Starting phenix.real_space_refine on Wed Jul 1 23:48:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ul2_26589/07_2026/7ul2_26589.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ul2_26589/07_2026/7ul2_26589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ul2_26589/07_2026/7ul2_26589.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ul2_26589/07_2026/7ul2_26589.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ul2_26589/07_2026/7ul2_26589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ul2_26589/07_2026/7ul2_26589.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ul2_26589/07_2026/7ul2_26589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ul2_26589/07_2026/7ul2_26589.map" } resolution = 2.4 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= -0.001 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1879 atoms to isotropic. 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 S 15 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 1724 2.51 5 N 428 2.21 5 O 455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2624 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2185 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 277} Chain breaks: 3 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 6, 'HIS:plan': 3, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 383 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 59} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TRP:plan': 1, 'TYR:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 56 Unusual residues: {' NA': 1, 'Q6Q': 1} Classifications: {'undetermined': 2, 'water': 13} Link IDs: {None: 14} Time building chain proxies: 0.86, per 1000 atoms: 0.33 Number of scatterers: 2624 At special positions: 0 Unit cell: (69.416, 50.3266, 103.256, 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) Cl 1 17.00 S 15 16.00 Na 1 11.00 O 455 8.00 N 428 7.00 C 1724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.05 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: 0.24 Conformation dependent library (CDL) restraints added in 96.3 milliseconds 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 73.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'R' and resid 60 through 90 removed outlier: 3.575A pdb=" N PHE R 86 " --> pdb=" O THR R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 118 removed outlier: 3.919A pdb=" N HIS R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 127 removed outlier: 3.775A pdb=" N VAL R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 removed outlier: 3.598A pdb=" N GLY R 140 " --> pdb=" O PHE R 136 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR R 145 " --> pdb=" O CYS R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 180 removed outlier: 3.784A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 200 Processing helix chain 'R' and resid 200 through 206 removed outlier: 4.015A pdb=" N LEU R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 245 through 264 Processing helix chain 'R' and resid 272 through 329 Proline residue: R 318 - end of helix removed outlier: 3.545A pdb=" N PHE R 326 " --> pdb=" O ARG R 322 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS R 327 " --> pdb=" O ARG R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 368 removed outlier: 3.505A pdb=" N PHE R 353 " --> pdb=" O THR R 349 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR R 354 " --> pdb=" O ASN R 350 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN R 360 " --> pdb=" O SER R 356 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 379 removed outlier: 3.512A pdb=" N ARG R 372 " --> pdb=" O SER R 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 207 through 212 Processing sheet with id=AA2, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.067A pdb=" N GLU D 100 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET D 36 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN D 98 " --> pdb=" O MET D 36 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.37 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 605 1.33 - 1.47: 939 1.47 - 1.60: 1106 1.60 - 1.74: 1 1.74 - 1.88: 24 Bond restraints: 2675 Sorted by residual: bond pdb=" C2 Q6Q R 501 " pdb=" O1 Q6Q R 501 " ideal model delta sigma weight residual 1.246 1.196 0.050 2.00e-02 2.50e+03 6.36e+00 bond pdb=" C2 Q6Q R 501 " pdb=" O2 Q6Q R 501 " ideal model delta sigma weight residual 1.244 1.194 0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 Q6Q R 501 " pdb=" C2 Q6Q R 501 " ideal model delta sigma weight residual 1.573 1.524 0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" CB CYS R 224 " pdb=" SG CYS R 224 " ideal model delta sigma weight residual 1.808 1.878 -0.070 3.30e-02 9.18e+02 4.44e+00 bond pdb=" CB ARG R 303 " pdb=" CG ARG R 303 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.09e+00 ... (remaining 2670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 3504 2.17 - 4.34: 133 4.34 - 6.51: 25 6.51 - 8.68: 2 8.68 - 10.85: 1 Bond angle restraints: 3665 Sorted by residual: angle pdb=" N ILE R 359 " pdb=" CA ILE R 359 " pdb=" C ILE R 359 " ideal model delta sigma weight residual 110.72 114.28 -3.56 1.01e+00 9.80e-01 1.24e+01 angle pdb=" N ASN R 360 " pdb=" CA ASN R 360 " pdb=" C ASN R 360 " ideal model delta sigma weight residual 109.81 117.53 -7.72 2.21e+00 2.05e-01 1.22e+01 angle pdb=" CA LEU R 258 " pdb=" CB LEU R 258 " pdb=" CG LEU R 258 " ideal model delta sigma weight residual 116.30 105.45 10.85 3.50e+00 8.16e-02 9.61e+00 angle pdb=" N TYR R 328 " pdb=" CA TYR R 328 " pdb=" C TYR R 328 " ideal model delta sigma weight residual 113.30 117.38 -4.08 1.34e+00 5.57e-01 9.28e+00 angle pdb=" CA TYR R 256 " pdb=" CB TYR R 256 " pdb=" CG TYR R 256 " ideal model delta sigma weight residual 113.90 108.43 5.47 1.80e+00 3.09e-01 9.25e+00 ... (remaining 3660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 1409 17.86 - 35.72: 60 35.72 - 53.58: 22 53.58 - 71.45: 3 71.45 - 89.31: 2 Dihedral angle restraints: 1496 sinusoidal: 479 harmonic: 1017 Sorted by residual: dihedral pdb=" N ASN R 126 " pdb=" CA ASN R 126 " pdb=" CB ASN R 126 " pdb=" CG ASN R 126 " ideal model delta sinusoidal sigma weight residual -180.00 -120.54 -59.46 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG R 323 " pdb=" CB ARG R 323 " pdb=" CG ARG R 323 " pdb=" CD ARG R 323 " ideal model delta sinusoidal sigma weight residual -60.00 -113.69 53.69 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CA ARG D 32 " pdb=" CB ARG D 32 " pdb=" CG ARG D 32 " pdb=" CD ARG D 32 " ideal model delta sinusoidal sigma weight residual -60.00 -111.39 51.39 3 1.50e+01 4.44e-03 9.01e+00 ... (remaining 1493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 280 0.052 - 0.103: 125 0.103 - 0.155: 28 0.155 - 0.207: 9 0.207 - 0.258: 1 Chirality restraints: 443 Sorted by residual: chirality pdb=" CA ASN R 360 " pdb=" N ASN R 360 " pdb=" C ASN R 360 " pdb=" CB ASN R 360 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA TYR R 145 " pdb=" N TYR R 145 " pdb=" C TYR R 145 " pdb=" CB TYR R 145 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA PHE R 127 " pdb=" N PHE R 127 " pdb=" C PHE R 127 " pdb=" CB PHE R 127 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 440 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C Q6Q R 501 " -0.015 2.00e-02 2.50e+03 2.26e-02 1.03e+01 pdb=" C12 Q6Q R 501 " 0.036 2.00e-02 2.50e+03 pdb=" C13 Q6Q R 501 " 0.006 2.00e-02 2.50e+03 pdb=" C14 Q6Q R 501 " -0.011 2.00e-02 2.50e+03 pdb=" C22 Q6Q R 501 " 0.009 2.00e-02 2.50e+03 pdb=" C23 Q6Q R 501 " 0.027 2.00e-02 2.50e+03 pdb=" N1 Q6Q R 501 " -0.014 2.00e-02 2.50e+03 pdb=" N2 Q6Q R 501 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 Q6Q R 501 " -0.046 2.00e-02 2.50e+03 1.77e-02 9.37e+00 pdb=" C24 Q6Q R 501 " 0.003 2.00e-02 2.50e+03 pdb=" C25 Q6Q R 501 " -0.010 2.00e-02 2.50e+03 pdb=" C26 Q6Q R 501 " -0.005 2.00e-02 2.50e+03 pdb=" C27 Q6Q R 501 " 0.008 2.00e-02 2.50e+03 pdb=" C28 Q6Q R 501 " 0.001 2.00e-02 2.50e+03 pdb=" C29 Q6Q R 501 " 0.001 2.00e-02 2.50e+03 pdb=" C30 Q6Q R 501 " 0.008 2.00e-02 2.50e+03 pdb=" C31 Q6Q R 501 " -0.001 2.00e-02 2.50e+03 pdb=" N2 Q6Q R 501 " 0.037 2.00e-02 2.50e+03 pdb=" N3 Q6Q R 501 " 0.000 2.00e-02 2.50e+03 pdb="CL Q6Q R 501 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 334 " 0.019 2.00e-02 2.50e+03 1.28e-02 4.11e+00 pdb=" CG TRP R 334 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP R 334 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 334 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 334 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 334 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP R 334 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 334 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 334 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 334 " 0.004 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 743 2.82 - 3.34: 2497 3.34 - 3.86: 4251 3.86 - 4.38: 4846 4.38 - 4.90: 8051 Nonbonded interactions: 20388 Sorted by model distance: nonbonded pdb=" N TYR D 39 " pdb=" O TYR D 96 " model vdw 2.306 3.120 nonbonded pdb=" O TYR D 39 " pdb=" N TYR D 96 " model vdw 2.371 3.120 nonbonded pdb=" O PHE R 74 " pdb=" OG1 THR R 78 " model vdw 2.379 3.040 nonbonded pdb=" OD1 ASP R 112 " pdb="NA NA R 502 " model vdw 2.385 2.470 nonbonded pdb=" O LYS R 63 " pdb=" OG1 THR R 67 " model vdw 2.428 3.040 ... (remaining 20383 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=0.00 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.520 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 0.070 2676 Z= 0.351 Angle : 1.024 10.850 3667 Z= 0.563 Chirality : 0.061 0.258 443 Planarity : 0.006 0.040 440 Dihedral : 12.803 89.306 833 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.84 % Allowed : 7.56 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 1.60 (0.41), residues: 329 helix: 1.95 (0.30), residues: 224 sheet: 1.57 (1.66), residues: 9 loop : -1.17 (0.52), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG R 299 TYR 0.031 0.004 TYR R 256 PHE 0.026 0.004 PHE R 337 TRP 0.032 0.004 TRP R 334 HIS 0.004 0.002 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.35 ( 2675) covalent geometry : angle 1.01588 / 0.56 ( 3665) SS BOND : bond 0.01850 / 0.97 ( 1) SS BOND : angle 5.44670 / 3.05 ( 2) hydrogen bonds : bond 0.26394 / 17.99 ( 203) hydrogen bonds : angle 6.47504 / 4.75 ( 597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.093 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.5040 time to fit residues: 25.8421 Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 ASN Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.149542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.129313 restraints weight = 2960.649| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.37 r_work: 0.3396 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2676 Z= 0.172 Angle : 0.580 8.873 3667 Z= 0.326 Chirality : 0.041 0.172 443 Planarity : 0.004 0.028 440 Dihedral : 5.877 50.184 379 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.10 % Allowed : 7.56 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 3.01 (0.44), residues: 329 helix: 3.31 (0.31), residues: 225 sheet: 1.57 (1.71), residues: 9 loop : -1.47 (0.50), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 102 TYR 0.014 0.002 TYR R 256 PHE 0.016 0.002 PHE R 375 TRP 0.010 0.001 TRP R 316 HIS 0.002 0.001 HIS R 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.17 ( 2675) covalent geometry : angle 0.57571 / 0.32 ( 3665) SS BOND : bond 0.00651 / 0.34 ( 1) SS BOND : angle 3.22671 / 1.78 ( 2) hydrogen bonds : bond 0.08174 / 5.71 ( 203) hydrogen bonds : angle 4.06009 / 2.89 ( 597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.101 Fit side-chains REVERT: R 65 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7274 (tt) outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 0.4696 time to fit residues: 20.2594 Evaluate side-chains 39 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125857 restraints weight = 2938.262| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.38 r_work: 0.3354 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2676 Z= 0.176 Angle : 0.573 8.197 3667 Z= 0.319 Chirality : 0.040 0.151 443 Planarity : 0.004 0.033 440 Dihedral : 5.078 44.571 377 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.94 % Allowed : 7.14 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.92 (0.44), residues: 329 helix: 3.22 (0.31), residues: 229 sheet: 1.40 (2.00), residues: 9 loop : -1.64 (0.51), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 102 TYR 0.016 0.002 TYR R 256 PHE 0.016 0.002 PHE R 375 TRP 0.010 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.18 ( 2675) covalent geometry : angle 0.56670 / 0.32 ( 3665) SS BOND : bond 0.00918 / 0.48 ( 1) SS BOND : angle 3.53861 / 1.95 ( 2) hydrogen bonds : bond 0.08493 / 5.95 ( 203) hydrogen bonds : angle 3.97539 / 2.85 ( 597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.106 Fit side-chains REVERT: R 65 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7245 (tt) REVERT: R 123 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: D 36 MET cc_start: 0.8599 (mtp) cc_final: 0.8322 (mtp) outliers start: 7 outliers final: 2 residues processed: 42 average time/residue: 0.4137 time to fit residues: 17.9737 Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.145895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125083 restraints weight = 2923.060| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.38 r_work: 0.3349 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 0.003 0.028 2676 Z= 0.177 Angle : 0.572 8.261 3667 Z= 0.319 Chirality : 0.040 0.151 443 Planarity : 0.005 0.037 440 Dihedral : 5.080 44.717 377 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.36 % Allowed : 7.56 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.71 (0.44), residues: 329 helix: 3.01 (0.31), residues: 235 sheet: 1.03 (1.83), residues: 9 loop : -1.89 (0.51), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 32 TYR 0.016 0.002 TYR R 256 PHE 0.015 0.002 PHE R 375 TRP 0.009 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.18 ( 2675) covalent geometry : angle 0.56652 / 0.32 ( 3665) SS BOND : bond 0.00921 / 0.48 ( 1) SS BOND : angle 3.52632 / 1.94 ( 2) hydrogen bonds : bond 0.08481 / 5.94 ( 203) hydrogen bonds : angle 3.98127 / 2.86 ( 597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.094 Fit side-chains REVERT: R 65 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7280 (tt) REVERT: R 123 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7844 (tt0) outliers start: 8 outliers final: 2 residues processed: 39 average time/residue: 0.4792 time to fit residues: 19.2378 Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.146003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125352 restraints weight = 2933.147| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.38 r_work: 0.3349 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2676 Z= 0.176 Angle : 0.568 8.301 3667 Z= 0.315 Chirality : 0.040 0.149 443 Planarity : 0.005 0.042 440 Dihedral : 5.049 44.624 377 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.36 % Allowed : 9.66 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.64 (0.44), residues: 329 helix: 2.98 (0.31), residues: 235 sheet: 0.51 (1.70), residues: 9 loop : -1.95 (0.51), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 32 TYR 0.016 0.002 TYR R 256 PHE 0.015 0.002 PHE R 375 TRP 0.009 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.18 ( 2675) covalent geometry : angle 0.56214 / 0.31 ( 3665) SS BOND : bond 0.00945 / 0.50 ( 1) SS BOND : angle 3.53444 / 1.94 ( 2) hydrogen bonds : bond 0.08417 / 5.90 ( 203) hydrogen bonds : angle 3.95461 / 2.84 ( 597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.098 Fit side-chains REVERT: R 65 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7272 (tt) REVERT: R 123 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7859 (tt0) outliers start: 8 outliers final: 3 residues processed: 40 average time/residue: 0.4584 time to fit residues: 18.8864 Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 31 optimal weight: 9.9990 chunk 13 optimal weight: 0.0470 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.151505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130465 restraints weight = 2899.696| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.44 r_work: 0.3473 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2676 Z= 0.162 Angle : 0.538 8.203 3667 Z= 0.300 Chirality : 0.039 0.147 443 Planarity : 0.005 0.043 440 Dihedral : 4.968 43.877 377 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.52 % Allowed : 12.18 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.73 (0.45), residues: 329 helix: 3.07 (0.31), residues: 235 sheet: 0.32 (1.69), residues: 9 loop : -1.95 (0.52), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 32 TYR 0.014 0.002 TYR R 256 PHE 0.015 0.002 PHE R 375 TRP 0.008 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 ( 2675) covalent geometry : angle 0.53311 / 0.30 ( 3665) SS BOND : bond 0.00791 / 0.42 ( 1) SS BOND : angle 3.28146 / 1.81 ( 2) hydrogen bonds : bond 0.07845 / 5.50 ( 203) hydrogen bonds : angle 3.88041 / 2.78 ( 597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.107 Fit side-chains REVERT: R 65 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7147 (mt) REVERT: R 123 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7883 (tt0) outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 0.4161 time to fit residues: 17.1226 Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.6980 chunk 19 optimal weight: 0.0170 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.152229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.131088 restraints weight = 2935.002| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.45 r_work: 0.3480 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2676 Z= 0.157 Angle : 0.526 8.162 3667 Z= 0.293 Chirality : 0.038 0.146 443 Planarity : 0.004 0.044 440 Dihedral : 4.921 43.740 377 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.52 % Allowed : 11.76 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.78 (0.45), residues: 329 helix: 3.12 (0.32), residues: 235 sheet: 0.26 (1.70), residues: 9 loop : -1.94 (0.52), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 32 TYR 0.014 0.002 TYR R 256 PHE 0.014 0.002 PHE R 375 TRP 0.008 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.16 ( 2675) covalent geometry : angle 0.52068 / 0.29 ( 3665) SS BOND : bond 0.00805 / 0.42 ( 1) SS BOND : angle 3.16991 / 1.75 ( 2) hydrogen bonds : bond 0.07612 / 5.34 ( 203) hydrogen bonds : angle 3.83700 / 2.75 ( 597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.097 Fit side-chains REVERT: R 65 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7120 (mt) REVERT: R 123 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7882 (tt0) outliers start: 6 outliers final: 3 residues processed: 39 average time/residue: 0.4570 time to fit residues: 18.3392 Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 30 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.150240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.129083 restraints weight = 2927.505| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.44 r_work: 0.3450 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2676 Z= 0.177 Angle : 0.565 8.348 3667 Z= 0.313 Chirality : 0.040 0.150 443 Planarity : 0.005 0.045 440 Dihedral : 5.016 44.709 377 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.94 % Allowed : 11.76 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.60 (0.44), residues: 329 helix: 2.98 (0.31), residues: 235 sheet: 0.07 (1.62), residues: 9 loop : -1.99 (0.52), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 32 TYR 0.015 0.002 TYR R 256 PHE 0.014 0.002 PHE R 375 TRP 0.009 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.18 ( 2675) covalent geometry : angle 0.55909 / 0.31 ( 3665) SS BOND : bond 0.00983 / 0.52 ( 1) SS BOND : angle 3.47039 / 1.90 ( 2) hydrogen bonds : bond 0.08431 / 5.91 ( 203) hydrogen bonds : angle 3.93425 / 2.82 ( 597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.082 Fit side-chains REVERT: R 123 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7895 (tt0) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.4488 time to fit residues: 18.9727 Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130333 restraints weight = 2971.795| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.45 r_work: 0.3467 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2676 Z= 0.164 Angle : 0.540 8.256 3667 Z= 0.300 Chirality : 0.039 0.149 443 Planarity : 0.005 0.046 440 Dihedral : 4.949 44.010 377 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.94 % Allowed : 12.18 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.68 (0.45), residues: 329 helix: 3.06 (0.32), residues: 235 sheet: -0.07 (1.59), residues: 9 loop : -2.01 (0.52), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 32 TYR 0.014 0.002 TYR R 256 PHE 0.014 0.002 PHE R 375 TRP 0.008 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 ( 2675) covalent geometry : angle 0.53429 / 0.30 ( 3665) SS BOND : bond 0.00882 / 0.46 ( 1) SS BOND : angle 3.28083 / 1.81 ( 2) hydrogen bonds : bond 0.07885 / 5.53 ( 203) hydrogen bonds : angle 3.86098 / 2.77 ( 597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.102 Fit side-chains REVERT: R 65 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7163 (mt) REVERT: R 123 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7902 (tt0) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.4410 time to fit residues: 18.6479 Evaluate side-chains 42 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128577 restraints weight = 2982.582| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.45 r_work: 0.3443 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2676 Z= 0.180 Angle : 0.571 8.385 3667 Z= 0.316 Chirality : 0.040 0.151 443 Planarity : 0.005 0.046 440 Dihedral : 5.027 44.861 377 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.94 % Allowed : 12.18 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.50 (0.44), residues: 329 helix: 2.94 (0.31), residues: 235 sheet: -0.59 (1.48), residues: 9 loop : -2.07 (0.50), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 32 TYR 0.016 0.002 TYR R 256 PHE 0.015 0.002 PHE R 375 TRP 0.009 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.18 ( 2675) covalent geometry : angle 0.56468 / 0.31 ( 3665) SS BOND : bond 0.01044 / 0.55 ( 1) SS BOND : angle 3.52942 / 1.93 ( 2) hydrogen bonds : bond 0.08556 / 6.00 ( 203) hydrogen bonds : angle 3.94359 / 2.83 ( 597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.097 Fit side-chains REVERT: R 65 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7204 (mt) REVERT: R 123 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7898 (tt0) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.4288 time to fit residues: 18.1357 Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.148447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127290 restraints weight = 2944.105| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.44 r_work: 0.3425 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2676 Z= 0.201 Angle : 0.610 8.526 3667 Z= 0.337 Chirality : 0.042 0.156 443 Planarity : 0.005 0.047 440 Dihedral : 5.131 45.675 377 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.94 % Allowed : 12.61 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.26 (0.44), residues: 329 helix: 2.80 (0.32), residues: 235 sheet: -1.19 (1.46), residues: 9 loop : -2.20 (0.49), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 32 TYR 0.017 0.002 TYR R 256 PHE 0.015 0.002 PHE R 375 TRP 0.010 0.002 TRP R 316 HIS 0.002 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.20 ( 2675) covalent geometry : angle 0.60399 / 0.33 ( 3665) SS BOND : bond 0.01175 / 0.62 ( 1) SS BOND : angle 3.80054 / 2.08 ( 2) hydrogen bonds : bond 0.09235 / 6.46 ( 203) hydrogen bonds : angle 4.03037 / 2.89 ( 597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1180.78 seconds wall clock time: 20 minutes 50.00 seconds (1250.00 seconds total)