Starting phenix.real_space_refine on Fri Aug 22 14:04:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k2w_36841/08_2025/8k2w_36841.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k2w_36841/08_2025/8k2w_36841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k2w_36841/08_2025/8k2w_36841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k2w_36841/08_2025/8k2w_36841.map" model { file = "/net/cci-nas-00/data/ceres_data/8k2w_36841/08_2025/8k2w_36841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k2w_36841/08_2025/8k2w_36841.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.152 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 18 5.16 5 C 2063 2.51 5 N 525 2.21 5 O 532 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3143 Number of models: 1 Model: "" Number of chains: 3 Chain: "N" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 2 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2223 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain: "R" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 157 Unusual residues: {'CLR': 1, 'FI6': 1, 'LPC': 1, 'PCW': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.31, per 1000 atoms: 0.42 Number of scatterers: 3143 At special positions: 0 Unit cell: (68.85, 53.55, 118.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 2 15.00 F 3 9.00 O 532 8.00 N 525 7.00 C 2063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 104.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 716 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 3 sheets defined 63.0% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'R' and resid 55 through 81 removed outlier: 4.001A pdb=" N ARG R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 104 Processing helix chain 'R' and resid 105 through 115 removed outlier: 3.600A pdb=" N TRP R 109 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 155 removed outlier: 3.892A pdb=" N PHE R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA R 139 " --> pdb=" O PHE R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 189 removed outlier: 3.526A pdb=" N THR R 171 " --> pdb=" O ARG R 167 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE R 182 " --> pdb=" O LEU R 178 " (cutoff:3.500A) Proline residue: R 185 - end of helix Processing helix chain 'R' and resid 208 through 244 removed outlier: 3.738A pdb=" N ALA R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Proline residue: R 227 - end of helix removed outlier: 4.063A pdb=" N SER R 244 " --> pdb=" O ALA R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 292 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 297 through 330 removed outlier: 4.259A pdb=" N ARG R 303 " --> pdb=" O GLY R 299 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL R 304 " --> pdb=" O ARG R 300 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL R 306 " --> pdb=" O SER R 302 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N CYS R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N CYS R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 338 removed outlier: 3.790A pdb=" N ARG R 334 " --> pdb=" O GLY R 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.514A pdb=" N SER N 27 " --> pdb=" O GLN N 5 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU N 22 " --> pdb=" O LEU N 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 59 through 61 removed outlier: 3.788A pdb=" N ALA N 51 " --> pdb=" O TRP N 38 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG N 32 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU N 100 " --> pdb=" O TYR N 34 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET N 36 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN N 98 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP N 38 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR N 96 " --> pdb=" O TRP N 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 59 through 61 removed outlier: 3.788A pdb=" N ALA N 51 " --> pdb=" O TRP N 38 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG N 32 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU N 100 " --> pdb=" O TYR N 34 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET N 36 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN N 98 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TRP N 38 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR N 96 " --> pdb=" O TRP N 38 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 609 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: 0.31 Time building geometry restraints manager: 0.34 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: 458 1.31 - 1.43: 907 1.43 - 1.56: 1818 1.56 - 1.68: 5 1.68 - 1.81: 24 Bond restraints: 3212 Sorted by residual: bond pdb=" C19 PCW R 402 " pdb=" C20 PCW R 402 " ideal model delta sigma weight residual 1.333 1.530 -0.197 2.00e-02 2.50e+03 9.70e+01 bond pdb=" C39 PCW R 402 " pdb=" C40 PCW R 402 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" C11 PCW R 402 " pdb=" O3 PCW R 402 " ideal model delta sigma weight residual 1.326 1.414 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C31 PCW R 402 " pdb=" O2 PCW R 402 " ideal model delta sigma weight residual 1.333 1.403 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N PCW R 402 " pdb=" C6 PCW R 402 " ideal model delta sigma weight residual 1.489 1.439 0.050 2.00e-02 2.50e+03 6.24e+00 ... (remaining 3207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 4299 3.00 - 6.00: 54 6.00 - 9.00: 5 9.00 - 12.00: 2 12.00 - 15.00: 5 Bond angle restraints: 4365 Sorted by residual: angle pdb=" C19 PCW R 402 " pdb=" C20 PCW R 402 " pdb=" C21 PCW R 402 " ideal model delta sigma weight residual 127.82 112.82 15.00 3.00e+00 1.11e-01 2.50e+01 angle pdb=" C18 PCW R 402 " pdb=" C19 PCW R 402 " pdb=" C20 PCW R 402 " ideal model delta sigma weight residual 127.82 112.95 14.87 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C38 PCW R 402 " pdb=" C39 PCW R 402 " pdb=" C40 PCW R 402 " ideal model delta sigma weight residual 127.57 112.87 14.70 3.00e+00 1.11e-01 2.40e+01 angle pdb=" C39 PCW R 402 " pdb=" C40 PCW R 402 " pdb=" C41 PCW R 402 " ideal model delta sigma weight residual 127.60 113.22 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O3P PCW R 402 " pdb=" P PCW R 402 " pdb=" O4P PCW R 402 " ideal model delta sigma weight residual 96.85 110.25 -13.40 3.00e+00 1.11e-01 1.99e+01 ... (remaining 4360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.51: 1893 34.51 - 69.03: 43 69.03 - 103.54: 4 103.54 - 138.05: 0 138.05 - 172.57: 1 Dihedral angle restraints: 1941 sinusoidal: 826 harmonic: 1115 Sorted by residual: dihedral pdb=" CB CYS R 124 " pdb=" SG CYS R 124 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual -86.00 -175.94 89.94 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" C2 PCW R 402 " pdb=" C31 PCW R 402 " pdb=" O2 PCW R 402 " pdb=" C32 PCW R 402 " ideal model delta sinusoidal sigma weight residual 175.43 -12.00 -172.57 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA LEU R 294 " pdb=" C LEU R 294 " pdb=" N ALA R 295 " pdb=" CA ALA R 295 " ideal model delta harmonic sigma weight residual -180.00 -165.41 -14.59 0 5.00e+00 4.00e-02 8.51e+00 ... (remaining 1938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 360 0.039 - 0.079: 109 0.079 - 0.118: 30 0.118 - 0.157: 3 0.157 - 0.196: 1 Chirality restraints: 503 Sorted by residual: chirality pdb=" C2 PCW R 402 " pdb=" C1 PCW R 402 " pdb=" C3 PCW R 402 " pdb=" O2 PCW R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA VAL R 245 " pdb=" N VAL R 245 " pdb=" C VAL R 245 " pdb=" CB VAL R 245 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA LEU R 106 " pdb=" N LEU R 106 " pdb=" C LEU R 106 " pdb=" CB LEU R 106 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 500 not shown) Planarity restraints: 522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 PCW R 402 " -0.318 2.00e-02 2.50e+03 3.16e-01 1.00e+03 pdb=" C19 PCW R 402 " 0.321 2.00e-02 2.50e+03 pdb=" C20 PCW R 402 " 0.311 2.00e-02 2.50e+03 pdb=" C21 PCW R 402 " -0.315 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 PCW R 402 " 0.198 2.00e-02 2.50e+03 1.98e-01 3.91e+02 pdb=" C39 PCW R 402 " -0.197 2.00e-02 2.50e+03 pdb=" C40 PCW R 402 " -0.198 2.00e-02 2.50e+03 pdb=" C41 PCW R 402 " 0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 FI6 R 404 " -0.075 2.00e-02 2.50e+03 7.99e-02 9.58e+01 pdb=" C18 FI6 R 404 " 0.109 2.00e-02 2.50e+03 pdb=" C24 FI6 R 404 " -0.031 2.00e-02 2.50e+03 pdb=" C25 FI6 R 404 " 0.110 2.00e-02 2.50e+03 pdb=" N4 FI6 R 404 " -0.031 2.00e-02 2.50e+03 pdb=" O3 FI6 R 404 " -0.082 2.00e-02 2.50e+03 ... (remaining 519 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 834 2.82 - 3.34: 2889 3.34 - 3.86: 4933 3.86 - 4.38: 5486 4.38 - 4.90: 9812 Nonbonded interactions: 23954 Sorted by model distance: nonbonded pdb=" O ALA R 273 " pdb=" OG1 THR R 277 " model vdw 2.294 3.040 nonbonded pdb=" NH2 ARG R 216 " pdb=" OD2 ASP R 290 " model vdw 2.314 3.120 nonbonded pdb=" OG SER R 191 " pdb=" OD1 ASN R 206 " model vdw 2.347 3.040 nonbonded pdb=" O SER R 244 " pdb=" OG SER R 244 " model vdw 2.348 3.040 nonbonded pdb=" OG SER R 309 " pdb=" O3 FI6 R 404 " model vdw 2.393 3.040 ... (remaining 23949 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.180 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:8.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.007 0.197 3214 Z= 0.329 Angle : 0.895 15.004 4369 Z= 0.367 Chirality : 0.040 0.196 503 Planarity : 0.017 0.316 522 Dihedral : 15.069 172.568 1219 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.45), residues: 378 helix: 1.50 (0.36), residues: 222 sheet: 0.17 (0.77), residues: 53 loop : -1.58 (0.61), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 259 TYR 0.010 0.001 TYR R 235 PHE 0.016 0.001 PHE R 207 TRP 0.005 0.001 TRP N 106 HIS 0.003 0.001 HIS R 193 Details of bonding type rmsd covalent geometry : bond 0.00661 ( 3212) covalent geometry : angle 0.89554 ( 4365) SS BOND : bond 0.00174 ( 2) SS BOND : angle 0.44127 ( 4) hydrogen bonds : bond 0.13550 ( 202) hydrogen bonds : angle 5.47258 ( 609) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.126 Fit side-chains REVERT: N 98 ASN cc_start: 0.7673 (t0) cc_final: 0.7254 (t0) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.3909 time to fit residues: 15.1173 Evaluate side-chains 30 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.182357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124626 restraints weight = 3057.979| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.15 r_work: 0.3290 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3214 Z= 0.174 Angle : 0.645 8.235 4369 Z= 0.312 Chirality : 0.041 0.145 503 Planarity : 0.004 0.026 522 Dihedral : 13.487 149.246 589 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.93 % Allowed : 11.58 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.44), residues: 378 helix: 1.19 (0.35), residues: 228 sheet: 0.59 (0.79), residues: 54 loop : -2.36 (0.56), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 259 TYR 0.014 0.002 TYR N 34 PHE 0.022 0.002 PHE R 207 TRP 0.006 0.001 TRP N 38 HIS 0.004 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 3212) covalent geometry : angle 0.64453 ( 4365) SS BOND : bond 0.00376 ( 2) SS BOND : angle 0.64857 ( 4) hydrogen bonds : bond 0.06038 ( 202) hydrogen bonds : angle 4.49665 ( 609) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.076 Fit side-chains REVERT: N 98 ASN cc_start: 0.7603 (t0) cc_final: 0.6997 (t0) REVERT: R 231 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7628 (mmt) REVERT: R 281 LEU cc_start: 0.8238 (mm) cc_final: 0.8029 (mt) REVERT: R 303 ARG cc_start: 0.7050 (mmt180) cc_final: 0.6687 (mmp-170) outliers start: 6 outliers final: 3 residues processed: 36 average time/residue: 0.5163 time to fit residues: 19.1873 Evaluate side-chains 35 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.182924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125589 restraints weight = 3067.996| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.14 r_work: 0.3291 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3214 Z= 0.137 Angle : 0.554 6.664 4369 Z= 0.273 Chirality : 0.038 0.135 503 Planarity : 0.003 0.028 522 Dihedral : 12.840 135.713 589 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.89 % Allowed : 14.15 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.45), residues: 378 helix: 1.41 (0.35), residues: 226 sheet: 0.61 (0.77), residues: 54 loop : -2.17 (0.58), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 259 TYR 0.010 0.001 TYR R 235 PHE 0.020 0.001 PHE R 207 TRP 0.005 0.001 TRP N 38 HIS 0.003 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3212) covalent geometry : angle 0.55428 ( 4365) SS BOND : bond 0.00305 ( 2) SS BOND : angle 0.58502 ( 4) hydrogen bonds : bond 0.05330 ( 202) hydrogen bonds : angle 4.28969 ( 609) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.115 Fit side-chains REVERT: N 98 ASN cc_start: 0.7698 (t0) cc_final: 0.7038 (t0) REVERT: R 231 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7614 (mmt) outliers start: 9 outliers final: 4 residues processed: 37 average time/residue: 0.3112 time to fit residues: 12.1764 Evaluate side-chains 32 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.179249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.122398 restraints weight = 3056.267| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.12 r_work: 0.3247 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3214 Z= 0.170 Angle : 0.611 7.139 4369 Z= 0.299 Chirality : 0.041 0.149 503 Planarity : 0.004 0.029 522 Dihedral : 12.893 134.577 589 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.22 % Allowed : 16.08 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.44), residues: 378 helix: 1.22 (0.34), residues: 229 sheet: 0.53 (0.77), residues: 54 loop : -2.53 (0.55), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 259 TYR 0.012 0.001 TYR R 235 PHE 0.021 0.002 PHE R 207 TRP 0.005 0.001 TRP N 38 HIS 0.003 0.001 HIS R 155 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3212) covalent geometry : angle 0.61050 ( 4365) SS BOND : bond 0.00361 ( 2) SS BOND : angle 0.69079 ( 4) hydrogen bonds : bond 0.06126 ( 202) hydrogen bonds : angle 4.37094 ( 609) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.117 Fit side-chains REVERT: N 98 ASN cc_start: 0.7846 (t0) cc_final: 0.7163 (t0) REVERT: R 231 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7747 (mmt) REVERT: R 303 ARG cc_start: 0.7264 (mmt180) cc_final: 0.6815 (mmp-170) outliers start: 10 outliers final: 5 residues processed: 35 average time/residue: 0.3857 time to fit residues: 14.1430 Evaluate side-chains 34 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.180105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123565 restraints weight = 3055.975| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.13 r_work: 0.3255 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3214 Z= 0.148 Angle : 0.572 6.995 4369 Z= 0.281 Chirality : 0.039 0.142 503 Planarity : 0.004 0.031 522 Dihedral : 12.667 131.859 589 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.54 % Allowed : 17.68 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.44), residues: 378 helix: 1.40 (0.34), residues: 227 sheet: 0.65 (0.76), residues: 54 loop : -2.27 (0.58), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 259 TYR 0.010 0.001 TYR R 235 PHE 0.019 0.001 PHE R 207 TRP 0.005 0.001 TRP N 38 HIS 0.002 0.001 HIS R 155 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3212) covalent geometry : angle 0.57234 ( 4365) SS BOND : bond 0.00357 ( 2) SS BOND : angle 0.62686 ( 4) hydrogen bonds : bond 0.05646 ( 202) hydrogen bonds : angle 4.28183 ( 609) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.162 Fit side-chains REVERT: N 98 ASN cc_start: 0.7849 (t0) cc_final: 0.7145 (t0) REVERT: R 231 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7803 (mmt) REVERT: R 290 ASP cc_start: 0.5837 (m-30) cc_final: 0.5360 (m-30) REVERT: R 303 ARG cc_start: 0.7267 (mmt180) cc_final: 0.6817 (mmp-170) outliers start: 11 outliers final: 6 residues processed: 36 average time/residue: 0.3560 time to fit residues: 13.5296 Evaluate side-chains 33 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.179678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123111 restraints weight = 3072.200| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.12 r_work: 0.3249 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3214 Z= 0.147 Angle : 0.571 6.887 4369 Z= 0.280 Chirality : 0.039 0.137 503 Planarity : 0.004 0.032 522 Dihedral : 12.480 129.632 589 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.22 % Allowed : 17.68 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.44), residues: 378 helix: 1.51 (0.34), residues: 227 sheet: 1.12 (0.84), residues: 45 loop : -2.32 (0.55), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 259 TYR 0.010 0.001 TYR R 235 PHE 0.019 0.002 PHE R 207 TRP 0.004 0.001 TRP N 38 HIS 0.003 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 3212) covalent geometry : angle 0.57129 ( 4365) SS BOND : bond 0.00348 ( 2) SS BOND : angle 0.65409 ( 4) hydrogen bonds : bond 0.05589 ( 202) hydrogen bonds : angle 4.25500 ( 609) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.118 Fit side-chains REVERT: N 98 ASN cc_start: 0.7833 (t0) cc_final: 0.7123 (t0) REVERT: R 231 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7718 (mmt) REVERT: R 290 ASP cc_start: 0.5866 (m-30) cc_final: 0.5392 (m-30) REVERT: R 303 ARG cc_start: 0.7248 (mmt180) cc_final: 0.6798 (mmp-170) outliers start: 10 outliers final: 8 residues processed: 34 average time/residue: 0.3891 time to fit residues: 13.8903 Evaluate side-chains 36 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN R 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.175743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119680 restraints weight = 3115.300| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.09 r_work: 0.3214 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3214 Z= 0.193 Angle : 0.642 7.910 4369 Z= 0.313 Chirality : 0.041 0.145 503 Planarity : 0.004 0.033 522 Dihedral : 12.701 132.391 589 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.18 % Allowed : 17.04 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.43), residues: 378 helix: 1.24 (0.34), residues: 230 sheet: 1.07 (0.85), residues: 45 loop : -2.73 (0.52), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 259 TYR 0.013 0.002 TYR R 235 PHE 0.020 0.002 PHE R 207 TRP 0.005 0.001 TRP N 38 HIS 0.004 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 3212) covalent geometry : angle 0.64126 ( 4365) SS BOND : bond 0.00433 ( 2) SS BOND : angle 0.87102 ( 4) hydrogen bonds : bond 0.06545 ( 202) hydrogen bonds : angle 4.43170 ( 609) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.115 Fit side-chains REVERT: N 98 ASN cc_start: 0.7830 (t0) cc_final: 0.7093 (t0) REVERT: R 231 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7761 (mmt) REVERT: R 290 ASP cc_start: 0.5929 (m-30) cc_final: 0.5443 (m-30) REVERT: R 303 ARG cc_start: 0.7304 (mmt180) cc_final: 0.6858 (mmp-170) outliers start: 13 outliers final: 8 residues processed: 37 average time/residue: 0.4723 time to fit residues: 18.1678 Evaluate side-chains 37 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.0070 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.179799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.123505 restraints weight = 3090.435| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.09 r_work: 0.3262 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3214 Z= 0.131 Angle : 0.562 6.548 4369 Z= 0.278 Chirality : 0.038 0.132 503 Planarity : 0.004 0.032 522 Dihedral : 12.354 127.531 589 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.22 % Allowed : 18.97 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.44), residues: 378 helix: 1.63 (0.34), residues: 227 sheet: 1.05 (0.83), residues: 45 loop : -2.39 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 259 TYR 0.009 0.001 TYR R 235 PHE 0.038 0.002 PHE R 189 TRP 0.005 0.001 TRP R 338 HIS 0.002 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3212) covalent geometry : angle 0.56213 ( 4365) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.64953 ( 4) hydrogen bonds : bond 0.05280 ( 202) hydrogen bonds : angle 4.25088 ( 609) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: N 98 ASN cc_start: 0.7856 (t0) cc_final: 0.7070 (t0) REVERT: R 231 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7530 (mmm) REVERT: R 290 ASP cc_start: 0.5852 (m-30) cc_final: 0.5385 (m-30) outliers start: 10 outliers final: 8 residues processed: 39 average time/residue: 0.3902 time to fit residues: 15.9728 Evaluate side-chains 38 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 294 LEU Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.179199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.123345 restraints weight = 3107.802| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.07 r_work: 0.3258 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3214 Z= 0.136 Angle : 0.571 7.544 4369 Z= 0.279 Chirality : 0.039 0.133 503 Planarity : 0.004 0.032 522 Dihedral : 12.268 126.315 589 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.89 % Allowed : 19.29 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.44), residues: 378 helix: 1.71 (0.34), residues: 227 sheet: 1.09 (0.83), residues: 45 loop : -2.40 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 259 TYR 0.009 0.001 TYR R 235 PHE 0.026 0.002 PHE R 189 TRP 0.004 0.001 TRP R 338 HIS 0.002 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 3212) covalent geometry : angle 0.57076 ( 4365) SS BOND : bond 0.00363 ( 2) SS BOND : angle 0.63803 ( 4) hydrogen bonds : bond 0.05335 ( 202) hydrogen bonds : angle 4.21320 ( 609) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: N 98 ASN cc_start: 0.7866 (t0) cc_final: 0.7134 (t0) REVERT: R 290 ASP cc_start: 0.5904 (m-30) cc_final: 0.5437 (m-30) outliers start: 9 outliers final: 8 residues processed: 37 average time/residue: 0.3775 time to fit residues: 14.6963 Evaluate side-chains 38 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 294 LEU Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.179300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124000 restraints weight = 3007.543| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.13 r_work: 0.3253 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3214 Z= 0.142 Angle : 0.579 7.633 4369 Z= 0.282 Chirality : 0.039 0.134 503 Planarity : 0.004 0.034 522 Dihedral : 12.162 124.837 589 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.22 % Allowed : 18.97 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.44), residues: 378 helix: 1.73 (0.34), residues: 227 sheet: 1.05 (0.83), residues: 45 loop : -2.40 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 212 TYR 0.008 0.001 TYR R 235 PHE 0.026 0.002 PHE R 189 TRP 0.004 0.001 TRP R 338 HIS 0.002 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3212) covalent geometry : angle 0.57943 ( 4365) SS BOND : bond 0.00368 ( 2) SS BOND : angle 0.64473 ( 4) hydrogen bonds : bond 0.05443 ( 202) hydrogen bonds : angle 4.23338 ( 609) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: N 98 ASN cc_start: 0.7802 (t0) cc_final: 0.7062 (t0) REVERT: R 290 ASP cc_start: 0.5879 (m-30) cc_final: 0.5411 (m-30) outliers start: 10 outliers final: 9 residues processed: 40 average time/residue: 0.4228 time to fit residues: 17.6444 Evaluate side-chains 39 residues out of total 319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 72 SER Chi-restraints excluded: chain N residue 110 LEU Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 294 LEU Chi-restraints excluded: chain R residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 20 optimal weight: 0.0070 chunk 7 optimal weight: 7.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.180440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124473 restraints weight = 3047.881| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.08 r_work: 0.3287 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3214 Z= 0.131 Angle : 0.559 7.611 4369 Z= 0.272 Chirality : 0.038 0.131 503 Planarity : 0.004 0.034 522 Dihedral : 12.066 126.569 589 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.89 % Allowed : 19.94 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.44), residues: 378 helix: 1.80 (0.34), residues: 227 sheet: 1.08 (0.83), residues: 45 loop : -2.38 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 212 TYR 0.008 0.001 TYR R 235 PHE 0.022 0.001 PHE R 189 TRP 0.005 0.001 TRP R 338 HIS 0.002 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3212) covalent geometry : angle 0.55890 ( 4365) SS BOND : bond 0.00352 ( 2) SS BOND : angle 0.59849 ( 4) hydrogen bonds : bond 0.05185 ( 202) hydrogen bonds : angle 4.19115 ( 609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1334.22 seconds wall clock time: 23 minutes 31.46 seconds (1411.46 seconds total)