Starting phenix.real_space_refine on Tue Mar 3 12:14:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wlv_21843/03_2026/6wlv_21843.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wlv_21843/03_2026/6wlv_21843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wlv_21843/03_2026/6wlv_21843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wlv_21843/03_2026/6wlv_21843.map" model { file = "/net/cci-nas-00/data/ceres_data/6wlv_21843/03_2026/6wlv_21843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wlv_21843/03_2026/6wlv_21843.cif" } resolution = 3.45 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= 1.000 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 K 3 8.98 5 S 14 5.16 5 C 2744 2.51 5 N 668 2.21 5 O 682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s 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: 4111 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2054 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "B" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2054 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.06, per 1000 atoms: 0.26 Number of scatterers: 4111 At special positions: 0 Unit cell: (94.371, 65.946, 78.453, 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) K 3 19.00 S 14 16.00 O 682 8.00 N 668 7.00 C 2744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS B 51 " 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: 0.42 Conformation dependent library (CDL) restraints added in 172.6 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 5 through 48 removed outlier: 3.812A pdb=" N THR A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 10 " --> pdb=" O PRO A 6 " (cutoff:3.500A) Proline residue: A 29 - end of helix Processing helix chain 'A' and resid 53 through 70 removed outlier: 3.594A pdb=" N GLN A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 96 Processing helix chain 'A' and resid 108 through 152 removed outlier: 3.686A pdb=" N PHE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.677A pdb=" N ARG A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.602A pdb=" N VAL A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 202 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'A' and resid 244 through 254 removed outlier: 4.442A pdb=" N MET A 248 " --> pdb=" O TRP A 244 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 removed outlier: 4.256A pdb=" N LYS A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 259' Processing helix chain 'B' and resid 7 through 49 Proline residue: B 29 - end of helix removed outlier: 3.586A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 84 through 96 removed outlier: 3.927A pdb=" N ILE B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 93 " --> pdb=" O MET B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 152 Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.724A pdb=" N VAL B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 Processing helix chain 'B' and resid 222 through 244 removed outlier: 3.710A pdb=" N LEU B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 254 Processing helix chain 'B' and resid 255 through 260 292 hydrogen bonds defined for protein. 876 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: 0.68 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1226 1.34 - 1.46: 886 1.46 - 1.57: 2104 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4236 Sorted by residual: bond pdb=" CB PRO B 179 " pdb=" CG PRO B 179 " ideal model delta sigma weight residual 1.492 1.453 0.039 5.00e-02 4.00e+02 6.15e-01 bond pdb=" CG1 ILE B 12 " pdb=" CD1 ILE B 12 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 5.85e-01 bond pdb=" CB PRO A 179 " pdb=" CG PRO A 179 " ideal model delta sigma weight residual 1.492 1.455 0.037 5.00e-02 4.00e+02 5.57e-01 bond pdb=" CB ILE A 199 " pdb=" CG2 ILE A 199 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.28e-01 bond pdb=" C PRO B 178 " pdb=" N PRO B 179 " ideal model delta sigma weight residual 1.333 1.344 -0.010 1.44e-02 4.82e+03 5.14e-01 ... (remaining 4231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 5489 1.08 - 2.16: 223 2.16 - 3.24: 33 3.24 - 4.32: 13 4.32 - 5.40: 10 Bond angle restraints: 5768 Sorted by residual: angle pdb=" N PRO A 178 " pdb=" CA PRO A 178 " pdb=" C PRO A 178 " ideal model delta sigma weight residual 110.70 113.67 -2.97 1.22e+00 6.72e-01 5.93e+00 angle pdb=" N TRP B 85 " pdb=" CA TRP B 85 " pdb=" C TRP B 85 " ideal model delta sigma weight residual 109.81 114.30 -4.49 2.21e+00 2.05e-01 4.13e+00 angle pdb=" N PRO B 178 " pdb=" CA PRO B 178 " pdb=" C PRO B 178 " ideal model delta sigma weight residual 110.70 113.14 -2.44 1.22e+00 6.72e-01 3.98e+00 angle pdb=" C TRP B 244 " pdb=" N LYS B 245 " pdb=" CA LYS B 245 " ideal model delta sigma weight residual 120.79 123.55 -2.76 1.39e+00 5.18e-01 3.95e+00 angle pdb=" CA TRP B 85 " pdb=" C TRP B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 118.44 121.55 -3.11 1.59e+00 3.96e-01 3.83e+00 ... (remaining 5763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 2142 16.04 - 32.08: 197 32.08 - 48.11: 52 48.11 - 64.15: 6 64.15 - 80.19: 2 Dihedral angle restraints: 2399 sinusoidal: 925 harmonic: 1474 Sorted by residual: dihedral pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " pdb=" SG CYS B 51 " pdb=" CB CYS B 51 " ideal model delta sinusoidal sigma weight residual 93.00 134.32 -41.32 1 1.00e+01 1.00e-02 2.39e+01 dihedral pdb=" CA ASN A 189 " pdb=" C ASN A 189 " pdb=" N TYR A 190 " pdb=" CA TYR A 190 " ideal model delta harmonic sigma weight residual -180.00 -163.83 -16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA GLY A 102 " pdb=" C GLY A 102 " pdb=" N ASN A 103 " pdb=" CA ASN A 103 " ideal model delta harmonic sigma weight residual 180.00 164.16 15.84 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 2396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 333 0.026 - 0.052: 189 0.052 - 0.079: 77 0.079 - 0.105: 33 0.105 - 0.131: 6 Chirality restraints: 638 Sorted by residual: chirality pdb=" CB VAL A 246 " pdb=" CA VAL A 246 " pdb=" CG1 VAL A 246 " pdb=" CG2 VAL A 246 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA PRO A 179 " pdb=" N PRO A 179 " pdb=" C PRO A 179 " pdb=" CB PRO A 179 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA THR A 98 " pdb=" N THR A 98 " pdb=" C THR A 98 " pdb=" CB THR A 98 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 635 not shown) Planarity restraints: 706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 178 " -0.027 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A 179 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 178 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO B 179 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 177 " 0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO A 178 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " 0.014 5.00e-02 4.00e+02 ... (remaining 703 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.80: 1122 2.80 - 3.38: 4936 3.38 - 3.97: 7710 3.97 - 4.55: 10811 4.55 - 5.14: 15422 Nonbonded interactions: 40001 Sorted by model distance: nonbonded pdb=" O ALA A 93 " pdb=" OG1 THR A 97 " model vdw 2.211 3.040 nonbonded pdb=" O LEU A 7 " pdb=" OG SER A 10 " model vdw 2.214 3.040 nonbonded pdb=" O GLU B 33 " pdb=" ND2 ASN B 37 " model vdw 2.284 3.120 nonbonded pdb=" NE2 GLN A 54 " pdb=" OD1 ASP A 58 " model vdw 2.321 3.120 nonbonded pdb=" O ALA B 236 " pdb=" OG SER B 239 " model vdw 2.357 3.040 ... (remaining 39996 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 5 through 260) selection = chain 'B' } 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: 0.270 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.170 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.004 0.039 4237 Z= 0.171 Angle : 0.558 5.404 5770 Z= 0.318 Chirality : 0.040 0.131 638 Planarity : 0.003 0.040 706 Dihedral : 13.212 80.190 1456 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % 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: -0.61 (0.36), residues: 508 helix: 0.28 (0.25), residues: 372 sheet: None (None), residues: 0 loop : -2.17 (0.54), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 112 TYR 0.016 0.001 TYR B 195 PHE 0.010 0.001 PHE B 241 TRP 0.009 0.001 TRP B 31 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 4236) covalent geometry : angle 0.55801 ( 5768) SS BOND : bond 0.00257 ( 1) SS BOND : angle 0.12407 ( 2) hydrogen bonds : bond 0.12216 ( 292) hydrogen bonds : angle 5.73037 ( 876) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: B 143 ARG cc_start: 0.7674 (ttp-170) cc_final: 0.7402 (tmm-80) REVERT: B 190 TYR cc_start: 0.8255 (t80) cc_final: 0.7818 (t80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0754 time to fit residues: 7.5320 Evaluate side-chains 55 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 218 ASN A 253 HIS B 174 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.102411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.078968 restraints weight = 10635.560| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.66 r_work: 0.3041 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4237 Z= 0.145 Angle : 0.558 5.778 5770 Z= 0.292 Chirality : 0.041 0.126 638 Planarity : 0.004 0.048 706 Dihedral : 3.822 14.458 552 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.41 % Allowed : 11.27 % Favored : 87.32 % 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: 1.06 (0.38), residues: 508 helix: 1.64 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -2.49 (0.54), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.017 0.001 TYR B 38 PHE 0.020 0.001 PHE B 147 TRP 0.017 0.001 TRP B 129 HIS 0.002 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4236) covalent geometry : angle 0.55785 ( 5768) SS BOND : bond 0.00290 ( 1) SS BOND : angle 0.50045 ( 2) hydrogen bonds : bond 0.03670 ( 292) hydrogen bonds : angle 4.40414 ( 876) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8935 (m-30) cc_final: 0.8533 (m-30) REVERT: B 143 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7495 (tmm-80) REVERT: B 190 TYR cc_start: 0.8641 (t80) cc_final: 0.8030 (t80) outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 0.0621 time to fit residues: 5.8780 Evaluate side-chains 64 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 162 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 21 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 24 optimal weight: 0.0670 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 6 optimal weight: 0.0970 overall best weight: 1.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.102101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.078748 restraints weight = 10600.950| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.66 r_work: 0.3038 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4237 Z= 0.152 Angle : 0.532 5.608 5770 Z= 0.279 Chirality : 0.041 0.127 638 Planarity : 0.004 0.051 706 Dihedral : 3.760 13.855 552 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.41 % Allowed : 13.38 % Favored : 85.21 % 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: 1.63 (0.38), residues: 508 helix: 2.01 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.18 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 112 TYR 0.013 0.002 TYR A 195 PHE 0.019 0.001 PHE B 147 TRP 0.022 0.001 TRP B 129 HIS 0.002 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 4236) covalent geometry : angle 0.53196 ( 5768) SS BOND : bond 0.00313 ( 1) SS BOND : angle 0.48841 ( 2) hydrogen bonds : bond 0.03440 ( 292) hydrogen bonds : angle 4.26581 ( 876) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8830 (m-30) cc_final: 0.8459 (m-30) REVERT: B 49 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7079 (m-80) REVERT: B 190 TYR cc_start: 0.8648 (t80) cc_final: 0.7982 (t80) outliers start: 6 outliers final: 5 residues processed: 72 average time/residue: 0.0535 time to fit residues: 5.2059 Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 0.4980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.102298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.079093 restraints weight = 10424.027| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.63 r_work: 0.3045 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4237 Z= 0.133 Angle : 0.519 5.799 5770 Z= 0.270 Chirality : 0.040 0.128 638 Planarity : 0.004 0.052 706 Dihedral : 3.674 13.653 552 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.58 % Allowed : 14.79 % Favored : 82.63 % 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: 1.96 (0.38), residues: 508 helix: 2.25 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.08 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 112 TYR 0.013 0.001 TYR B 223 PHE 0.018 0.001 PHE B 147 TRP 0.014 0.001 TRP B 129 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4236) covalent geometry : angle 0.51855 ( 5768) SS BOND : bond 0.00314 ( 1) SS BOND : angle 0.44100 ( 2) hydrogen bonds : bond 0.03202 ( 292) hydrogen bonds : angle 4.15145 ( 876) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8795 (t0) cc_final: 0.8535 (t0) REVERT: A 195 TYR cc_start: 0.9060 (t80) cc_final: 0.8729 (t80) REVERT: B 49 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.6934 (m-80) REVERT: B 148 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6315 (mm) REVERT: B 190 TYR cc_start: 0.8669 (t80) cc_final: 0.8043 (t80) outliers start: 11 outliers final: 5 residues processed: 78 average time/residue: 0.0457 time to fit residues: 4.9533 Evaluate side-chains 74 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.103466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.080455 restraints weight = 10475.114| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.65 r_work: 0.3073 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4237 Z= 0.106 Angle : 0.511 6.007 5770 Z= 0.262 Chirality : 0.039 0.147 638 Planarity : 0.004 0.053 706 Dihedral : 3.564 13.230 552 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.58 % Allowed : 15.96 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.39), residues: 508 helix: 2.43 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.05 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 112 TYR 0.014 0.001 TYR B 223 PHE 0.017 0.001 PHE B 147 TRP 0.026 0.001 TRP B 129 HIS 0.003 0.000 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 4236) covalent geometry : angle 0.51133 ( 5768) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.32475 ( 2) hydrogen bonds : bond 0.03015 ( 292) hydrogen bonds : angle 4.05585 ( 876) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8790 (t0) cc_final: 0.8552 (t0) REVERT: A 195 TYR cc_start: 0.9037 (t80) cc_final: 0.8694 (t80) REVERT: B 44 HIS cc_start: 0.8945 (t-90) cc_final: 0.8684 (t-90) REVERT: B 49 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.6963 (m-80) REVERT: B 148 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6276 (mm) REVERT: B 190 TYR cc_start: 0.8667 (t80) cc_final: 0.8152 (t80) outliers start: 11 outliers final: 7 residues processed: 82 average time/residue: 0.0501 time to fit residues: 5.6585 Evaluate side-chains 78 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 0.0770 chunk 46 optimal weight: 0.0370 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.2418 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.102926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.079953 restraints weight = 10591.396| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.68 r_work: 0.3056 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4237 Z= 0.131 Angle : 0.530 6.698 5770 Z= 0.273 Chirality : 0.040 0.134 638 Planarity : 0.004 0.053 706 Dihedral : 3.547 13.409 552 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.11 % Allowed : 18.54 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.38), residues: 508 helix: 2.39 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.05 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 112 TYR 0.016 0.001 TYR B 223 PHE 0.018 0.001 PHE B 147 TRP 0.019 0.001 TRP B 129 HIS 0.002 0.000 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4236) covalent geometry : angle 0.52973 ( 5768) SS BOND : bond 0.00222 ( 1) SS BOND : angle 0.41966 ( 2) hydrogen bonds : bond 0.03063 ( 292) hydrogen bonds : angle 4.09628 ( 876) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8848 (t0) cc_final: 0.8563 (t0) REVERT: A 195 TYR cc_start: 0.9081 (t80) cc_final: 0.8726 (t80) REVERT: B 44 HIS cc_start: 0.8944 (t-90) cc_final: 0.8664 (t-90) REVERT: B 49 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6943 (m-80) REVERT: B 148 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6271 (mm) REVERT: B 190 TYR cc_start: 0.8686 (t80) cc_final: 0.8131 (t80) outliers start: 9 outliers final: 5 residues processed: 81 average time/residue: 0.0520 time to fit residues: 5.7391 Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.103443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.080294 restraints weight = 10584.600| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.67 r_work: 0.3077 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4237 Z= 0.111 Angle : 0.526 8.018 5770 Z= 0.267 Chirality : 0.039 0.147 638 Planarity : 0.004 0.053 706 Dihedral : 3.511 13.212 552 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.64 % Allowed : 18.78 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.38), residues: 508 helix: 2.44 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.05 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 112 TYR 0.013 0.001 TYR B 38 PHE 0.017 0.001 PHE B 147 TRP 0.017 0.001 TRP B 129 HIS 0.002 0.000 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 4236) covalent geometry : angle 0.52563 ( 5768) SS BOND : bond 0.00206 ( 1) SS BOND : angle 0.36220 ( 2) hydrogen bonds : bond 0.02933 ( 292) hydrogen bonds : angle 4.06996 ( 876) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8802 (t0) cc_final: 0.8532 (t0) REVERT: A 195 TYR cc_start: 0.9054 (t80) cc_final: 0.8689 (t80) REVERT: B 44 HIS cc_start: 0.8937 (t-90) cc_final: 0.8649 (t-90) REVERT: B 62 GLN cc_start: 0.8739 (tp40) cc_final: 0.8493 (tp-100) REVERT: B 81 ASN cc_start: 0.8212 (t0) cc_final: 0.7772 (t0) REVERT: B 148 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6010 (mm) REVERT: B 190 TYR cc_start: 0.8655 (t80) cc_final: 0.8099 (t80) outliers start: 7 outliers final: 4 residues processed: 75 average time/residue: 0.0545 time to fit residues: 5.5639 Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 0.0570 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.103264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.080123 restraints weight = 10398.696| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.63 r_work: 0.3074 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4237 Z= 0.120 Angle : 0.530 8.118 5770 Z= 0.275 Chirality : 0.039 0.145 638 Planarity : 0.004 0.053 706 Dihedral : 3.497 13.378 552 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.41 % Allowed : 20.42 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.38), residues: 508 helix: 2.47 (0.26), residues: 387 sheet: None (None), residues: 0 loop : -1.99 (0.54), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 112 TYR 0.020 0.001 TYR B 223 PHE 0.017 0.001 PHE B 147 TRP 0.024 0.001 TRP B 129 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4236) covalent geometry : angle 0.53013 ( 5768) SS BOND : bond 0.00243 ( 1) SS BOND : angle 0.49768 ( 2) hydrogen bonds : bond 0.02959 ( 292) hydrogen bonds : angle 4.12241 ( 876) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8835 (t0) cc_final: 0.8486 (t0) REVERT: A 195 TYR cc_start: 0.9072 (t80) cc_final: 0.8705 (t80) REVERT: B 44 HIS cc_start: 0.8944 (t-90) cc_final: 0.8664 (t-90) REVERT: B 49 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.6887 (m-80) REVERT: B 81 ASN cc_start: 0.8227 (t0) cc_final: 0.7786 (t0) REVERT: B 148 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6009 (mm) REVERT: B 190 TYR cc_start: 0.8664 (t80) cc_final: 0.8099 (t80) outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 0.0512 time to fit residues: 5.1115 Evaluate side-chains 72 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 0.0030 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.103518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.080369 restraints weight = 10575.795| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.65 r_work: 0.3073 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4237 Z= 0.116 Angle : 0.520 6.581 5770 Z= 0.271 Chirality : 0.039 0.149 638 Planarity : 0.004 0.053 706 Dihedral : 3.484 13.444 552 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.41 % Allowed : 20.66 % Favored : 77.93 % 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: 2.33 (0.38), residues: 508 helix: 2.50 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.87 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 112 TYR 0.016 0.001 TYR B 223 PHE 0.023 0.001 PHE A 226 TRP 0.027 0.001 TRP B 129 HIS 0.002 0.000 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4236) covalent geometry : angle 0.52012 ( 5768) SS BOND : bond 0.00235 ( 1) SS BOND : angle 0.45141 ( 2) hydrogen bonds : bond 0.02953 ( 292) hydrogen bonds : angle 4.09608 ( 876) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8860 (t0) cc_final: 0.8570 (t0) REVERT: A 195 TYR cc_start: 0.9067 (t80) cc_final: 0.8699 (t80) REVERT: B 44 HIS cc_start: 0.8942 (t-90) cc_final: 0.8671 (t-90) REVERT: B 49 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: B 81 ASN cc_start: 0.8197 (t0) cc_final: 0.7755 (t0) REVERT: B 148 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.5981 (mm) REVERT: B 190 TYR cc_start: 0.8666 (t80) cc_final: 0.8146 (t80) REVERT: B 260 ARG cc_start: 0.5524 (ttt180) cc_final: 0.5280 (ttt-90) outliers start: 6 outliers final: 4 residues processed: 72 average time/residue: 0.0501 time to fit residues: 4.8629 Evaluate side-chains 74 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.103864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.080705 restraints weight = 10214.166| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.65 r_work: 0.3072 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4237 Z= 0.119 Angle : 0.537 7.477 5770 Z= 0.280 Chirality : 0.039 0.150 638 Planarity : 0.004 0.053 706 Dihedral : 3.518 13.368 552 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.41 % Allowed : 20.89 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.38), residues: 508 helix: 2.51 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.87 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 112 TYR 0.016 0.001 TYR B 223 PHE 0.017 0.001 PHE B 147 TRP 0.027 0.001 TRP B 129 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4236) covalent geometry : angle 0.53746 ( 5768) SS BOND : bond 0.00256 ( 1) SS BOND : angle 0.44779 ( 2) hydrogen bonds : bond 0.03007 ( 292) hydrogen bonds : angle 4.11334 ( 876) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8868 (t0) cc_final: 0.8609 (t0) REVERT: A 195 TYR cc_start: 0.9103 (t80) cc_final: 0.8754 (t80) REVERT: B 44 HIS cc_start: 0.8969 (t-90) cc_final: 0.8694 (t-90) REVERT: B 49 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6907 (m-80) REVERT: B 81 ASN cc_start: 0.8209 (t0) cc_final: 0.7762 (t0) REVERT: B 148 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.5990 (mm) REVERT: B 190 TYR cc_start: 0.8684 (t80) cc_final: 0.8149 (t80) REVERT: B 260 ARG cc_start: 0.5562 (ttt180) cc_final: 0.5311 (ttt-90) outliers start: 6 outliers final: 4 residues processed: 76 average time/residue: 0.0545 time to fit residues: 5.5724 Evaluate side-chains 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 0.0000 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.104242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081161 restraints weight = 10321.001| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.62 r_work: 0.3088 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4237 Z= 0.110 Angle : 0.530 6.983 5770 Z= 0.274 Chirality : 0.039 0.143 638 Planarity : 0.004 0.054 706 Dihedral : 3.472 13.061 552 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.64 % Allowed : 20.42 % Favored : 77.93 % 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: 2.42 (0.38), residues: 508 helix: 2.56 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.82 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 224 TYR 0.022 0.001 TYR B 223 PHE 0.028 0.001 PHE A 226 TRP 0.026 0.001 TRP B 129 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4236) covalent geometry : angle 0.53018 ( 5768) SS BOND : bond 0.00238 ( 1) SS BOND : angle 0.43450 ( 2) hydrogen bonds : bond 0.02936 ( 292) hydrogen bonds : angle 4.09628 ( 876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1021.26 seconds wall clock time: 18 minutes 9.29 seconds (1089.29 seconds total)