Starting phenix.real_space_refine on Fri Aug 22 12:38:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggi_40009/08_2025/8ggi_40009.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggi_40009/08_2025/8ggi_40009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ggi_40009/08_2025/8ggi_40009.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggi_40009/08_2025/8ggi_40009.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ggi_40009/08_2025/8ggi_40009.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggi_40009/08_2025/8ggi_40009.map" } resolution = 3.5 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= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 1470 2.51 5 N 348 2.21 5 O 370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 2203 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 4, 'TRP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 0.92, per 1000 atoms: 0.42 Number of scatterers: 2203 At special positions: 0 Unit cell: (54.6651, 83.2992, 63.3421, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 370 8.00 N 348 7.00 C 1470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=1.41 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: 0.21 Conformation dependent library (CDL) restraints added in 87.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 544 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'R' and resid 29 through 61 removed outlier: 3.553A pdb=" N VAL R 33 " --> pdb=" O ASP R 29 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE R 55 " --> pdb=" O ASN R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 97 removed outlier: 4.624A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 removed outlier: 4.114A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP R 109 " --> pdb=" O TRP R 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA R 134 " --> pdb=" O ASP R 130 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR R 136 " --> pdb=" O TYR R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 163 removed outlier: 3.657A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 178 through 186 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.686A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 238 removed outlier: 3.953A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL R 222 " --> pdb=" O VAL R 218 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE R 223 " --> pdb=" O TYR R 219 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 280 Processing helix chain 'R' and resid 286 through 299 removed outlier: 3.692A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.569A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 340 153 hydrogen bonds defined for protein. 459 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: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 651 1.34 - 1.46: 581 1.46 - 1.58: 1004 1.58 - 1.70: 0 1.70 - 1.83: 21 Bond restraints: 2257 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.439 -0.045 2.00e-02 2.50e+03 5.06e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.567 -0.044 2.00e-02 2.50e+03 4.87e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.563 -0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C CYS R 191 " pdb=" O CYS R 191 " ideal model delta sigma weight residual 1.235 1.220 0.015 7.50e-03 1.78e+04 4.18e+00 ... (remaining 2252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 3021 1.88 - 3.75: 44 3.75 - 5.63: 16 5.63 - 7.51: 3 7.51 - 9.38: 3 Bond angle restraints: 3087 Sorted by residual: angle pdb=" N THR R 189 " pdb=" CA THR R 189 " pdb=" C THR R 189 " ideal model delta sigma weight residual 114.04 104.66 9.38 1.24e+00 6.50e-01 5.73e+01 angle pdb=" N PHE R 193 " pdb=" CA PHE R 193 " pdb=" C PHE R 193 " ideal model delta sigma weight residual 108.67 116.73 -8.06 1.55e+00 4.16e-01 2.70e+01 angle pdb=" N CYS R 191 " pdb=" CA CYS R 191 " pdb=" C CYS R 191 " ideal model delta sigma weight residual 113.21 106.63 6.58 1.40e+00 5.10e-01 2.21e+01 angle pdb=" N CYS R 190 " pdb=" CA CYS R 190 " pdb=" C CYS R 190 " ideal model delta sigma weight residual 109.96 115.88 -5.92 1.50e+00 4.44e-01 1.56e+01 angle pdb=" N CYS R 191 " pdb=" CA CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sigma weight residual 110.65 115.26 -4.61 1.71e+00 3.42e-01 7.28e+00 ... (remaining 3082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 1151 16.08 - 32.17: 122 32.17 - 48.25: 25 48.25 - 64.33: 3 64.33 - 80.42: 3 Dihedral angle restraints: 1304 sinusoidal: 467 harmonic: 837 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -162.92 -17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA SER R 207 " pdb=" C SER R 207 " pdb=" N PHE R 208 " pdb=" CA PHE R 208 " ideal model delta harmonic sigma weight residual -180.00 -164.16 -15.84 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CB MET R 171 " pdb=" CG MET R 171 " pdb=" SD MET R 171 " pdb=" CE MET R 171 " ideal model delta sinusoidal sigma weight residual 60.00 117.75 -57.75 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 1301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 232 0.033 - 0.066: 102 0.066 - 0.098: 33 0.098 - 0.131: 10 0.131 - 0.164: 1 Chirality restraints: 378 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.56 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA LEU R 287 " pdb=" N LEU R 287 " pdb=" C LEU R 287 " pdb=" CB LEU R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.02e-01 chirality pdb=" CA PRO R 88 " pdb=" N PRO R 88 " pdb=" C PRO R 88 " pdb=" CB PRO R 88 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 375 not shown) Planarity restraints: 368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS R 190 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" C CYS R 190 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS R 190 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS R 191 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU R 237 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" CD GLU R 237 " -0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU R 237 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU R 237 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 313 " -0.006 2.00e-02 2.50e+03 7.40e-03 1.37e+00 pdb=" CG TRP R 313 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP R 313 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 313 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 313 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 313 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 313 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 313 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 313 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 313 " -0.000 2.00e-02 2.50e+03 ... (remaining 365 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 445 2.77 - 3.31: 2101 3.31 - 3.84: 3493 3.84 - 4.37: 3684 4.37 - 4.90: 6782 Nonbonded interactions: 16505 Sorted by model distance: nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.242 3.040 nonbonded pdb=" N GLU R 306 " pdb=" OE1 GLU R 306 " model vdw 2.333 3.120 nonbonded pdb=" OH TYR R 326 " pdb=" O HOH R 601 " model vdw 2.407 3.040 nonbonded pdb=" OH TYR R 209 " pdb=" O PHE R 290 " model vdw 2.450 3.040 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.495 3.120 ... (remaining 16500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.290 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.700 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 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 : 0.014 0.622 2259 Z= 0.684 Angle : 0.805 18.619 3091 Z= 0.435 Chirality : 0.042 0.164 378 Planarity : 0.004 0.030 368 Dihedral : 13.755 80.416 754 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.47 (0.51), residues: 280 helix: 1.60 (0.37), residues: 204 sheet: None (None), residues: 0 loop : -0.70 (0.71), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 63 TYR 0.007 0.001 TYR R 132 PHE 0.007 0.001 PHE R 193 TRP 0.019 0.001 TRP R 313 HIS 0.005 0.002 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 2257) covalent geometry : angle 0.69241 ( 3087) SS BOND : bond 0.43999 ( 2) SS BOND : angle 11.40898 ( 4) hydrogen bonds : bond 0.16886 ( 153) hydrogen bonds : angle 5.56873 ( 459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.087 Fit side-chains REVERT: R 82 MET cc_start: 0.8318 (ttm) cc_final: 0.8052 (ttm) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.0784 time to fit residues: 3.9897 Evaluate side-chains 34 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.095166 restraints weight = 3083.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.097529 restraints weight = 1755.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.099105 restraints weight = 1240.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.100201 restraints weight = 993.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.100599 restraints weight = 855.837| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2259 Z= 0.155 Angle : 0.538 7.072 3091 Z= 0.285 Chirality : 0.040 0.106 378 Planarity : 0.003 0.027 368 Dihedral : 4.616 20.801 316 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.33 % Allowed : 8.00 % Favored : 90.67 % 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: 1.40 (0.51), residues: 280 helix: 1.37 (0.36), residues: 221 sheet: None (None), residues: 0 loop : -0.58 (0.77), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 63 TYR 0.008 0.001 TYR R 132 PHE 0.009 0.001 PHE R 332 TRP 0.007 0.001 TRP R 109 HIS 0.006 0.002 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 2257) covalent geometry : angle 0.53166 ( 3087) SS BOND : bond 0.00245 ( 2) SS BOND : angle 2.32255 ( 4) hydrogen bonds : bond 0.05461 ( 153) hydrogen bonds : angle 4.24954 ( 459) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.078 Fit side-chains REVERT: R 279 MET cc_start: 0.8562 (mmm) cc_final: 0.8243 (mmm) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.0878 time to fit residues: 3.7093 Evaluate side-chains 35 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.111675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.094465 restraints weight = 3147.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.096910 restraints weight = 1788.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.098515 restraints weight = 1263.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.099626 restraints weight = 1013.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.100257 restraints weight = 876.743| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2259 Z= 0.163 Angle : 0.539 9.547 3091 Z= 0.279 Chirality : 0.040 0.107 378 Planarity : 0.003 0.027 368 Dihedral : 4.596 18.095 316 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.22 % Allowed : 10.22 % Favored : 87.56 % 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: 1.40 (0.51), residues: 280 helix: 1.38 (0.36), residues: 221 sheet: None (None), residues: 0 loop : -0.63 (0.78), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 63 TYR 0.008 0.001 TYR R 132 PHE 0.008 0.001 PHE R 332 TRP 0.007 0.001 TRP R 109 HIS 0.006 0.002 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 2257) covalent geometry : angle 0.53701 ( 3087) SS BOND : bond 0.00299 ( 2) SS BOND : angle 1.40898 ( 4) hydrogen bonds : bond 0.05435 ( 153) hydrogen bonds : angle 4.16550 ( 459) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.099 Fit side-chains REVERT: R 279 MET cc_start: 0.8592 (mmm) cc_final: 0.8225 (mmm) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.0889 time to fit residues: 3.7582 Evaluate side-chains 37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.096973 restraints weight = 3019.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.099486 restraints weight = 1701.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.101102 restraints weight = 1190.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.102167 restraints weight = 947.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.102778 restraints weight = 819.432| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2259 Z= 0.123 Angle : 0.487 7.951 3091 Z= 0.254 Chirality : 0.039 0.104 378 Planarity : 0.003 0.026 368 Dihedral : 4.327 17.392 316 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.33 % Allowed : 10.67 % Favored : 88.00 % 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: 1.52 (0.51), residues: 280 helix: 1.49 (0.36), residues: 221 sheet: None (None), residues: 0 loop : -0.68 (0.78), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 63 TYR 0.007 0.001 TYR R 132 PHE 0.006 0.001 PHE R 332 TRP 0.007 0.001 TRP R 109 HIS 0.004 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 2257) covalent geometry : angle 0.48477 ( 3087) SS BOND : bond 0.00266 ( 2) SS BOND : angle 1.48590 ( 4) hydrogen bonds : bond 0.04803 ( 153) hydrogen bonds : angle 3.98111 ( 459) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.101 Fit side-chains REVERT: R 279 MET cc_start: 0.8605 (mmm) cc_final: 0.8240 (mmm) outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 0.0913 time to fit residues: 3.8604 Evaluate side-chains 38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.113995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.096813 restraints weight = 3036.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.099318 restraints weight = 1716.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.100966 restraints weight = 1203.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.102175 restraints weight = 960.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.102824 restraints weight = 825.194| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2259 Z= 0.135 Angle : 0.508 10.182 3091 Z= 0.260 Chirality : 0.039 0.104 378 Planarity : 0.003 0.026 368 Dihedral : 4.339 17.394 316 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.33 % Allowed : 12.44 % Favored : 86.22 % 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: 1.47 (0.51), residues: 280 helix: 1.44 (0.35), residues: 223 sheet: None (None), residues: 0 loop : -0.74 (0.79), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 63 TYR 0.008 0.001 TYR R 132 PHE 0.006 0.001 PHE R 332 TRP 0.007 0.001 TRP R 109 HIS 0.004 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 2257) covalent geometry : angle 0.50575 ( 3087) SS BOND : bond 0.00154 ( 2) SS BOND : angle 1.34016 ( 4) hydrogen bonds : bond 0.04934 ( 153) hydrogen bonds : angle 3.95485 ( 459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.082 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 38 average time/residue: 0.0881 time to fit residues: 3.8174 Evaluate side-chains 36 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.110969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.094201 restraints weight = 3058.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.096674 restraints weight = 1751.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.098180 restraints weight = 1222.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.099258 restraints weight = 985.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.099762 restraints weight = 854.221| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2259 Z= 0.156 Angle : 0.529 9.668 3091 Z= 0.272 Chirality : 0.040 0.107 378 Planarity : 0.003 0.026 368 Dihedral : 4.399 17.419 316 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.78 % Allowed : 12.89 % Favored : 85.33 % 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: 1.41 (0.50), residues: 280 helix: 1.43 (0.35), residues: 222 sheet: None (None), residues: 0 loop : -0.86 (0.75), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 63 TYR 0.009 0.001 TYR R 132 PHE 0.008 0.001 PHE R 332 TRP 0.007 0.001 TRP R 109 HIS 0.004 0.002 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 2257) covalent geometry : angle 0.52736 ( 3087) SS BOND : bond 0.00170 ( 2) SS BOND : angle 1.34690 ( 4) hydrogen bonds : bond 0.05278 ( 153) hydrogen bonds : angle 3.99139 ( 459) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.085 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 0.0895 time to fit residues: 3.6887 Evaluate side-chains 36 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 6 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.095193 restraints weight = 3044.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.097632 restraints weight = 1710.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.099259 restraints weight = 1202.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.100309 restraints weight = 958.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.101047 restraints weight = 825.880| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2259 Z= 0.134 Angle : 0.512 8.979 3091 Z= 0.263 Chirality : 0.039 0.104 378 Planarity : 0.003 0.026 368 Dihedral : 4.399 17.438 316 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.33 % Allowed : 13.78 % Favored : 84.89 % 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: 1.36 (0.50), residues: 280 helix: 1.43 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -1.14 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 63 TYR 0.008 0.001 TYR R 132 PHE 0.006 0.001 PHE R 332 TRP 0.007 0.001 TRP R 109 HIS 0.007 0.002 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2257) covalent geometry : angle 0.50657 ( 3087) SS BOND : bond 0.00112 ( 2) SS BOND : angle 2.08498 ( 4) hydrogen bonds : bond 0.04984 ( 153) hydrogen bonds : angle 3.96817 ( 459) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.082 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 35 average time/residue: 0.0919 time to fit residues: 3.6809 Evaluate side-chains 37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.111664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.094884 restraints weight = 3077.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.097343 restraints weight = 1727.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.099008 restraints weight = 1210.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.099944 restraints weight = 963.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.100693 restraints weight = 838.267| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2259 Z= 0.141 Angle : 0.513 8.626 3091 Z= 0.264 Chirality : 0.040 0.105 378 Planarity : 0.003 0.028 368 Dihedral : 4.392 17.458 316 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.78 % Allowed : 13.33 % Favored : 84.89 % 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: 1.34 (0.50), residues: 280 helix: 1.42 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -1.20 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 63 TYR 0.008 0.001 TYR R 132 PHE 0.007 0.001 PHE R 61 TRP 0.007 0.001 TRP R 109 HIS 0.008 0.002 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 2257) covalent geometry : angle 0.50796 ( 3087) SS BOND : bond 0.00161 ( 2) SS BOND : angle 2.03447 ( 4) hydrogen bonds : bond 0.05020 ( 153) hydrogen bonds : angle 3.96548 ( 459) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.108 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 0.0961 time to fit residues: 3.9116 Evaluate side-chains 37 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 0.0270 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.113025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.096136 restraints weight = 3046.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.098588 restraints weight = 1729.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.100096 restraints weight = 1221.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.101229 restraints weight = 982.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.101893 restraints weight = 844.395| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2259 Z= 0.127 Angle : 0.498 8.303 3091 Z= 0.257 Chirality : 0.039 0.104 378 Planarity : 0.003 0.029 368 Dihedral : 4.308 17.422 316 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.22 % Allowed : 12.44 % Favored : 85.33 % 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: 1.46 (0.51), residues: 280 helix: 1.50 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -1.12 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 63 TYR 0.008 0.001 TYR R 132 PHE 0.006 0.001 PHE R 61 TRP 0.008 0.001 TRP R 109 HIS 0.004 0.002 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 2257) covalent geometry : angle 0.49434 ( 3087) SS BOND : bond 0.00107 ( 2) SS BOND : angle 1.74917 ( 4) hydrogen bonds : bond 0.04810 ( 153) hydrogen bonds : angle 3.88989 ( 459) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.059 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 37 average time/residue: 0.0891 time to fit residues: 3.7664 Evaluate side-chains 38 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 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 178 HIS R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.111756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.094910 restraints weight = 3089.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.097302 restraints weight = 1743.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.098919 restraints weight = 1240.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.100072 restraints weight = 990.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.100656 restraints weight = 851.493| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2259 Z= 0.153 Angle : 0.523 8.348 3091 Z= 0.271 Chirality : 0.040 0.108 378 Planarity : 0.004 0.032 368 Dihedral : 4.383 17.292 316 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.78 % Allowed : 12.89 % Favored : 85.33 % 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: 1.39 (0.50), residues: 280 helix: 1.44 (0.36), residues: 224 sheet: None (None), residues: 0 loop : -1.08 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 63 TYR 0.011 0.001 TYR R 132 PHE 0.007 0.001 PHE R 332 TRP 0.007 0.001 TRP R 109 HIS 0.006 0.002 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 2257) covalent geometry : angle 0.51894 ( 3087) SS BOND : bond 0.00121 ( 2) SS BOND : angle 1.88808 ( 4) hydrogen bonds : bond 0.05145 ( 153) hydrogen bonds : angle 3.96829 ( 459) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.087 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 0.0800 time to fit residues: 3.3886 Evaluate side-chains 39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 283 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.112012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.095324 restraints weight = 3090.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.097833 restraints weight = 1727.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.099513 restraints weight = 1205.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.100468 restraints weight = 956.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.101184 restraints weight = 830.661| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2259 Z= 0.151 Angle : 0.522 8.250 3091 Z= 0.271 Chirality : 0.040 0.107 378 Planarity : 0.004 0.032 368 Dihedral : 4.396 17.325 316 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.78 % Allowed : 12.89 % Favored : 85.33 % 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: 1.38 (0.50), residues: 280 helix: 1.45 (0.36), residues: 223 sheet: None (None), residues: 0 loop : -1.09 (0.71), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 63 TYR 0.010 0.001 TYR R 132 PHE 0.007 0.001 PHE R 332 TRP 0.007 0.001 TRP R 109 HIS 0.005 0.002 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 2257) covalent geometry : angle 0.51755 ( 3087) SS BOND : bond 0.00106 ( 2) SS BOND : angle 1.86976 ( 4) hydrogen bonds : bond 0.05160 ( 153) hydrogen bonds : angle 3.99288 ( 459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 678.39 seconds wall clock time: 12 minutes 48.38 seconds (768.38 seconds total)