 ILE cc_start: 0.8682 (tp) cc_final: 0.8348 (tp) outliers start: 13 outliers final: 8 residues processed: 41 average time/residue: 0.1083 time to fit residues: 5.5278 Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 360 LEU Chi-restraints excluded: chain R residue 378 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.0670 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.159893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.148424 restraints weight = 3661.057| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.94 r_work: 0.3736 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2098 Z= 0.137 Angle : 0.647 7.372 2865 Z= 0.329 Chirality : 0.044 0.135 352 Planarity : 0.007 0.074 339 Dihedral : 8.285 54.468 316 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 6.40 % Allowed : 13.79 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -6.38 (0.38), residues: 257 helix: -4.48 (0.22), residues: 180 sheet: None (None), residues: 0 loop : -2.86 (0.69), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 241 HIS 0.003 0.001 HIS R 219 PHE 0.010 0.001 PHE R 177 TYR 0.009 0.001 TYR R 294 ARG 0.003 0.001 ARG R 311 Details of bonding type rmsd hydrogen bonds : bond 0.02305 ( 31) hydrogen bonds : angle 5.79845 ( 78) covalent geometry : bond 0.00337 ( 2098) covalent geometry : angle 0.64730 ( 2865) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: R 191 PHE cc_start: 0.6086 (t80) cc_final: 0.4453 (m-10) REVERT: R 297 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7423 (mp) REVERT: R 353 ILE cc_start: 0.8832 (tp) cc_final: 0.8503 (tp) outliers start: 13 outliers final: 10 residues processed: 41 average time/residue: 0.1057 time to fit residues: 5.4747 Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 291 VAL Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 378 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 3 optimal weight: 0.0470 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.0370 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.162782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.151450 restraints weight = 3647.476| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.94 r_work: 0.3747 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 2098 Z= 0.094 Angle : 0.598 8.220 2865 Z= 0.301 Chirality : 0.042 0.140 352 Planarity : 0.006 0.075 339 Dihedral : 7.638 55.630 316 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 4.93 % Allowed : 16.26 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -6.05 (0.41), residues: 257 helix: -4.29 (0.24), residues: 179 sheet: None (None), residues: 0 loop : -2.64 (0.73), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 356 HIS 0.002 0.000 HIS R 178 PHE 0.008 0.001 PHE R 408 TYR 0.009 0.001 TYR R 292 ARG 0.002 0.000 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.01697 ( 31) hydrogen bonds : angle 5.44741 ( 78) covalent geometry : bond 0.00239 ( 2098) covalent geometry : angle 0.59825 ( 2865) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.216 Fit side-chains REVERT: R 297 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7440 (mp) REVERT: R 353 ILE cc_start: 0.8818 (tp) cc_final: 0.8536 (tp) outliers start: 10 outliers final: 6 residues processed: 37 average time/residue: 0.0878 time to fit residues: 4.1354 Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 378 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.0000 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 18 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.162162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.150341 restraints weight = 3653.795| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.19 r_work: 0.3611 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 2098 Z= 0.107 Angle : 0.621 7.324 2865 Z= 0.314 Chirality : 0.043 0.137 352 Planarity : 0.006 0.074 339 Dihedral : 7.639 54.290 316 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 4.93 % Allowed : 17.24 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -5.88 (0.42), residues: 257 helix: -4.20 (0.24), residues: 180 sheet: None (None), residues: 0 loop : -2.40 (0.77), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 356 HIS 0.002 0.001 HIS R 178 PHE 0.009 0.001 PHE R 237 TYR 0.005 0.001 TYR R 275 ARG 0.002 0.000 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.01900 ( 31) hydrogen bonds : angle 5.58792 ( 78) covalent geometry : bond 0.00270 ( 2098) covalent geometry : angle 0.62139 ( 2865) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: R 297 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7200 (mp) REVERT: R 353 ILE cc_start: 0.8705 (tp) cc_final: 0.8419 (tp) outliers start: 10 outliers final: 8 residues processed: 35 average time/residue: 0.0953 time to fit residues: 4.2914 Evaluate side-chains 34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 25 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 378 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.0070 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.0060 chunk 16 optimal weight: 0.0980 chunk 3 optimal weight: 0.0670 chunk 10 optimal weight: 0.9990 overall best weight: 0.0552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.162427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.150489 restraints weight = 3716.957| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.28 r_work: 0.3783 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 2098 Z= 0.092 Angle : 0.584 7.579 2865 Z= 0.293 Chirality : 0.041 0.139 352 Planarity : 0.006 0.076 339 Dihedral : 7.212 56.532 316 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.97 % Allowed : 20.20 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -5.23 (0.45), residues: 257 helix: -3.71 (0.27), residues: 177 sheet: None (None), residues: 0 loop : -2.27 (0.77), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP R 356 HIS 0.002 0.000 HIS R 181 PHE 0.007 0.001 PHE R 408 TYR 0.002 0.000 TYR R 292 ARG 0.003 0.000 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.01392 ( 31) hydrogen bonds : angle 5.17656 ( 78) covalent geometry : bond 0.00242 ( 2098) covalent geometry : angle 0.58419 ( 2865) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.226 Fit side-chains REVERT: R 353 ILE cc_start: 0.8665 (tp) cc_final: 0.8405 (tp) outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.0996 time to fit residues: 3.8699 Evaluate side-chains 29 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 359 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.3980 chunk 14 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.157788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145709 restraints weight = 3584.132| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.26 r_work: 0.3689 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 2098 Z= 0.117 Angle : 0.615 7.358 2865 Z= 0.305 Chirality : 0.044 0.156 352 Planarity : 0.006 0.074 339 Dihedral : 7.437 53.370 316 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.96 % Allowed : 19.21 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -5.42 (0.44), residues: 257 helix: -3.86 (0.26), residues: 182 sheet: None (None), residues: 0 loop : -2.14 (0.80), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 356 HIS 0.003 0.001 HIS R 178 PHE 0.009 0.001 PHE R 237 TYR 0.006 0.001 TYR R 296 ARG 0.003 0.000 ARG R 148 Details of bonding type rmsd hydrogen bonds : bond 0.01911 ( 31) hydrogen bonds : angle 5.63225 ( 78) covalent geometry : bond 0.00314 ( 2098) covalent geometry : angle 0.61460 ( 2865) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 514 Ramachandran restraints generated. 257 Oldfield, 0 Emsley, 257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: R 353 ILE cc_start: 0.8658 (tp) cc_final: 0.8370 (tp) outliers start: 6 outliers final: 5 residues processed: 30 average time/residue: 0.0891 time to fit residues: 3.4747 Evaluate side-chains 29 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 378 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.0000 chunk 23 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.0040 chunk 0 optimal weight: 1.9990 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.164841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153171 restraints weight = 3650.191| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.18 r_work: 0.3763 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 2098 Z= 0.092 Angle : 0.576 7.656 2865 Z= 0.283 Chirality : 0.042 0.140 352 Planarity : 0.006 0.075 339 Dihedral : 7.226 55.227 316 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.94 % Allowed : 18.23 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -5.13 (0.45), residues: 257 helix: -3.63 (0.28), residues: 181 sheet: None (None), residues: 0 loop : -2.12 (0.80), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 356 HIS 0.001 0.000 HIS R 178 PHE 0.008 0.001 PHE R 408 TYR 0.004 0.001 TYR R 275 ARG 0.002 0.000 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.01594 ( 31) hydrogen bonds : angle 5.49323 ( 78) covalent geometry : bond 0.00263 ( 2098) covalent geometry : angle 0.57597 ( 2865) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1584.93 seconds wall clock time: 28 minutes 25.36 seconds (1705.36 seconds total)