Starting phenix.real_space_refine on Tue Mar 3 12:43:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iei_35382/03_2026/8iei_35382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iei_35382/03_2026/8iei_35382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iei_35382/03_2026/8iei_35382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iei_35382/03_2026/8iei_35382.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iei_35382/03_2026/8iei_35382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iei_35382/03_2026/8iei_35382.map" } resolution = 2.62 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= 0.011 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 35 5.16 5 C 2961 2.51 5 N 704 2.21 5 O 767 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4469 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2135 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2230 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain breaks: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 1.19, per 1000 atoms: 0.27 Number of scatterers: 4469 At special positions: 0 Unit cell: (68.04, 89.1, 102.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 2 15.00 O 767 8.00 N 704 7.00 C 2961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 216 " 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: 0.35 Conformation dependent library (CDL) restraints added in 258.5 milliseconds 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1048 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 1 sheets defined 78.3% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 46 through 74 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 84 through 105 removed outlier: 3.560A pdb=" N ILE A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 150 Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 161 through 187 removed outlier: 3.782A pdb=" N LEU A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 246 removed outlier: 4.099A pdb=" N TRP A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 281 removed outlier: 3.558A pdb=" N ASN A 265 " --> pdb=" O MET A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 327 Proline residue: A 310 - end of helix Processing helix chain 'B' and resid 46 through 74 Processing helix chain 'B' and resid 77 through 83 removed outlier: 3.692A pdb=" N SER B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 105 removed outlier: 3.664A pdb=" N VAL B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 149 Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 169 through 187 Processing helix chain 'B' and resid 220 through 246 removed outlier: 3.597A pdb=" N TRP B 224 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 281 Processing helix chain 'B' and resid 284 through 332 Proline residue: B 310 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 216 removed outlier: 3.508A pdb=" N PHE A 215 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 195 " --> pdb=" O MET B 199 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 215 " --> pdb=" O LEU B 192 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1140 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: 0.67 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 645 1.31 - 1.44: 1215 1.44 - 1.56: 2638 1.56 - 1.69: 12 1.69 - 1.81: 50 Bond restraints: 4560 Sorted by residual: bond pdb=" C39 PC1 B 601 " pdb=" C3A PC1 B 601 " ideal model delta sigma weight residual 1.524 1.324 0.200 2.00e-02 2.50e+03 9.99e+01 bond pdb=" C39 PC1 A 601 " pdb=" C3A PC1 A 601 " ideal model delta sigma weight residual 1.524 1.327 0.197 2.00e-02 2.50e+03 9.74e+01 bond pdb=" C31 PC1 A 601 " pdb=" O31 PC1 A 601 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C31 PC1 B 601 " pdb=" O31 PC1 B 601 " ideal model delta sigma weight residual 1.330 1.424 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C21 PC1 B 601 " pdb=" O21 PC1 B 601 " ideal model delta sigma weight residual 1.331 1.383 -0.052 2.00e-02 2.50e+03 6.74e+00 ... (remaining 4555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 6109 2.82 - 5.63: 64 5.63 - 8.45: 14 8.45 - 11.26: 0 11.26 - 14.08: 2 Bond angle restraints: 6189 Sorted by residual: angle pdb=" O12 PC1 B 601 " pdb=" P PC1 B 601 " pdb=" O14 PC1 B 601 " ideal model delta sigma weight residual 123.67 109.59 14.08 3.00e+00 1.11e-01 2.20e+01 angle pdb=" O12 PC1 A 601 " pdb=" P PC1 A 601 " pdb=" O14 PC1 A 601 " ideal model delta sigma weight residual 123.67 109.95 13.72 3.00e+00 1.11e-01 2.09e+01 angle pdb=" CB TRP B 229 " pdb=" CG TRP B 229 " pdb=" CD2 TRP B 229 " ideal model delta sigma weight residual 126.80 131.57 -4.77 1.40e+00 5.10e-01 1.16e+01 angle pdb=" CB TRP B 229 " pdb=" CG TRP B 229 " pdb=" CD1 TRP B 229 " ideal model delta sigma weight residual 126.90 122.30 4.60 1.50e+00 4.44e-01 9.41e+00 angle pdb=" C32 PC1 A 601 " pdb=" C31 PC1 A 601 " pdb=" O31 PC1 A 601 " ideal model delta sigma weight residual 111.44 119.80 -8.36 3.00e+00 1.11e-01 7.76e+00 ... (remaining 6184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 2452 17.56 - 35.12: 196 35.12 - 52.68: 42 52.68 - 70.25: 7 70.25 - 87.81: 5 Dihedral angle restraints: 2702 sinusoidal: 1080 harmonic: 1622 Sorted by residual: dihedral pdb=" CA ILE B 228 " pdb=" C ILE B 228 " pdb=" N TRP B 229 " pdb=" CA TRP B 229 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ILE A 307 " pdb=" C ILE A 307 " pdb=" N PHE A 308 " pdb=" CA PHE A 308 " 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=" CA ILE B 307 " pdb=" C ILE B 307 " pdb=" N PHE B 308 " pdb=" CA PHE B 308 " ideal model delta harmonic sigma weight residual -180.00 -161.73 -18.27 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 2699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 560 0.040 - 0.080: 152 0.080 - 0.119: 46 0.119 - 0.159: 3 0.159 - 0.199: 1 Chirality restraints: 762 Sorted by residual: chirality pdb=" CA TRP B 229 " pdb=" N TRP B 229 " pdb=" C TRP B 229 " pdb=" CB TRP B 229 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CB ILE B 225 " pdb=" CA ILE B 225 " pdb=" CG1 ILE B 225 " pdb=" CG2 ILE B 225 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 759 not shown) Planarity restraints: 721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 229 " -0.028 2.00e-02 2.50e+03 2.95e-02 2.17e+01 pdb=" CG TRP B 229 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP B 229 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 229 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 229 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 229 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 229 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 229 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 229 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 229 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 229 " -0.016 2.00e-02 2.50e+03 1.95e-02 9.53e+00 pdb=" CG TRP A 229 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 229 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 229 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 229 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 229 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 229 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 229 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 229 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 229 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 252 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO A 253 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " 0.035 5.00e-02 4.00e+02 ... (remaining 718 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 714 2.76 - 3.30: 4279 3.30 - 3.83: 7391 3.83 - 4.37: 8110 4.37 - 4.90: 15202 Nonbonded interactions: 35696 Sorted by model distance: nonbonded pdb=" OG SER A 84 " pdb=" NH2 ARG A 144 " model vdw 2.227 3.120 nonbonded pdb=" OG SER B 58 " pdb=" OH TYR B 103 " model vdw 2.246 3.040 nonbonded pdb=" OG SER A 132 " pdb=" OD2 ASP A 176 " model vdw 2.320 3.040 nonbonded pdb=" O VAL A 298 " pdb=" OG1 THR A 302 " model vdw 2.329 3.040 nonbonded pdb=" OG1 THR A 202 " pdb=" OD1 ASP A 205 " model vdw 2.347 3.040 ... (remaining 35691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 44 through 111 or resid 115 through 601)) selection = (chain 'B' and (resid 44 through 151 or (resid 152 and (name N or name CA or nam \ e C or name O or name CB )) or resid 160 or (resid 161 and (name N or name CA or \ name C or name O or name CB )) or resid 162 through 327 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.590 Find NCS groups from input model: 0.050 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:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.200 4562 Z= 0.349 Angle : 0.798 14.077 6193 Z= 0.379 Chirality : 0.040 0.199 762 Planarity : 0.005 0.062 721 Dihedral : 14.107 87.807 1648 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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 (0.35), residues: 555 helix: 2.86 (0.23), residues: 421 sheet: 1.83 (0.89), residues: 38 loop : -2.06 (0.56), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 75 TYR 0.010 0.001 TYR B 103 PHE 0.011 0.001 PHE A 308 TRP 0.080 0.003 TRP B 229 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00717 ( 4560) covalent geometry : angle 0.79852 ( 6189) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.26980 ( 4) hydrogen bonds : bond 0.12636 ( 381) hydrogen bonds : angle 4.89650 ( 1140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.126 Fit side-chains REVERT: A 79 ILE cc_start: 0.7930 (mm) cc_final: 0.7647 (mm) REVERT: A 199 MET cc_start: 0.7318 (ttm) cc_final: 0.6938 (ttm) REVERT: A 275 PHE cc_start: 0.8136 (t80) cc_final: 0.7924 (t80) REVERT: B 174 MET cc_start: 0.6158 (mmm) cc_final: 0.5737 (mmm) REVERT: B 193 GLN cc_start: 0.7231 (tt0) cc_final: 0.6882 (tt0) REVERT: B 283 SER cc_start: 0.8344 (m) cc_final: 0.8064 (t) REVERT: B 312 LEU cc_start: 0.7856 (mp) cc_final: 0.7587 (mt) outliers start: 0 outliers final: 1 residues processed: 81 average time/residue: 0.3249 time to fit residues: 27.9223 Evaluate side-chains 69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 0.0980 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.0980 chunk 53 optimal weight: 0.3980 overall best weight: 0.1156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN B 256 GLN B 311 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.138470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.116891 restraints weight = 5678.068| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.01 r_work: 0.3481 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.002 0.023 4562 Z= 0.122 Angle : 0.510 7.115 6193 Z= 0.269 Chirality : 0.038 0.176 762 Planarity : 0.005 0.059 721 Dihedral : 11.062 76.566 686 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.01 % Allowed : 7.85 % Favored : 91.15 % 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: 3.56 (0.34), residues: 555 helix: 3.21 (0.22), residues: 426 sheet: 3.01 (1.24), residues: 18 loop : -1.53 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 75 TYR 0.010 0.001 TYR A 280 PHE 0.026 0.001 PHE B 215 TRP 0.017 0.001 TRP B 229 HIS 0.001 0.000 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 4560) covalent geometry : angle 0.51010 ( 6189) SS BOND : bond 0.00416 ( 2) SS BOND : angle 0.50805 ( 4) hydrogen bonds : bond 0.04248 ( 381) hydrogen bonds : angle 4.08151 ( 1140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.156 Fit side-chains REVERT: A 79 ILE cc_start: 0.8120 (mm) cc_final: 0.7836 (mm) REVERT: A 103 TYR cc_start: 0.7969 (m-80) cc_final: 0.7760 (m-80) REVERT: B 174 MET cc_start: 0.6518 (mmm) cc_final: 0.6107 (mmm) REVERT: B 199 MET cc_start: 0.7396 (mtm) cc_final: 0.7114 (mtm) REVERT: B 312 LEU cc_start: 0.8586 (mp) cc_final: 0.8333 (mt) outliers start: 5 outliers final: 0 residues processed: 68 average time/residue: 0.2700 time to fit residues: 19.6455 Evaluate side-chains 62 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 31 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 35 optimal weight: 0.1980 chunk 30 optimal weight: 0.4980 chunk 33 optimal weight: 0.0870 chunk 28 optimal weight: 0.2980 chunk 47 optimal weight: 0.0020 overall best weight: 0.0964 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.139236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.118113 restraints weight = 5635.598| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.95 r_work: 0.3506 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4562 Z= 0.109 Angle : 0.495 9.317 6193 Z= 0.259 Chirality : 0.038 0.178 762 Planarity : 0.005 0.061 721 Dihedral : 10.025 72.639 684 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.81 % Allowed : 9.26 % Favored : 88.93 % 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: 3.83 (0.34), residues: 555 helix: 3.40 (0.22), residues: 431 sheet: 2.99 (1.58), residues: 12 loop : -1.37 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 75 TYR 0.008 0.001 TYR A 280 PHE 0.019 0.001 PHE B 215 TRP 0.008 0.001 TRP B 284 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 4560) covalent geometry : angle 0.49478 ( 6189) SS BOND : bond 0.00262 ( 2) SS BOND : angle 0.40939 ( 4) hydrogen bonds : bond 0.03908 ( 381) hydrogen bonds : angle 3.85996 ( 1140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.117 Fit side-chains REVERT: A 68 LEU cc_start: 0.8502 (tp) cc_final: 0.8300 (tp) REVERT: A 79 ILE cc_start: 0.8091 (mm) cc_final: 0.7845 (mm) REVERT: B 75 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7727 (ttp80) REVERT: B 174 MET cc_start: 0.6591 (mmm) cc_final: 0.6175 (mmm) outliers start: 9 outliers final: 2 residues processed: 70 average time/residue: 0.2780 time to fit residues: 20.8271 Evaluate side-chains 62 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 181 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.0000 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.135639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.114751 restraints weight = 5544.956| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.94 r_work: 0.3445 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4562 Z= 0.225 Angle : 0.574 9.041 6193 Z= 0.302 Chirality : 0.043 0.196 762 Planarity : 0.005 0.058 721 Dihedral : 10.797 79.886 684 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.61 % Allowed : 10.26 % Favored : 88.13 % 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: 3.48 (0.34), residues: 555 helix: 3.12 (0.22), residues: 432 sheet: 2.67 (1.48), residues: 12 loop : -1.40 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 75 TYR 0.017 0.001 TYR B 280 PHE 0.014 0.002 PHE B 318 TRP 0.011 0.002 TRP A 183 HIS 0.002 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00548 ( 4560) covalent geometry : angle 0.57440 ( 6189) SS BOND : bond 0.00424 ( 2) SS BOND : angle 0.59284 ( 4) hydrogen bonds : bond 0.04894 ( 381) hydrogen bonds : angle 4.00409 ( 1140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.171 Fit side-chains REVERT: A 79 ILE cc_start: 0.8201 (mm) cc_final: 0.7976 (mm) REVERT: B 72 ILE cc_start: 0.8628 (mm) cc_final: 0.8376 (mt) REVERT: B 174 MET cc_start: 0.6799 (mmm) cc_final: 0.6365 (mmm) REVERT: B 193 GLN cc_start: 0.7734 (tt0) cc_final: 0.7488 (tt0) REVERT: B 199 MET cc_start: 0.7726 (mtm) cc_final: 0.7455 (mtm) REVERT: B 209 THR cc_start: 0.8551 (m) cc_final: 0.8344 (t) outliers start: 8 outliers final: 3 residues processed: 74 average time/residue: 0.2490 time to fit residues: 19.7966 Evaluate side-chains 68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 195 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 32 optimal weight: 0.0980 chunk 45 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 21 optimal weight: 0.2980 chunk 52 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 0.0970 chunk 28 optimal weight: 0.2980 overall best weight: 0.2378 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.137141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.116217 restraints weight = 5570.666| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.95 r_work: 0.3468 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4562 Z= 0.137 Angle : 0.520 10.696 6193 Z= 0.272 Chirality : 0.039 0.169 762 Planarity : 0.005 0.058 721 Dihedral : 10.522 76.312 684 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.21 % Allowed : 12.68 % Favored : 86.12 % 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: 3.71 (0.34), residues: 555 helix: 3.34 (0.22), residues: 430 sheet: 2.32 (1.41), residues: 12 loop : -1.40 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 75 TYR 0.009 0.001 TYR B 280 PHE 0.031 0.001 PHE B 215 TRP 0.008 0.001 TRP B 284 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4560) covalent geometry : angle 0.52020 ( 6189) SS BOND : bond 0.00387 ( 2) SS BOND : angle 0.41880 ( 4) hydrogen bonds : bond 0.04253 ( 381) hydrogen bonds : angle 3.84231 ( 1140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.111 Fit side-chains REVERT: A 79 ILE cc_start: 0.8144 (mm) cc_final: 0.7925 (mm) REVERT: A 200 THR cc_start: 0.8242 (m) cc_final: 0.7883 (p) REVERT: A 279 ARG cc_start: 0.8430 (tpp80) cc_final: 0.8010 (ttt90) REVERT: B 72 ILE cc_start: 0.8634 (mm) cc_final: 0.8431 (mt) REVERT: B 174 MET cc_start: 0.6778 (mmm) cc_final: 0.6312 (mmm) REVERT: B 193 GLN cc_start: 0.7692 (tt0) cc_final: 0.7458 (tt0) REVERT: B 199 MET cc_start: 0.7741 (mtm) cc_final: 0.7472 (mtm) REVERT: B 209 THR cc_start: 0.8526 (m) cc_final: 0.8290 (t) outliers start: 6 outliers final: 4 residues processed: 67 average time/residue: 0.2754 time to fit residues: 19.7266 Evaluate side-chains 67 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 195 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 0.3980 chunk 2 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 9 optimal weight: 0.4980 chunk 41 optimal weight: 0.1980 chunk 47 optimal weight: 0.0770 overall best weight: 0.2538 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.137107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.116037 restraints weight = 5681.248| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.97 r_work: 0.3463 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4562 Z= 0.141 Angle : 0.498 8.798 6193 Z= 0.266 Chirality : 0.040 0.213 762 Planarity : 0.005 0.059 721 Dihedral : 10.435 78.204 684 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.41 % Allowed : 12.47 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.74 (0.34), residues: 555 helix: 3.35 (0.22), residues: 431 sheet: 2.05 (1.38), residues: 12 loop : -1.34 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.009 0.001 TYR B 280 PHE 0.030 0.002 PHE B 215 TRP 0.008 0.001 TRP B 284 HIS 0.001 0.000 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4560) covalent geometry : angle 0.49829 ( 6189) SS BOND : bond 0.00351 ( 2) SS BOND : angle 0.49686 ( 4) hydrogen bonds : bond 0.04214 ( 381) hydrogen bonds : angle 3.80754 ( 1140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.177 Fit side-chains REVERT: A 79 ILE cc_start: 0.8134 (mm) cc_final: 0.7913 (mm) REVERT: A 200 THR cc_start: 0.8189 (m) cc_final: 0.7896 (p) REVERT: B 174 MET cc_start: 0.6859 (mmm) cc_final: 0.6395 (mmm) REVERT: B 193 GLN cc_start: 0.7717 (tt0) cc_final: 0.7483 (tt0) REVERT: B 199 MET cc_start: 0.7774 (mtm) cc_final: 0.7459 (mtm) outliers start: 12 outliers final: 6 residues processed: 68 average time/residue: 0.2974 time to fit residues: 21.5933 Evaluate side-chains 67 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 246 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.0980 chunk 37 optimal weight: 0.0270 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 23 optimal weight: 0.2980 overall best weight: 0.2638 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.137092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116053 restraints weight = 5574.406| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.96 r_work: 0.3464 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4562 Z= 0.143 Angle : 0.519 10.699 6193 Z= 0.270 Chirality : 0.040 0.178 762 Planarity : 0.005 0.059 721 Dihedral : 10.368 78.682 684 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.01 % Allowed : 12.88 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.77 (0.34), residues: 555 helix: 3.36 (0.22), residues: 431 sheet: 1.84 (1.37), residues: 12 loop : -1.29 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.010 0.001 TYR B 280 PHE 0.030 0.001 PHE B 215 TRP 0.008 0.001 TRP B 284 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4560) covalent geometry : angle 0.51936 ( 6189) SS BOND : bond 0.00336 ( 2) SS BOND : angle 0.45060 ( 4) hydrogen bonds : bond 0.04268 ( 381) hydrogen bonds : angle 3.78670 ( 1140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.162 Fit side-chains REVERT: A 79 ILE cc_start: 0.8131 (mm) cc_final: 0.7904 (mm) REVERT: A 200 THR cc_start: 0.8192 (m) cc_final: 0.7895 (p) REVERT: A 279 ARG cc_start: 0.8502 (tpp80) cc_final: 0.8047 (ttm170) REVERT: B 149 PHE cc_start: 0.7576 (m-80) cc_final: 0.6423 (t80) REVERT: B 174 MET cc_start: 0.6921 (mmm) cc_final: 0.6437 (mmm) REVERT: B 193 GLN cc_start: 0.7707 (tt0) cc_final: 0.7485 (tt0) REVERT: B 199 MET cc_start: 0.7803 (mtm) cc_final: 0.7500 (mtm) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.3047 time to fit residues: 22.1722 Evaluate side-chains 70 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 246 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 25 optimal weight: 0.0370 chunk 3 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 8 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 overall best weight: 0.3058 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.136415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115611 restraints weight = 5536.267| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.94 r_work: 0.3456 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4562 Z= 0.155 Angle : 0.514 9.214 6193 Z= 0.272 Chirality : 0.040 0.223 762 Planarity : 0.005 0.059 721 Dihedral : 10.418 80.374 684 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.81 % Allowed : 13.08 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.71 (0.34), residues: 555 helix: 3.32 (0.22), residues: 431 sheet: 1.63 (1.39), residues: 12 loop : -1.29 (0.59), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 279 TYR 0.010 0.001 TYR B 280 PHE 0.030 0.002 PHE B 215 TRP 0.008 0.001 TRP B 284 HIS 0.000 0.000 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4560) covalent geometry : angle 0.51362 ( 6189) SS BOND : bond 0.00366 ( 2) SS BOND : angle 0.47470 ( 4) hydrogen bonds : bond 0.04360 ( 381) hydrogen bonds : angle 3.80722 ( 1140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.157 Fit side-chains REVERT: A 79 ILE cc_start: 0.8136 (mm) cc_final: 0.7871 (mm) REVERT: A 200 THR cc_start: 0.8177 (m) cc_final: 0.7898 (p) REVERT: A 279 ARG cc_start: 0.8510 (tpp80) cc_final: 0.8196 (tpp-160) REVERT: B 149 PHE cc_start: 0.7578 (m-80) cc_final: 0.6425 (t80) REVERT: B 174 MET cc_start: 0.6961 (mmm) cc_final: 0.6479 (mmm) REVERT: B 193 GLN cc_start: 0.7706 (tt0) cc_final: 0.7483 (tt0) REVERT: B 199 MET cc_start: 0.7757 (mtm) cc_final: 0.7459 (mtm) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 0.3154 time to fit residues: 22.1750 Evaluate side-chains 69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 246 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 10 optimal weight: 0.0970 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.135241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.115070 restraints weight = 5639.665| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.83 r_work: 0.3458 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4562 Z= 0.171 Angle : 0.542 11.587 6193 Z= 0.282 Chirality : 0.041 0.185 762 Planarity : 0.005 0.059 721 Dihedral : 10.590 82.068 684 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.21 % Allowed : 14.49 % Favored : 84.31 % 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: 3.75 (0.33), residues: 555 helix: 3.28 (0.22), residues: 431 sheet: 2.20 (0.88), residues: 24 loop : -1.42 (0.62), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.012 0.001 TYR B 280 PHE 0.030 0.002 PHE B 215 TRP 0.008 0.001 TRP B 284 HIS 0.000 0.000 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 4560) covalent geometry : angle 0.54243 ( 6189) SS BOND : bond 0.00372 ( 2) SS BOND : angle 0.46384 ( 4) hydrogen bonds : bond 0.04520 ( 381) hydrogen bonds : angle 3.81940 ( 1140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.117 Fit side-chains REVERT: A 200 THR cc_start: 0.8174 (m) cc_final: 0.7928 (p) REVERT: A 279 ARG cc_start: 0.8508 (tpp80) cc_final: 0.8206 (tpp-160) REVERT: B 149 PHE cc_start: 0.7590 (m-80) cc_final: 0.6451 (t80) REVERT: B 174 MET cc_start: 0.7019 (mmm) cc_final: 0.6536 (mmm) REVERT: B 193 GLN cc_start: 0.7702 (tt0) cc_final: 0.7488 (tt0) REVERT: B 199 MET cc_start: 0.7751 (mtm) cc_final: 0.7448 (mtm) outliers start: 6 outliers final: 7 residues processed: 67 average time/residue: 0.2999 time to fit residues: 21.3667 Evaluate side-chains 70 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 246 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 7 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 48 optimal weight: 0.0060 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.134642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114494 restraints weight = 5624.881| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.84 r_work: 0.3453 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4562 Z= 0.191 Angle : 0.555 8.923 6193 Z= 0.289 Chirality : 0.042 0.237 762 Planarity : 0.005 0.060 721 Dihedral : 10.739 83.250 684 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.61 % Allowed : 13.88 % Favored : 84.51 % 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: 3.65 (0.33), residues: 555 helix: 3.23 (0.22), residues: 429 sheet: 2.22 (0.88), residues: 24 loop : -1.47 (0.61), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 279 TYR 0.012 0.001 TYR B 280 PHE 0.030 0.002 PHE B 215 TRP 0.009 0.001 TRP A 183 HIS 0.001 0.000 HIS B 248 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 4560) covalent geometry : angle 0.55543 ( 6189) SS BOND : bond 0.00394 ( 2) SS BOND : angle 0.45992 ( 4) hydrogen bonds : bond 0.04571 ( 381) hydrogen bonds : angle 3.84488 ( 1140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.169 Fit side-chains REVERT: A 79 ILE cc_start: 0.8204 (mm) cc_final: 0.7978 (mm) REVERT: A 200 THR cc_start: 0.8175 (m) cc_final: 0.7928 (p) REVERT: B 149 PHE cc_start: 0.7590 (m-80) cc_final: 0.6355 (t80) REVERT: B 174 MET cc_start: 0.7054 (mmm) cc_final: 0.6588 (mmm) REVERT: B 193 GLN cc_start: 0.7714 (tt0) cc_final: 0.7500 (tt0) REVERT: B 199 MET cc_start: 0.7732 (mtm) cc_final: 0.7441 (mtm) outliers start: 8 outliers final: 7 residues processed: 67 average time/residue: 0.2896 time to fit residues: 20.7695 Evaluate side-chains 70 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 246 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 31 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 17 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.135518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115333 restraints weight = 5673.241| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.85 r_work: 0.3464 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4562 Z= 0.154 Angle : 0.536 11.847 6193 Z= 0.278 Chirality : 0.040 0.191 762 Planarity : 0.005 0.059 721 Dihedral : 10.730 83.333 684 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.61 % Allowed : 14.08 % Favored : 84.31 % 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: 3.78 (0.33), residues: 555 helix: 3.35 (0.22), residues: 425 sheet: 2.29 (0.86), residues: 24 loop : -1.39 (0.59), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.010 0.001 TYR B 280 PHE 0.029 0.002 PHE B 215 TRP 0.009 0.001 TRP B 315 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4560) covalent geometry : angle 0.53637 ( 6189) SS BOND : bond 0.00350 ( 2) SS BOND : angle 0.43464 ( 4) hydrogen bonds : bond 0.04381 ( 381) hydrogen bonds : angle 3.80103 ( 1140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1753.56 seconds wall clock time: 30 minutes 37.10 seconds (1837.10 seconds total)