Starting phenix.real_space_refine on Sat Apr 4 20:08:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggn_40014/04_2026/8ggn_40014.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggn_40014/04_2026/8ggn_40014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ggn_40014/04_2026/8ggn_40014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggn_40014/04_2026/8ggn_40014.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggn_40014/04_2026/8ggn_40014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggn_40014/04_2026/8ggn_40014.cif" } resolution = 3.3 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= 0.028 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 1446 2.51 5 N 344 2.21 5 O 363 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-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2168 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2153 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 7, 'TRP:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 89 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.53, per 1000 atoms: 0.24 Number of scatterers: 2168 At special positions: 0 Unit cell: (58.1359, 83.2992, 61.6067, 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 363 8.00 N 344 7.00 C 1446 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 87.6 milliseconds 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 88.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.753A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.251A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.958A 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 102 through 137 removed outlier: 3.640A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.696A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.583A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 299 removed outlier: 4.007A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.619A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.567A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 327 removed outlier: 3.765A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 168 hydrogen bonds defined for protein. 504 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: 0.24 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 325 1.32 - 1.44: 650 1.44 - 1.56: 1228 1.56 - 1.69: 1 1.69 - 1.81: 21 Bond restraints: 2225 Sorted by residual: bond pdb=" CA ARG R 63 " pdb=" C ARG R 63 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.37e-02 5.33e+03 9.74e+00 bond pdb=" C LEU R 64 " pdb=" O LEU R 64 " ideal model delta sigma weight residual 1.235 1.199 0.037 1.33e-02 5.65e+03 7.54e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.29e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.56e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.441 -0.047 2.00e-02 2.50e+03 5.42e+00 ... (remaining 2220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 2898 1.12 - 2.25: 120 2.25 - 3.37: 17 3.37 - 4.50: 8 4.50 - 5.62: 7 Bond angle restraints: 3050 Sorted by residual: angle pdb=" N GLU R 62 " pdb=" CA GLU R 62 " pdb=" CB GLU R 62 " ideal model delta sigma weight residual 110.49 105.04 5.45 1.48e+00 4.57e-01 1.36e+01 angle pdb=" N GLU R 62 " pdb=" CA GLU R 62 " pdb=" C GLU R 62 " ideal model delta sigma weight residual 113.17 116.58 -3.41 1.26e+00 6.30e-01 7.33e+00 angle pdb=" N ARG R 63 " pdb=" CA ARG R 63 " pdb=" C ARG R 63 " ideal model delta sigma weight residual 113.23 109.94 3.29 1.24e+00 6.50e-01 7.02e+00 angle pdb=" C ALA R 85 " pdb=" N VAL R 86 " pdb=" CA VAL R 86 " ideal model delta sigma weight residual 120.82 117.78 3.04 1.55e+00 4.16e-01 3.85e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 117.96 -5.33 3.00e+00 1.11e-01 3.16e+00 ... (remaining 3045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 1147 16.05 - 32.09: 99 32.09 - 48.14: 20 48.14 - 64.18: 2 64.18 - 80.23: 4 Dihedral angle restraints: 1272 sinusoidal: 432 harmonic: 840 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 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CG ARG R 175 " pdb=" CD ARG R 175 " pdb=" NE ARG R 175 " pdb=" CZ ARG R 175 " ideal model delta sinusoidal sigma weight residual -180.00 -139.14 -40.86 2 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" CB GLU R 122 " pdb=" CG GLU R 122 " pdb=" CD GLU R 122 " pdb=" OE1 GLU R 122 " ideal model delta sinusoidal sigma weight residual 0.00 80.23 -80.23 1 3.00e+01 1.11e-03 8.86e+00 ... (remaining 1269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 243 0.034 - 0.068: 99 0.068 - 0.101: 23 0.101 - 0.135: 7 0.135 - 0.169: 2 Chirality restraints: 374 Sorted by residual: chirality pdb=" CA LEU R 64 " pdb=" N LEU R 64 " pdb=" C LEU R 64 " pdb=" CB LEU R 64 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.11e-01 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 2.54 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA PRO R 288 " pdb=" N PRO R 288 " pdb=" C PRO R 288 " pdb=" CB PRO R 288 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.83e-01 ... (remaining 371 not shown) Planarity restraints: 366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 61 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C PHE R 61 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE R 61 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU R 62 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 173 " -0.009 2.00e-02 2.50e+03 6.35e-03 1.01e+00 pdb=" CG TRP R 173 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP R 173 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 173 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 173 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 173 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.017 5.00e-02 4.00e+02 2.49e-02 9.89e-01 pdb=" N PRO R 211 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.014 5.00e-02 4.00e+02 ... (remaining 363 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 472 2.78 - 3.31: 2101 3.31 - 3.84: 3495 3.84 - 4.37: 3607 4.37 - 4.90: 6804 Nonbonded interactions: 16479 Sorted by model distance: nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.248 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.294 3.040 nonbonded pdb=" OG SER R 203 " pdb=" OAK G1I R 501 " model vdw 2.438 3.040 nonbonded pdb=" O ALA R 92 " pdb=" OG1 THR R 96 " model vdw 2.448 3.040 nonbonded pdb=" O THR R 189 " pdb=" OG1 THR R 189 " model vdw 2.462 3.040 ... (remaining 16474 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=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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.920 Find NCS groups from input model: 0.010 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 0.005 0.050 2226 Z= 0.240 Angle : 0.584 5.623 3052 Z= 0.330 Chirality : 0.040 0.169 374 Planarity : 0.003 0.025 366 Dihedral : 13.181 80.230 723 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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 are not related in a simple way. whole: 2.26 (0.49), residues: 281 helix: 2.30 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.40 (0.63), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 63 TYR 0.010 0.001 TYR R 199 PHE 0.013 0.001 PHE R 108 TRP 0.017 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 2225) covalent geometry : angle 0.58387 ( 3050) SS BOND : bond 0.00123 ( 1) SS BOND : angle 0.45990 ( 2) hydrogen bonds : bond 0.17307 ( 168) hydrogen bonds : angle 5.37967 ( 504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.076 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0743 time to fit residues: 2.0288 Evaluate side-chains 18 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.075 ------------------------------------------------------------------------------- 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: 2.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.0770 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.127640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.110274 restraints weight = 2693.663| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.51 r_work: 0.3107 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2226 Z= 0.139 Angle : 0.479 5.435 3052 Z= 0.270 Chirality : 0.038 0.127 374 Planarity : 0.003 0.026 366 Dihedral : 4.896 20.447 316 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.40 % Allowed : 6.07 % Favored : 92.52 % 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 are not related in a simple way. whole: 2.79 (0.49), residues: 281 helix: 2.65 (0.34), residues: 224 sheet: None (None), residues: 0 loop : -1.68 (0.66), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 63 TYR 0.009 0.001 TYR R 308 PHE 0.011 0.001 PHE R 108 TRP 0.012 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 2225) covalent geometry : angle 0.47949 ( 3050) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.44226 ( 2) hydrogen bonds : bond 0.06397 ( 168) hydrogen bonds : angle 3.97093 ( 504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.057 Fit side-chains REVERT: R 63 ARG cc_start: 0.8244 (ptp90) cc_final: 0.6359 (mmt90) outliers start: 3 outliers final: 1 residues processed: 28 average time/residue: 0.0680 time to fit residues: 2.2073 Evaluate side-chains 23 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.0470 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.125864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.108572 restraints weight = 2771.239| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.54 r_work: 0.3081 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2226 Z= 0.142 Angle : 0.479 5.679 3052 Z= 0.263 Chirality : 0.038 0.122 374 Planarity : 0.003 0.027 366 Dihedral : 4.663 20.458 316 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.27 % Allowed : 8.88 % Favored : 87.85 % 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 are not related in a simple way. whole: 2.90 (0.49), residues: 281 helix: 2.76 (0.33), residues: 224 sheet: None (None), residues: 0 loop : -1.77 (0.66), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.009 0.001 TYR R 199 PHE 0.008 0.001 PHE R 217 TRP 0.009 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 2225) covalent geometry : angle 0.47917 ( 3050) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.46838 ( 2) hydrogen bonds : bond 0.06356 ( 168) hydrogen bonds : angle 3.79599 ( 504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.078 Fit side-chains REVERT: R 63 ARG cc_start: 0.8086 (ptp90) cc_final: 0.6301 (mmt90) REVERT: R 101 PHE cc_start: 0.8325 (m-80) cc_final: 0.7951 (m-80) outliers start: 7 outliers final: 4 residues processed: 27 average time/residue: 0.0609 time to fit residues: 2.0438 Evaluate side-chains 23 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 165 SER 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 2 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 0 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.126005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.109044 restraints weight = 2699.219| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.49 r_work: 0.3092 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2226 Z= 0.135 Angle : 0.461 5.355 3052 Z= 0.255 Chirality : 0.037 0.123 374 Planarity : 0.003 0.026 366 Dihedral : 4.565 20.149 316 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 11.21 % Favored : 85.98 % 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 are not related in a simple way. whole: 3.06 (0.49), residues: 281 helix: 2.85 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -1.72 (0.68), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.009 0.001 TYR R 199 PHE 0.008 0.001 PHE R 217 TRP 0.009 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2225) covalent geometry : angle 0.46094 ( 3050) SS BOND : bond 0.00068 ( 1) SS BOND : angle 0.47029 ( 2) hydrogen bonds : bond 0.06093 ( 168) hydrogen bonds : angle 3.72907 ( 504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.072 Fit side-chains REVERT: R 63 ARG cc_start: 0.8000 (ptp90) cc_final: 0.6264 (mmt90) REVERT: R 101 PHE cc_start: 0.8275 (m-80) cc_final: 0.7912 (m-80) outliers start: 6 outliers final: 5 residues processed: 26 average time/residue: 0.0603 time to fit residues: 1.9056 Evaluate side-chains 25 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 165 SER 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 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.0870 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.126856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.109889 restraints weight = 2739.625| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.51 r_work: 0.3103 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2226 Z= 0.127 Angle : 0.446 5.306 3052 Z= 0.247 Chirality : 0.037 0.120 374 Planarity : 0.003 0.026 366 Dihedral : 4.402 20.266 316 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 11.68 % Favored : 85.51 % 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 are not related in a simple way. whole: 3.17 (0.50), residues: 281 helix: 2.94 (0.34), residues: 225 sheet: None (None), residues: 0 loop : -1.74 (0.68), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.009 0.001 TYR R 199 PHE 0.007 0.001 PHE R 217 TRP 0.010 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 2225) covalent geometry : angle 0.44611 ( 3050) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.49396 ( 2) hydrogen bonds : bond 0.05820 ( 168) hydrogen bonds : angle 3.65927 ( 504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.082 Fit side-chains REVERT: R 63 ARG cc_start: 0.7985 (ptp90) cc_final: 0.6205 (mmt90) REVERT: R 101 PHE cc_start: 0.8263 (m-80) cc_final: 0.7949 (m-80) outliers start: 6 outliers final: 5 residues processed: 25 average time/residue: 0.0690 time to fit residues: 2.1000 Evaluate side-chains 24 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.124879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107999 restraints weight = 2728.544| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.50 r_work: 0.3073 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2226 Z= 0.141 Angle : 0.460 5.341 3052 Z= 0.256 Chirality : 0.038 0.121 374 Planarity : 0.003 0.026 366 Dihedral : 4.459 20.126 316 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.27 % Allowed : 12.15 % Favored : 84.58 % 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 are not related in a simple way. whole: 3.08 (0.50), residues: 281 helix: 2.87 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -1.72 (0.70), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 221 TYR 0.009 0.001 TYR R 199 PHE 0.008 0.001 PHE R 290 TRP 0.010 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 2225) covalent geometry : angle 0.45996 ( 3050) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.48569 ( 2) hydrogen bonds : bond 0.06241 ( 168) hydrogen bonds : angle 3.70785 ( 504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.046 Fit side-chains REVERT: R 63 ARG cc_start: 0.8008 (ptp90) cc_final: 0.6197 (mmt90) REVERT: R 101 PHE cc_start: 0.8313 (m-80) cc_final: 0.8000 (m-80) outliers start: 7 outliers final: 5 residues processed: 26 average time/residue: 0.0667 time to fit residues: 2.0583 Evaluate side-chains 25 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.122588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.105621 restraints weight = 2761.543| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.51 r_work: 0.3048 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2226 Z= 0.161 Angle : 0.484 5.362 3052 Z= 0.272 Chirality : 0.038 0.123 374 Planarity : 0.003 0.027 366 Dihedral : 4.472 20.340 316 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 13.55 % Favored : 83.64 % 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 are not related in a simple way. whole: 2.89 (0.49), residues: 281 helix: 2.71 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -1.67 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 175 TYR 0.010 0.001 TYR R 308 PHE 0.009 0.001 PHE R 290 TRP 0.010 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 2225) covalent geometry : angle 0.48435 ( 3050) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.45843 ( 2) hydrogen bonds : bond 0.06811 ( 168) hydrogen bonds : angle 3.81792 ( 504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.8031 (ptp90) cc_final: 0.6203 (mmt90) REVERT: R 101 PHE cc_start: 0.8313 (m-80) cc_final: 0.7991 (m-80) outliers start: 6 outliers final: 6 residues processed: 27 average time/residue: 0.0804 time to fit residues: 2.5323 Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 20 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.124426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.107584 restraints weight = 2747.492| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.50 r_work: 0.3072 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2226 Z= 0.137 Angle : 0.459 5.313 3052 Z= 0.257 Chirality : 0.037 0.121 374 Planarity : 0.003 0.027 366 Dihedral : 4.376 20.449 316 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 13.55 % Favored : 83.64 % 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 are not related in a simple way. whole: 3.03 (0.50), residues: 281 helix: 2.81 (0.34), residues: 225 sheet: None (None), residues: 0 loop : -1.63 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 131 TYR 0.009 0.001 TYR R 308 PHE 0.007 0.001 PHE R 290 TRP 0.011 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 2225) covalent geometry : angle 0.45926 ( 3050) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.48756 ( 2) hydrogen bonds : bond 0.06196 ( 168) hydrogen bonds : angle 3.71661 ( 504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.060 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.8006 (ptp90) cc_final: 0.6197 (mmt90) REVERT: R 101 PHE cc_start: 0.8304 (m-80) cc_final: 0.8091 (m-80) outliers start: 6 outliers final: 5 residues processed: 27 average time/residue: 0.0720 time to fit residues: 2.2716 Evaluate side-chains 27 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 0.0980 chunk 1 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.127521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110278 restraints weight = 2761.511| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.55 r_work: 0.3097 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2226 Z= 0.119 Angle : 0.438 5.278 3052 Z= 0.244 Chirality : 0.037 0.117 374 Planarity : 0.003 0.026 366 Dihedral : 4.225 20.415 316 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.27 % Allowed : 13.08 % Favored : 83.64 % 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 are not related in a simple way. whole: 3.16 (0.50), residues: 281 helix: 2.96 (0.34), residues: 224 sheet: None (None), residues: 0 loop : -1.77 (0.71), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.008 0.001 TYR R 199 PHE 0.007 0.001 PHE R 217 TRP 0.012 0.001 TRP R 173 HIS 0.002 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 2225) covalent geometry : angle 0.43839 ( 3050) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.56354 ( 2) hydrogen bonds : bond 0.05559 ( 168) hydrogen bonds : angle 3.60709 ( 504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.7980 (ptp90) cc_final: 0.6189 (mmt90) REVERT: R 101 PHE cc_start: 0.8268 (m-80) cc_final: 0.8039 (m-80) outliers start: 7 outliers final: 6 residues processed: 28 average time/residue: 0.0620 time to fit residues: 2.1192 Evaluate side-chains 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 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 = 0.3356 r_free = 0.3356 target = 0.123812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106801 restraints weight = 2807.175| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.52 r_work: 0.3062 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2226 Z= 0.150 Angle : 0.469 5.345 3052 Z= 0.263 Chirality : 0.038 0.120 374 Planarity : 0.003 0.027 366 Dihedral : 4.390 20.226 316 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 14.02 % Favored : 83.18 % 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 are not related in a simple way. whole: 2.99 (0.50), residues: 281 helix: 2.79 (0.34), residues: 225 sheet: None (None), residues: 0 loop : -1.68 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 175 TYR 0.010 0.001 TYR R 199 PHE 0.009 0.001 PHE R 290 TRP 0.013 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 2225) covalent geometry : angle 0.46943 ( 3050) SS BOND : bond 0.00105 ( 1) SS BOND : angle 0.48201 ( 2) hydrogen bonds : bond 0.06442 ( 168) hydrogen bonds : angle 3.73752 ( 504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.047 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.8019 (ptp90) cc_final: 0.6174 (mmt90) REVERT: R 101 PHE cc_start: 0.8304 (m-80) cc_final: 0.8079 (m-80) outliers start: 6 outliers final: 6 residues processed: 29 average time/residue: 0.0686 time to fit residues: 2.3184 Evaluate side-chains 30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 135 ILE Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 0.0030 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.125654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108664 restraints weight = 2821.881| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.52 r_work: 0.3088 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2226 Z= 0.127 Angle : 0.447 5.283 3052 Z= 0.249 Chirality : 0.037 0.118 374 Planarity : 0.003 0.026 366 Dihedral : 4.303 20.373 316 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 14.02 % Favored : 83.18 % 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 are not related in a simple way. whole: 3.12 (0.50), residues: 281 helix: 2.93 (0.34), residues: 224 sheet: None (None), residues: 0 loop : -1.77 (0.70), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 63 TYR 0.008 0.001 TYR R 308 PHE 0.007 0.001 PHE R 290 TRP 0.014 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 2225) covalent geometry : angle 0.44703 ( 3050) SS BOND : bond 0.00078 ( 1) SS BOND : angle 0.51685 ( 2) hydrogen bonds : bond 0.05854 ( 168) hydrogen bonds : angle 3.64751 ( 504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 756.94 seconds wall clock time: 13 minutes 32.62 seconds (812.62 seconds total)