Starting phenix.real_space_refine on Fri May 9 13:41:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggn_40014/05_2025/8ggn_40014.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggn_40014/05_2025/8ggn_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_40014/05_2025/8ggn_40014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggn_40014/05_2025/8ggn_40014.map" model { file = "/net/cci-nas-00/data/ceres_data/8ggn_40014/05_2025/8ggn_40014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggn_40014/05_2025/8ggn_40014.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} 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: 2.35, per 1000 atoms: 1.08 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: 0.60 Conformation dependent library (CDL) restraints added in 373.8 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: 0.21 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: 0.53 Time building geometry restraints manager: 0.69 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: 1.450 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.260 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.490 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.017 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.013 0.001 PHE R 108 TYR 0.010 0.001 TYR R 199 ARG 0.002 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.17307 ( 168) hydrogen bonds : angle 5.37967 ( 504) SS BOND : bond 0.00123 ( 1) SS BOND : angle 0.45990 ( 2) covalent geometry : bond 0.00464 ( 2225) covalent geometry : angle 0.58387 ( 3050) *********************** 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 : 0.265 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1524 time to fit residues: 4.3109 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 : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.127022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.109568 restraints weight = 2709.515| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.54 r_work: 0.3096 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 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 = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.0929 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= 0.144 Angle : 0.486 5.507 3052 Z= 0.274 Chirality : 0.038 0.126 374 Planarity : 0.003 0.026 366 Dihedral : 4.934 20.523 316 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.40 % Allowed : 6.54 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.49), residues: 281 helix: 2.64 (0.33), residues: 224 sheet: None (None), residues: 0 loop : -1.69 (0.67), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE R 108 TYR 0.009 0.001 TYR R 308 ARG 0.002 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.06507 ( 168) hydrogen bonds : angle 3.99304 ( 504) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.42394 ( 2) covalent geometry : bond 0.00306 ( 2225) covalent geometry : angle 0.48612 ( 3050) *********************** 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 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.237 Fit side-chains REVERT: R 63 ARG cc_start: 0.8241 (ptp90) cc_final: 0.6361 (mmt90) outliers start: 3 outliers final: 1 residues processed: 27 average time/residue: 0.1750 time to fit residues: 5.5938 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 : 0.188 ------------------------------------------------------------------------------- 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 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.127339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110075 restraints weight = 2749.902| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.53 r_work: 0.3097 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 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 = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1206 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 : 0.456 5.327 3052 Z= 0.255 Chirality : 0.037 0.123 374 Planarity : 0.003 0.026 366 Dihedral : 4.615 20.494 316 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.80 % Allowed : 7.48 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.49), residues: 281 helix: 2.79 (0.33), residues: 224 sheet: None (None), residues: 0 loop : -1.79 (0.66), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 217 TYR 0.009 0.001 TYR R 199 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.06118 ( 168) hydrogen bonds : angle 3.76156 ( 504) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.46788 ( 2) covalent geometry : bond 0.00290 ( 2225) covalent geometry : angle 0.45632 ( 3050) *********************** 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 27 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.228 Fit side-chains REVERT: R 63 ARG cc_start: 0.8073 (ptp90) cc_final: 0.6296 (mmt90) outliers start: 6 outliers final: 4 residues processed: 26 average time/residue: 0.1405 time to fit residues: 4.5005 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 : 0.223 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.122006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.105036 restraints weight = 2748.827| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.49 r_work: 0.3032 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2226 Z= 0.174 Angle : 0.498 5.402 3052 Z= 0.281 Chirality : 0.039 0.124 374 Planarity : 0.003 0.029 366 Dihedral : 4.799 20.639 316 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.34 % Allowed : 11.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.49), residues: 281 helix: 2.66 (0.33), residues: 224 sheet: None (None), residues: 0 loop : -1.72 (0.68), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 173 HIS 0.005 0.001 HIS R 296 PHE 0.010 0.001 PHE R 290 TYR 0.010 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.07252 ( 168) hydrogen bonds : angle 3.92367 ( 504) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.41642 ( 2) covalent geometry : bond 0.00399 ( 2225) covalent geometry : angle 0.49838 ( 3050) *********************** 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: 5 poor density : 22 time to evaluate : 0.247 Fit side-chains REVERT: R 63 ARG cc_start: 0.8068 (ptp90) cc_final: 0.6284 (mmt90) REVERT: R 101 PHE cc_start: 0.8320 (m-80) cc_final: 0.7947 (m-80) outliers start: 5 outliers final: 5 residues processed: 26 average time/residue: 0.1813 time to fit residues: 5.5749 Evaluate side-chains 26 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 12 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.125557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108512 restraints weight = 2739.751| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.51 r_work: 0.3079 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 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 = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1413 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= 0.136 Angle : 0.452 5.320 3052 Z= 0.254 Chirality : 0.037 0.122 374 Planarity : 0.003 0.028 366 Dihedral : 4.530 20.699 316 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.34 % Allowed : 11.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.50), residues: 281 helix: 2.79 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -1.72 (0.71), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.008 0.001 PHE R 217 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.06230 ( 168) hydrogen bonds : angle 3.74988 ( 504) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.46359 ( 2) covalent geometry : bond 0.00290 ( 2225) covalent geometry : angle 0.45201 ( 3050) *********************** 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: 5 poor density : 21 time to evaluate : 0.233 Fit side-chains REVERT: R 63 ARG cc_start: 0.8032 (ptp90) cc_final: 0.6197 (mmt90) REVERT: R 101 PHE cc_start: 0.8288 (m-80) cc_final: 0.7956 (m-80) outliers start: 5 outliers final: 4 residues processed: 25 average time/residue: 0.1432 time to fit residues: 4.4169 Evaluate side-chains 24 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.0270 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.126102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.109267 restraints weight = 2723.243| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.50 r_work: 0.3094 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 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 = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1507 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= 0.128 Angle : 0.440 5.291 3052 Z= 0.246 Chirality : 0.037 0.118 374 Planarity : 0.003 0.027 366 Dihedral : 4.362 20.571 316 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 : 3.27 % Allowed : 11.68 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.50), residues: 281 helix: 2.89 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -1.73 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.007 0.001 PHE R 290 TYR 0.009 0.001 TYR R 199 ARG 0.001 0.000 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.05833 ( 168) hydrogen bonds : angle 3.65418 ( 504) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.47558 ( 2) covalent geometry : bond 0.00271 ( 2225) covalent geometry : angle 0.44008 ( 3050) *********************** 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 29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.234 Fit side-chains REVERT: R 63 ARG cc_start: 0.7996 (ptp90) cc_final: 0.6205 (mmt90) outliers start: 7 outliers final: 5 residues processed: 28 average time/residue: 0.1352 time to fit residues: 4.6702 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 : 0.233 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.124103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.107089 restraints weight = 2789.665| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.51 r_work: 0.3066 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 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 = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1538 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= 0.146 Angle : 0.464 5.306 3052 Z= 0.261 Chirality : 0.038 0.121 374 Planarity : 0.003 0.027 366 Dihedral : 4.374 20.456 316 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 13.08 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.50), residues: 281 helix: 2.79 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -1.73 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 101 TYR 0.009 0.001 TYR R 199 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.06329 ( 168) hydrogen bonds : angle 3.73592 ( 504) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.46095 ( 2) covalent geometry : bond 0.00324 ( 2225) covalent geometry : angle 0.46388 ( 3050) *********************** 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 26 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.226 Fit side-chains REVERT: R 63 ARG cc_start: 0.8017 (ptp90) cc_final: 0.6176 (mmt90) outliers start: 6 outliers final: 6 residues processed: 25 average time/residue: 0.1598 time to fit residues: 4.8127 Evaluate side-chains 25 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.0070 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.124987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.108051 restraints weight = 2789.286| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.51 r_work: 0.3080 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 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 = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1588 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= 0.134 Angle : 0.451 5.299 3052 Z= 0.253 Chirality : 0.037 0.120 374 Planarity : 0.003 0.027 366 Dihedral : 4.334 20.518 316 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.27 % Allowed : 12.62 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.50), residues: 281 helix: 2.86 (0.34), residues: 225 sheet: None (None), residues: 0 loop : -1.67 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 101 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.06035 ( 168) hydrogen bonds : angle 3.68997 ( 504) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.49269 ( 2) covalent geometry : bond 0.00290 ( 2225) covalent geometry : angle 0.45076 ( 3050) *********************** 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 27 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.245 Fit side-chains REVERT: R 63 ARG cc_start: 0.8010 (ptp90) cc_final: 0.6177 (mmt90) outliers start: 7 outliers final: 6 residues processed: 26 average time/residue: 0.1595 time to fit residues: 5.0050 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 : 0.237 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.125001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108122 restraints weight = 2773.342| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.50 r_work: 0.3082 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 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 = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1623 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= 0.132 Angle : 0.448 5.290 3052 Z= 0.251 Chirality : 0.037 0.119 374 Planarity : 0.003 0.027 366 Dihedral : 4.298 20.446 316 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.27 % Allowed : 12.62 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.50), residues: 281 helix: 2.87 (0.34), residues: 225 sheet: None (None), residues: 0 loop : -1.66 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 101 TYR 0.009 0.001 TYR R 199 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.05964 ( 168) hydrogen bonds : angle 3.68278 ( 504) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.53092 ( 2) covalent geometry : bond 0.00283 ( 2225) covalent geometry : angle 0.44821 ( 3050) *********************** 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 28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.7995 (ptp90) cc_final: 0.6163 (mmt90) outliers start: 7 outliers final: 6 residues processed: 27 average time/residue: 0.1708 time to fit residues: 5.4438 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 : 0.214 ------------------------------------------------------------------------------- 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 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.123791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.106996 restraints weight = 2713.307| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.49 r_work: 0.3065 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 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 = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1614 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= 0.142 Angle : 0.459 5.317 3052 Z= 0.258 Chirality : 0.038 0.120 374 Planarity : 0.003 0.027 366 Dihedral : 4.372 20.470 316 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 13.08 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.50), residues: 281 helix: 2.81 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -1.67 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 173 HIS 0.003 0.001 HIS R 296 PHE 0.009 0.001 PHE R 101 TYR 0.009 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.06294 ( 168) hydrogen bonds : angle 3.73275 ( 504) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.49265 ( 2) covalent geometry : bond 0.00314 ( 2225) covalent geometry : angle 0.45898 ( 3050) ********************** 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 27 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: R 63 ARG cc_start: 0.8011 (ptp90) cc_final: 0.6172 (mmt90) outliers start: 6 outliers final: 6 residues processed: 26 average time/residue: 0.1702 time to fit residues: 5.2466 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 : 0.221 ------------------------------------------------------------------------------- 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 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.123145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.105916 restraints weight = 2750.984| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.55 r_work: 0.3039 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.004 0.026 2226 Z= 0.156 Angle : 0.475 5.352 3052 Z= 0.267 Chirality : 0.038 0.122 374 Planarity : 0.003 0.028 366 Dihedral : 4.474 20.581 316 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.80 % Allowed : 13.08 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.49), residues: 281 helix: 2.73 (0.33), residues: 225 sheet: None (None), residues: 0 loop : -1.66 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.009 0.001 PHE R 290 TYR 0.010 0.001 TYR R 308 ARG 0.001 0.000 ARG R 221 Details of bonding type rmsd hydrogen bonds : bond 0.06721 ( 168) hydrogen bonds : angle 3.81519 ( 504) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.45329 ( 2) covalent geometry : bond 0.00355 ( 2225) covalent geometry : angle 0.47492 ( 3050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1575.90 seconds wall clock time: 28 minutes 7.35 seconds (1687.35 seconds total)