Starting phenix.real_space_refine on Wed Jun 4 10:17:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dgi_46828/06_2025/9dgi_46828_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dgi_46828/06_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_46828/06_2025/9dgi_46828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dgi_46828/06_2025/9dgi_46828.map" model { file = "/net/cci-nas-00/data/ceres_data/9dgi_46828/06_2025/9dgi_46828_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dgi_46828/06_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-5710/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: 2.32, per 1000 atoms: 1.13 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: 0.73 Conformation dependent library (CDL) restraints added in 253.0 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: 0.22 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: 0.35 Time building geometry restraints manager: 0.61 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: 1.340 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: 0.020 Process input model: 10.600 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.690 ------------------------------------------------------------------------------- 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 : 0.238 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: 0.1949 time to fit residues: 11.0700 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 : 0.245 ------------------------------------------------------------------------------- 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: 0.3698 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- 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 : 0.234 Fit side-chains revert: symmetry clash REVERT: R 126 LEU cc_start: 0.8684 (mp) cc_final: 0.8396 (tp) REVERT: R 343 LYS cc_start: 0.8126 (pttp) cc_final: 0.7810 (mttt) outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 0.1088 time to fit residues: 4.8912 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 : 0.226 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.0170 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.162677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.151101 restraints weight = 3649.218| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.95 r_work: 0.3637 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2098 Z= 0.115 Angle : 0.672 7.649 2865 Z= 0.343 Chirality : 0.044 0.176 352 Planarity : 0.007 0.078 339 Dihedral : 10.220 56.186 316 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % 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: -7.11 (0.33), residues: 257 helix: -4.75 (0.20), residues: 181 sheet: None (None), residues: 0 loop : -3.92 (0.57), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 241 HIS 0.003 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 0.02557 ( 31) hydrogen bonds : angle 5.52569 ( 78) covalent geometry : bond 0.00283 ( 2098) covalent geometry : angle 0.67188 ( 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 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.200 Fit side-chains REVERT: R 343 LYS cc_start: 0.8201 (pttp) cc_final: 0.7732 (mttt) outliers start: 8 outliers final: 6 residues processed: 34 average time/residue: 0.1025 time to fit residues: 4.3992 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 : 0.232 ------------------------------------------------------------------------------- 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 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: 0.0770 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 22 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.0170 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.164455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.152995 restraints weight = 3532.526| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.87 r_work: 0.3786 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2631 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= 0.096 Angle : 0.622 7.357 2865 Z= 0.315 Chirality : 0.043 0.146 352 Planarity : 0.006 0.077 339 Dihedral : 8.236 55.257 316 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.43 % Allowed : 12.32 % 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: -6.68 (0.36), residues: 257 helix: -4.65 (0.21), residues: 179 sheet: None (None), residues: 0 loop : -3.18 (0.65), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 356 HIS 0.002 0.001 HIS R 178 PHE 0.011 0.001 PHE R 408 TYR 0.007 0.001 TYR R 294 ARG 0.004 0.000 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.01978 ( 31) hydrogen bonds : angle 5.38926 ( 78) covalent geometry : bond 0.00227 ( 2098) covalent geometry : angle 0.62206 ( 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 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.228 Fit side-chains REVERT: R 343 LYS cc_start: 0.8091 (pttp) cc_final: 0.7877 (mttt) outliers start: 9 outliers final: 5 residues processed: 37 average time/residue: 0.1033 time to fit residues: 4.7774 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 : 0.200 ------------------------------------------------------------------------------- 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: 0.5980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.0000 chunk 17 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.3502 ------------------------------------------------------------------------------- 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 = 0.3899 r_free = 0.3899 target = 0.161509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.149287 restraints weight = 3570.899| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.17 r_work: 0.3767 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2863 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= 0.093 Angle : 0.602 7.359 2865 Z= 0.304 Chirality : 0.042 0.135 352 Planarity : 0.006 0.076 339 Dihedral : 7.714 54.484 316 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 5.42 % Allowed : 11.33 % 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: -6.34 (0.39), residues: 257 helix: -4.47 (0.22), residues: 179 sheet: None (None), residues: 0 loop : -2.84 (0.70), 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 0.009 0.001 PHE R 408 TYR 0.005 0.001 TYR R 294 ARG 0.003 0.000 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.01844 ( 31) hydrogen bonds : angle 5.24812 ( 78) covalent geometry : bond 0.00225 ( 2098) covalent geometry : angle 0.60168 ( 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 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.213 Fit side-chains REVERT: R 297 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7266 (mp) REVERT: R 343 LYS cc_start: 0.8092 (pttp) cc_final: 0.7764 (mttt) outliers start: 11 outliers final: 7 residues processed: 36 average time/residue: 0.1088 time to fit residues: 4.9071 Evaluate side-chains 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 378 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 8 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.0670 chunk 9 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.0470 chunk 1 optimal weight: 0.0770 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.2174 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.166860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155171 restraints weight = 3567.830| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.07 r_work: 0.3685 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 2098 Z= 0.084 Angle : 0.575 7.277 2865 Z= 0.291 Chirality : 0.041 0.133 352 Planarity : 0.006 0.075 339 Dihedral : 7.425 54.527 316 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.43 % Allowed : 13.79 % 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: -6.15 (0.39), residues: 257 helix: -4.14 (0.24), residues: 183 sheet: None (None), residues: 0 loop : -3.20 (0.70), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 294 ARG 0.002 0.000 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.01637 ( 31) hydrogen bonds : angle 5.01644 ( 78) covalent geometry : bond 0.00206 ( 2098) covalent geometry : angle 0.57525 ( 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 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.226 Fit side-chains REVERT: R 297 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7242 (mp) REVERT: R 343 LYS cc_start: 0.8036 (pttp) cc_final: 0.7699 (mttt) outliers start: 9 outliers final: 5 residues processed: 36 average time/residue: 0.1055 time to fit residues: 4.7529 Evaluate side-chains 34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 234 VAL Chi-restraints excluded: chain R residue 267 ILE Chi-restraints excluded: chain R residue 297 ILE 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: 0.0770 chunk 11 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.0060 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.0270 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.2412 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.167955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.156253 restraints weight = 3590.043| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.11 r_work: 0.3753 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 2098 Z= 0.088 Angle : 0.578 7.140 2865 Z= 0.295 Chirality : 0.042 0.132 352 Planarity : 0.006 0.075 339 Dihedral : 7.240 53.897 316 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.93 % Allowed : 13.79 % Favored : 81.28 % 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: -5.84 (0.40), residues: 257 helix: -3.93 (0.26), residues: 183 sheet: None (None), residues: 0 loop : -2.99 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 356 HIS 0.002 0.000 HIS R 178 PHE 0.008 0.001 PHE R 408 TYR 0.004 0.000 TYR R 294 ARG 0.002 0.000 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.01625 ( 31) hydrogen bonds : angle 5.06452 ( 78) covalent geometry : bond 0.00219 ( 2098) covalent geometry : angle 0.57823 ( 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 : 0.234 Fit side-chains REVERT: R 297 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7316 (mp) REVERT: R 343 LYS cc_start: 0.8015 (pttp) cc_final: 0.7788 (mttt) REVERT: R 353 ILE cc_start: 0.8643 (tp) cc_final: 0.8335 (tp) outliers start: 10 outliers final: 8 residues processed: 38 average time/residue: 0.1096 time to fit residues: 5.3169 Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 250 LEU 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 378 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 16 optimal weight: 0.0070 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.0020 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.0170 chunk 22 optimal weight: 1.9990 overall best weight: 0.1822 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.167534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155749 restraints weight = 3613.631| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.17 r_work: 0.3741 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 2098 Z= 0.086 Angle : 0.564 7.201 2865 Z= 0.284 Chirality : 0.041 0.133 352 Planarity : 0.006 0.074 339 Dihedral : 7.126 54.033 316 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.45 % Allowed : 16.26 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.55 (0.42), residues: 257 helix: -3.74 (0.27), residues: 183 sheet: None (None), residues: 0 loop : -2.84 (0.73), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 356 HIS 0.002 0.000 HIS R 178 PHE 0.008 0.001 PHE R 408 TYR 0.003 0.000 TYR R 275 ARG 0.002 0.000 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.01493 ( 31) hydrogen bonds : angle 4.99448 ( 78) covalent geometry : bond 0.00224 ( 2098) covalent geometry : angle 0.56409 ( 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: 7 poor density : 29 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: R 297 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7343 (mp) REVERT: R 353 ILE cc_start: 0.8638 (tp) cc_final: 0.8333 (tp) outliers start: 7 outliers final: 5 residues processed: 35 average time/residue: 0.1300 time to fit residues: 5.4731 Evaluate side-chains 33 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 297 ILE 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: 0.6980 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 5 optimal weight: 0.3980 chunk 23 optimal weight: 0.3980 chunk 21 optimal weight: 0.0040 chunk 16 optimal weight: 0.0980 chunk 3 optimal weight: 0.0000 chunk 10 optimal weight: 0.9980 overall best weight: 0.1154 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.169367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157742 restraints weight = 3672.561| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.18 r_work: 0.3810 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 2098 Z= 0.087 Angle : 0.558 7.270 2865 Z= 0.282 Chirality : 0.041 0.132 352 Planarity : 0.006 0.075 339 Dihedral : 6.914 54.183 316 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.94 % Allowed : 16.26 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.45), residues: 257 helix: -3.45 (0.30), residues: 179 sheet: None (None), residues: 0 loop : -2.35 (0.75), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP R 356 HIS 0.001 0.000 HIS R 181 PHE 0.007 0.001 PHE R 408 TYR 0.003 0.000 TYR R 294 ARG 0.002 0.000 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.01458 ( 31) hydrogen bonds : angle 4.84780 ( 78) covalent geometry : bond 0.00232 ( 2098) covalent geometry : angle 0.55835 ( 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 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: R 353 ILE cc_start: 0.8592 (tp) cc_final: 0.8304 (tp) outliers start: 8 outliers final: 5 residues processed: 37 average time/residue: 0.1215 time to fit residues: 5.5059 Evaluate side-chains 34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 378 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 8 optimal weight: 0.0470 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.163868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.152315 restraints weight = 3528.926| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.10 r_work: 0.3774 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 2098 Z= 0.105 Angle : 0.606 7.252 2865 Z= 0.300 Chirality : 0.042 0.132 352 Planarity : 0.006 0.073 339 Dihedral : 7.123 52.870 316 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.96 % Allowed : 18.72 % Favored : 78.33 % 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: -5.09 (0.45), residues: 257 helix: -3.51 (0.28), residues: 184 sheet: None (None), residues: 0 loop : -2.25 (0.81), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 356 HIS 0.003 0.001 HIS R 178 PHE 0.008 0.001 PHE R 237 TYR 0.006 0.001 TYR R 275 ARG 0.002 0.000 ARG R 148 Details of bonding type rmsd hydrogen bonds : bond 0.01768 ( 31) hydrogen bonds : angle 5.25155 ( 78) covalent geometry : bond 0.00284 ( 2098) covalent geometry : angle 0.60563 ( 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 34 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.233 Fit side-chains REVERT: R 191 PHE cc_start: 0.5717 (t80) cc_final: 0.4078 (m-10) REVERT: R 353 ILE cc_start: 0.8622 (tp) cc_final: 0.8330 (tp) outliers start: 6 outliers final: 5 residues processed: 33 average time/residue: 0.1012 time to fit residues: 4.3008 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 : 0.242 ------------------------------------------------------------------------------- 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 378 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 16 optimal weight: 0.0670 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.0270 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.0870 chunk 17 optimal weight: 0.2980 chunk 24 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 overall best weight: 0.1152 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.168417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.156601 restraints weight = 3567.455| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.12 r_work: 0.3810 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 2098 Z= 0.091 Angle : 0.578 7.441 2865 Z= 0.282 Chirality : 0.041 0.136 352 Planarity : 0.006 0.073 339 Dihedral : 6.935 54.435 316 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.97 % Allowed : 19.70 % Favored : 78.33 % 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: -4.71 (0.47), residues: 257 helix: -3.24 (0.31), residues: 181 sheet: None (None), residues: 0 loop : -2.18 (0.78), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 356 HIS 0.001 0.000 HIS R 178 PHE 0.007 0.001 PHE R 408 TYR 0.003 0.000 TYR R 275 ARG 0.002 0.000 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.01401 ( 31) hydrogen bonds : angle 5.03332 ( 78) covalent geometry : bond 0.00260 ( 2098) covalent geometry : angle 0.57836 ( 2865) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1618.75 seconds wall clock time: 28 minutes 37.10 seconds (1717.10 seconds total)