Starting phenix.real_space_refine on Wed Jul 1 23:53:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8de9_27388/07_2026/8de9_27388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de9_27388/07_2026/8de9_27388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8de9_27388/07_2026/8de9_27388.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8de9_27388/07_2026/8de9_27388.cif" model { file = "/net/cci-nas-00/data/ceres_data/8de9_27388/07_2026/8de9_27388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de9_27388/07_2026/8de9_27388.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8de9_27388/07_2026/8de9_27388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de9_27388/07_2026/8de9_27388.map" } resolution = 3.4 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= 0.002 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: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 1 5.49 5 S 16 5.16 5 C 2760 2.51 5 N 626 2.21 5 O 709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4115 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2035 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain: "B" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2028 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {' K': 3, 'PEV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 0.91, per 1000 atoms: 0.22 Number of scatterers: 4115 At special positions: 0 Unit cell: (80.514, 97.128, 79.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 16 16.00 P 1 15.00 O 709 8.00 N 626 7.00 C 2760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS B 93 " 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: 0.33 Conformation dependent library (CDL) restraints added in 154.7 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 43 through 91 removed outlier: 3.569A pdb=" N ALA A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 95 through 113 Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 152 through 196 removed outlier: 3.561A pdb=" N ILE A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 202 through 234 removed outlier: 3.894A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 269 through 298 removed outlier: 3.702A pdb=" N ILE A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 91 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 95 through 113 removed outlier: 3.580A pdb=" N ALA B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 152 through 193 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 204 through 223 Processing helix chain 'B' and resid 223 through 235 removed outlier: 3.713A pdb=" N ALA B 227 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 Processing helix chain 'B' and resid 269 through 297 323 hydrogen bonds defined for protein. 969 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: 0.38 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 623 1.31 - 1.44: 1184 1.44 - 1.56: 2381 1.56 - 1.69: 3 1.69 - 1.81: 26 Bond restraints: 4217 Sorted by residual: bond pdb=" CA ILE B 264 " pdb=" C ILE B 264 " ideal model delta sigma weight residual 1.530 1.584 -0.053 1.12e-02 7.97e+03 2.27e+01 bond pdb=" C31 PEV A 401 " pdb=" O2 PEV A 401 " ideal model delta sigma weight residual 1.330 1.409 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C11 PEV A 401 " pdb=" O3 PEV A 401 " ideal model delta sigma weight residual 1.335 1.398 -0.063 2.00e-02 2.50e+03 9.77e+00 bond pdb=" CA THR A 251 " pdb=" C THR A 251 " ideal model delta sigma weight residual 1.525 1.488 0.037 1.40e-02 5.10e+03 7.01e+00 bond pdb=" N THR A 251 " pdb=" CA THR A 251 " ideal model delta sigma weight residual 1.461 1.431 0.031 1.49e-02 4.50e+03 4.26e+00 ... (remaining 4212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 5583 3.27 - 6.55: 121 6.55 - 9.82: 12 9.82 - 13.09: 4 13.09 - 16.36: 1 Bond angle restraints: 5721 Sorted by residual: angle pdb=" C ILE B 264 " pdb=" CA ILE B 264 " pdb=" CB ILE B 264 " ideal model delta sigma weight residual 112.19 102.19 10.00 1.15e+00 7.56e-01 7.56e+01 angle pdb=" N GLU B 263 " pdb=" CA GLU B 263 " pdb=" C GLU B 263 " ideal model delta sigma weight residual 111.17 122.10 -10.93 1.41e+00 5.03e-01 6.01e+01 angle pdb=" C GLU B 263 " pdb=" CA GLU B 263 " pdb=" CB GLU B 263 " ideal model delta sigma weight residual 112.06 101.34 10.72 1.57e+00 4.06e-01 4.66e+01 angle pdb=" N TRP A 199 " pdb=" CA TRP A 199 " pdb=" C TRP A 199 " ideal model delta sigma weight residual 108.52 118.91 -10.39 1.63e+00 3.76e-01 4.06e+01 angle pdb=" O3P PEV A 401 " pdb=" P PEV A 401 " pdb=" O4P PEV A 401 " ideal model delta sigma weight residual 93.57 109.93 -16.36 3.00e+00 1.11e-01 2.98e+01 ... (remaining 5716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 2139 16.15 - 32.30: 204 32.30 - 48.45: 47 48.45 - 64.60: 11 64.60 - 80.75: 4 Dihedral angle restraints: 2405 sinusoidal: 936 harmonic: 1469 Sorted by residual: dihedral pdb=" CA GLN B 122 " pdb=" C GLN B 122 " pdb=" N GLU B 123 " pdb=" CA GLU B 123 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU B 68 " pdb=" C LEU B 68 " pdb=" N GLU B 69 " pdb=" CA GLU B 69 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU A 68 " pdb=" C LEU A 68 " pdb=" N GLU A 69 " pdb=" CA GLU A 69 " ideal model delta harmonic sigma weight residual -180.00 -162.14 -17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 591 0.089 - 0.178: 68 0.178 - 0.266: 5 0.266 - 0.355: 1 0.355 - 0.444: 2 Chirality restraints: 667 Sorted by residual: chirality pdb=" CA THR A 251 " pdb=" N THR A 251 " pdb=" C THR A 251 " pdb=" CB THR A 251 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CA ILE B 264 " pdb=" N ILE B 264 " pdb=" C ILE B 264 " pdb=" CB ILE B 264 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA LEU A 249 " pdb=" N LEU A 249 " pdb=" C LEU A 249 " pdb=" CB LEU A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 664 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 119 " 0.057 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO A 120 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 120 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 120 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 115 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO A 116 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 196 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C PHE A 196 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE A 196 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL A 197 " -0.013 2.00e-02 2.50e+03 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.88: 1450 2.88 - 3.44: 5034 3.44 - 4.01: 7273 4.01 - 4.57: 10264 4.57 - 5.14: 14449 Nonbonded interactions: 38470 Sorted by model distance: nonbonded pdb=" OE2 GLU A 234 " pdb=" OH TYR A 266 " model vdw 2.309 3.040 nonbonded pdb=" O PRO A 116 " pdb=" NZ LYS B 84 " model vdw 2.335 3.120 nonbonded pdb=" NZ LYS A 84 " pdb=" O PRO B 116 " model vdw 2.349 3.120 nonbonded pdb=" C ILE A 264 " pdb=" OE1 GLU A 265 " model vdw 2.376 3.270 nonbonded pdb=" OE1 GLN A 231 " pdb=" OG SER A 241 " model vdw 2.414 3.040 ... (remaining 38465 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 40 through 297) 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.430 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 4218 Z= 0.268 Angle : 1.125 16.364 5723 Z= 0.634 Chirality : 0.059 0.444 667 Planarity : 0.008 0.088 685 Dihedral : 13.796 80.752 1464 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.23 % Allowed : 2.06 % Favored : 97.71 % 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: 2.27 (0.35), residues: 513 helix: 2.42 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -1.75 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 207 TYR 0.016 0.002 TYR B 284 PHE 0.039 0.003 PHE A 276 TRP 0.031 0.002 TRP A 127 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.27 ( 4217) covalent geometry : angle 1.12476 / 0.63 ( 5721) SS BOND : bond 0.00323 / 0.17 ( 1) SS BOND : angle 0.51756 / 0.27 ( 2) hydrogen bonds : bond 0.10107 / 5.47 ( 323) hydrogen bonds : angle 4.66508 / 3.42 ( 969) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8274 (tttt) cc_final: 0.7236 (ttmm) REVERT: A 77 LYS cc_start: 0.9185 (mttm) cc_final: 0.8962 (mtpt) REVERT: A 82 GLN cc_start: 0.8363 (pt0) cc_final: 0.7628 (pp30) REVERT: A 86 ASP cc_start: 0.8291 (m-30) cc_final: 0.7641 (m-30) REVERT: A 104 LYS cc_start: 0.9424 (ttpp) cc_final: 0.9103 (ttpp) REVERT: A 105 GLN cc_start: 0.8742 (mt0) cc_final: 0.8438 (pt0) REVERT: A 195 MET cc_start: 0.8544 (tmm) cc_final: 0.7503 (tmm) REVERT: A 268 ASP cc_start: 0.7318 (t70) cc_final: 0.6973 (t0) REVERT: B 66 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8204 (ttmm) REVERT: B 77 LYS cc_start: 0.9451 (mtmt) cc_final: 0.9248 (mtpt) REVERT: B 120 PRO cc_start: 0.8391 (Cg_endo) cc_final: 0.7370 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.0541 time to fit residues: 15.4031 Evaluate side-chains 188 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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: 0.6980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 0.0870 chunk 22 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN B 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.156346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.118149 restraints weight = 7306.335| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 4.24 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4218 Z= 0.165 Angle : 0.774 10.661 5723 Z= 0.401 Chirality : 0.045 0.187 667 Planarity : 0.005 0.041 685 Dihedral : 8.090 58.250 575 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.20 % Allowed : 15.33 % 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: 2.69 (0.36), residues: 513 helix: 2.65 (0.24), residues: 397 sheet: None (None), residues: 0 loop : -1.51 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 156 TYR 0.019 0.002 TYR B 57 PHE 0.021 0.002 PHE A 158 TRP 0.029 0.002 TRP A 199 HIS 0.006 0.002 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 4217) covalent geometry : angle 0.77427 / 0.40 ( 5721) SS BOND : bond 0.00171 / 0.09 ( 1) SS BOND : angle 0.31726 / 0.16 ( 2) hydrogen bonds : bond 0.04385 / 2.93 ( 323) hydrogen bonds : angle 4.01253 / 2.98 ( 969) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8385 (tttt) cc_final: 0.7474 (ttmm) REVERT: A 70 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7954 (mm110) REVERT: A 73 GLU cc_start: 0.9083 (pt0) cc_final: 0.8672 (pt0) REVERT: A 79 ARG cc_start: 0.8672 (tmt-80) cc_final: 0.8072 (tpt90) REVERT: A 82 GLN cc_start: 0.8637 (pt0) cc_final: 0.7973 (pp30) REVERT: A 83 GLU cc_start: 0.8337 (tp30) cc_final: 0.8126 (tp30) REVERT: A 86 ASP cc_start: 0.8448 (m-30) cc_final: 0.8074 (m-30) REVERT: A 101 ASP cc_start: 0.8764 (t0) cc_final: 0.8431 (t0) REVERT: A 104 LYS cc_start: 0.9464 (ttpp) cc_final: 0.9115 (ttpp) REVERT: A 180 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8164 (tp40) REVERT: A 240 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8032 (mt-10) REVERT: A 263 GLU cc_start: 0.8478 (tt0) cc_final: 0.8046 (tt0) REVERT: A 268 ASP cc_start: 0.7971 (t70) cc_final: 0.7528 (t70) REVERT: A 269 TYR cc_start: 0.7307 (m-80) cc_final: 0.7081 (m-80) REVERT: A 284 TYR cc_start: 0.8615 (t80) cc_final: 0.8278 (t80) REVERT: B 44 TRP cc_start: 0.7287 (m-90) cc_final: 0.7047 (m-10) REVERT: B 45 LYS cc_start: 0.8439 (mtmm) cc_final: 0.7945 (mmtt) REVERT: B 48 LEU cc_start: 0.9210 (mt) cc_final: 0.8956 (mt) REVERT: B 50 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8285 (tt) REVERT: B 66 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8257 (ttmt) REVERT: B 70 GLN cc_start: 0.8869 (mt0) cc_final: 0.8487 (mm-40) REVERT: B 73 GLU cc_start: 0.8988 (pt0) cc_final: 0.8289 (pt0) REVERT: B 115 ASN cc_start: 0.9200 (p0) cc_final: 0.8966 (p0) REVERT: B 122 GLN cc_start: 0.7476 (mp-120) cc_final: 0.6574 (mp10) REVERT: B 222 PHE cc_start: 0.7803 (m-80) cc_final: 0.7233 (m-10) REVERT: B 240 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8269 (mt-10) REVERT: B 284 TYR cc_start: 0.8871 (t80) cc_final: 0.8631 (t80) outliers start: 14 outliers final: 5 residues processed: 214 average time/residue: 0.0572 time to fit residues: 15.3162 Evaluate side-chains 203 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 196 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 0.0870 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.146818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110017 restraints weight = 7598.209| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 4.38 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4218 Z= 0.161 Angle : 0.775 10.608 5723 Z= 0.391 Chirality : 0.045 0.189 667 Planarity : 0.004 0.048 685 Dihedral : 8.039 58.978 575 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.58 % Allowed : 19.68 % Favored : 75.74 % 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: 2.66 (0.36), residues: 513 helix: 2.59 (0.24), residues: 397 sheet: None (None), residues: 0 loop : -1.35 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 207 TYR 0.022 0.002 TYR A 162 PHE 0.022 0.002 PHE A 217 TRP 0.022 0.001 TRP A 295 HIS 0.001 0.000 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 4217) covalent geometry : angle 0.77502 / 0.39 ( 5721) SS BOND : bond 0.00168 / 0.09 ( 1) SS BOND : angle 0.09365 / 0.04 ( 2) hydrogen bonds : bond 0.04151 / 2.78 ( 323) hydrogen bonds : angle 3.93644 / 2.93 ( 969) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8311 (tttt) cc_final: 0.7399 (ttmm) REVERT: A 70 GLN cc_start: 0.8235 (mm110) cc_final: 0.8012 (mm110) REVERT: A 82 GLN cc_start: 0.8640 (pt0) cc_final: 0.7853 (pp30) REVERT: A 86 ASP cc_start: 0.8551 (m-30) cc_final: 0.7963 (m-30) REVERT: A 101 ASP cc_start: 0.8943 (t0) cc_final: 0.8636 (t0) REVERT: A 104 LYS cc_start: 0.9413 (ttpp) cc_final: 0.9130 (ttpp) REVERT: A 162 TYR cc_start: 0.8734 (t80) cc_final: 0.8528 (t80) REVERT: A 187 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7595 (pttt) REVERT: A 268 ASP cc_start: 0.8244 (t70) cc_final: 0.7753 (t0) REVERT: A 269 TYR cc_start: 0.7571 (m-80) cc_final: 0.7279 (m-80) REVERT: A 284 TYR cc_start: 0.8621 (t80) cc_final: 0.8271 (t80) REVERT: B 44 TRP cc_start: 0.7403 (m-90) cc_final: 0.7098 (m-10) REVERT: B 48 LEU cc_start: 0.8987 (mt) cc_final: 0.8717 (mt) REVERT: B 50 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8328 (tt) REVERT: B 66 LYS cc_start: 0.8909 (ttpt) cc_final: 0.8199 (ttmm) REVERT: B 68 LEU cc_start: 0.8930 (mp) cc_final: 0.8726 (mp) REVERT: B 70 GLN cc_start: 0.8896 (mt0) cc_final: 0.8469 (mm-40) REVERT: B 73 GLU cc_start: 0.9068 (pt0) cc_final: 0.8608 (pt0) REVERT: B 158 PHE cc_start: 0.9153 (t80) cc_final: 0.8925 (t80) REVERT: B 222 PHE cc_start: 0.8062 (m-80) cc_final: 0.7854 (m-10) REVERT: B 240 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8270 (mt-10) REVERT: B 295 TRP cc_start: 0.7925 (OUTLIER) cc_final: 0.7241 (m100) outliers start: 20 outliers final: 11 residues processed: 214 average time/residue: 0.0599 time to fit residues: 15.9605 Evaluate side-chains 211 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 295 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.144999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110473 restraints weight = 7514.345| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 4.08 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4218 Z= 0.177 Angle : 0.799 10.587 5723 Z= 0.404 Chirality : 0.044 0.192 667 Planarity : 0.004 0.037 685 Dihedral : 7.973 57.559 575 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.89 % Allowed : 22.88 % Favored : 73.23 % 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: 2.48 (0.36), residues: 513 helix: 2.45 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.35 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 207 TYR 0.020 0.002 TYR A 162 PHE 0.021 0.002 PHE A 158 TRP 0.017 0.001 TRP A 295 HIS 0.002 0.000 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 4217) covalent geometry : angle 0.79940 / 0.40 ( 5721) SS BOND : bond 0.00053 / 0.03 ( 1) SS BOND : angle 0.37786 / 0.19 ( 2) hydrogen bonds : bond 0.04372 / 2.87 ( 323) hydrogen bonds : angle 3.91225 / 2.93 ( 969) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8640 (tppt) cc_final: 0.8361 (tppt) REVERT: A 66 LYS cc_start: 0.8447 (tttt) cc_final: 0.7628 (ttmm) REVERT: A 70 GLN cc_start: 0.8330 (mm110) cc_final: 0.7905 (mm110) REVERT: A 79 ARG cc_start: 0.8504 (ttm110) cc_final: 0.8201 (ptp-110) REVERT: A 82 GLN cc_start: 0.8648 (pt0) cc_final: 0.7755 (pp30) REVERT: A 83 GLU cc_start: 0.8743 (tp30) cc_final: 0.8444 (tp30) REVERT: A 84 LYS cc_start: 0.8090 (mtmm) cc_final: 0.7826 (mtmm) REVERT: A 86 ASP cc_start: 0.8579 (m-30) cc_final: 0.7974 (m-30) REVERT: A 104 LYS cc_start: 0.9457 (ttpp) cc_final: 0.9217 (ttpp) REVERT: A 187 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7639 (pttt) REVERT: A 284 TYR cc_start: 0.8759 (t80) cc_final: 0.8481 (t80) REVERT: B 43 LYS cc_start: 0.8070 (tptt) cc_final: 0.7640 (tptt) REVERT: B 45 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8394 (pttp) REVERT: B 58 LEU cc_start: 0.8628 (mt) cc_final: 0.8343 (mt) REVERT: B 66 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8584 (ptmm) REVERT: B 70 GLN cc_start: 0.8929 (mt0) cc_final: 0.8607 (mm-40) REVERT: B 73 GLU cc_start: 0.9020 (pt0) cc_final: 0.8754 (pt0) REVERT: B 86 ASP cc_start: 0.9080 (p0) cc_final: 0.8790 (p0) REVERT: B 100 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8490 (tp30) REVERT: B 104 LYS cc_start: 0.9402 (ttmm) cc_final: 0.9051 (mtmm) REVERT: B 158 PHE cc_start: 0.9202 (t80) cc_final: 0.8955 (t80) REVERT: B 195 MET cc_start: 0.7607 (mmm) cc_final: 0.7241 (mpp) REVERT: B 222 PHE cc_start: 0.8030 (m-80) cc_final: 0.7785 (m-10) REVERT: B 240 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8267 (mt-10) REVERT: B 291 MET cc_start: 0.8706 (tmm) cc_final: 0.7941 (mmp) outliers start: 17 outliers final: 8 residues processed: 221 average time/residue: 0.0636 time to fit residues: 17.4519 Evaluate side-chains 206 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 197 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.143066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.108242 restraints weight = 7680.774| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 4.17 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4218 Z= 0.184 Angle : 0.819 10.978 5723 Z= 0.412 Chirality : 0.045 0.191 667 Planarity : 0.004 0.034 685 Dihedral : 7.973 57.896 575 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.81 % Allowed : 26.54 % Favored : 68.65 % 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: 2.32 (0.36), residues: 513 helix: 2.34 (0.24), residues: 397 sheet: None (None), residues: 0 loop : -1.46 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 207 TYR 0.018 0.002 TYR B 57 PHE 0.017 0.002 PHE A 217 TRP 0.016 0.001 TRP A 295 HIS 0.007 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 4217) covalent geometry : angle 0.81925 / 0.41 ( 5721) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 0.40264 / 0.20 ( 2) hydrogen bonds : bond 0.04378 / 2.90 ( 323) hydrogen bonds : angle 3.90682 / 2.93 ( 969) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8715 (tppt) cc_final: 0.8415 (tppt) REVERT: A 66 LYS cc_start: 0.8473 (tttt) cc_final: 0.7620 (ttmm) REVERT: A 70 GLN cc_start: 0.8367 (mm110) cc_final: 0.7900 (mm110) REVERT: A 79 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8175 (ptp-110) REVERT: A 82 GLN cc_start: 0.8625 (pt0) cc_final: 0.7815 (pp30) REVERT: A 83 GLU cc_start: 0.8727 (tp30) cc_final: 0.8401 (tp30) REVERT: A 84 LYS cc_start: 0.8308 (mtmm) cc_final: 0.8103 (mtmm) REVERT: A 86 ASP cc_start: 0.8625 (m-30) cc_final: 0.8149 (m-30) REVERT: A 104 LYS cc_start: 0.9471 (ttpp) cc_final: 0.9224 (ttpp) REVERT: A 122 GLN cc_start: 0.8091 (pp30) cc_final: 0.7878 (pp30) REVERT: A 174 LEU cc_start: 0.8545 (tp) cc_final: 0.8263 (tp) REVERT: A 179 ASP cc_start: 0.8578 (t0) cc_final: 0.8350 (t0) REVERT: A 187 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7803 (pttt) REVERT: A 263 GLU cc_start: 0.8755 (tt0) cc_final: 0.8367 (tm-30) REVERT: A 268 ASP cc_start: 0.8256 (t0) cc_final: 0.7408 (t70) REVERT: A 284 TYR cc_start: 0.8769 (t80) cc_final: 0.8475 (t80) REVERT: B 43 LYS cc_start: 0.8087 (tptt) cc_final: 0.7830 (tptt) REVERT: B 45 LYS cc_start: 0.8753 (mtmm) cc_final: 0.8259 (pttt) REVERT: B 48 LEU cc_start: 0.8951 (mt) cc_final: 0.8666 (mt) REVERT: B 66 LYS cc_start: 0.8962 (ttpt) cc_final: 0.8581 (ptmm) REVERT: B 70 GLN cc_start: 0.8944 (mt0) cc_final: 0.8612 (mm-40) REVERT: B 73 GLU cc_start: 0.8999 (pt0) cc_final: 0.8729 (pt0) REVERT: B 86 ASP cc_start: 0.8983 (p0) cc_final: 0.8633 (p0) REVERT: B 104 LYS cc_start: 0.9393 (ttmm) cc_final: 0.9059 (mtmm) REVERT: B 158 PHE cc_start: 0.9195 (t80) cc_final: 0.8967 (t80) REVERT: B 240 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8302 (mt-10) REVERT: B 282 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8189 (tp) outliers start: 21 outliers final: 13 residues processed: 201 average time/residue: 0.0618 time to fit residues: 15.3341 Evaluate side-chains 203 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.0050 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.145306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111398 restraints weight = 7718.168| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 4.17 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4218 Z= 0.161 Angle : 0.831 11.782 5723 Z= 0.411 Chirality : 0.045 0.204 667 Planarity : 0.004 0.046 685 Dihedral : 7.913 59.491 575 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.35 % Allowed : 26.77 % Favored : 68.88 % 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: 2.31 (0.36), residues: 513 helix: 2.40 (0.25), residues: 396 sheet: None (None), residues: 0 loop : -1.68 (0.54), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 207 TYR 0.021 0.002 TYR A 162 PHE 0.019 0.002 PHE A 158 TRP 0.014 0.001 TRP A 295 HIS 0.002 0.000 HIS A 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 4217) covalent geometry : angle 0.83101 / 0.41 ( 5721) SS BOND : bond 0.00037 / 0.02 ( 1) SS BOND : angle 0.27516 / 0.13 ( 2) hydrogen bonds : bond 0.04263 / 2.81 ( 323) hydrogen bonds : angle 3.93956 / 2.97 ( 969) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8702 (tppt) cc_final: 0.8394 (tppt) REVERT: A 66 LYS cc_start: 0.8458 (tttt) cc_final: 0.7457 (ttmm) REVERT: A 70 GLN cc_start: 0.8354 (mm110) cc_final: 0.8102 (mm110) REVERT: A 79 ARG cc_start: 0.8662 (ttm110) cc_final: 0.8122 (ptp-110) REVERT: A 82 GLN cc_start: 0.8627 (pt0) cc_final: 0.7809 (pp30) REVERT: A 83 GLU cc_start: 0.8604 (tp30) cc_final: 0.8210 (tp30) REVERT: A 86 ASP cc_start: 0.8606 (m-30) cc_final: 0.8134 (m-30) REVERT: A 187 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7834 (pttt) REVERT: A 195 MET cc_start: 0.8375 (tpp) cc_final: 0.7671 (tpt) REVERT: A 207 ARG cc_start: 0.9027 (mtm180) cc_final: 0.8732 (mtm180) REVERT: A 263 GLU cc_start: 0.8732 (tt0) cc_final: 0.8348 (tm-30) REVERT: A 268 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7740 (t70) REVERT: A 269 TYR cc_start: 0.7752 (m-80) cc_final: 0.7506 (m-80) REVERT: A 284 TYR cc_start: 0.8780 (t80) cc_final: 0.8517 (t80) REVERT: B 43 LYS cc_start: 0.8036 (tptt) cc_final: 0.7382 (tptt) REVERT: B 45 LYS cc_start: 0.8735 (mtmm) cc_final: 0.8197 (pttt) REVERT: B 48 LEU cc_start: 0.8951 (mt) cc_final: 0.8633 (mt) REVERT: B 66 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8187 (ttmt) REVERT: B 70 GLN cc_start: 0.8924 (mt0) cc_final: 0.8508 (mm-40) REVERT: B 73 GLU cc_start: 0.8971 (pt0) cc_final: 0.8721 (pt0) REVERT: B 86 ASP cc_start: 0.9030 (p0) cc_final: 0.8688 (p0) REVERT: B 104 LYS cc_start: 0.9360 (ttmm) cc_final: 0.9122 (mtmm) REVERT: B 158 PHE cc_start: 0.9200 (t80) cc_final: 0.8981 (t80) REVERT: B 240 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8308 (mt-10) REVERT: B 282 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8171 (tp) REVERT: B 291 MET cc_start: 0.8675 (tmm) cc_final: 0.7525 (mmp) outliers start: 19 outliers final: 10 residues processed: 197 average time/residue: 0.0607 time to fit residues: 14.7791 Evaluate side-chains 199 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.0170 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.0170 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.145410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.110356 restraints weight = 7890.677| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 4.32 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4218 Z= 0.166 Angle : 0.885 12.264 5723 Z= 0.436 Chirality : 0.045 0.187 667 Planarity : 0.004 0.038 685 Dihedral : 7.794 59.473 575 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.43 % Allowed : 30.66 % Favored : 65.90 % 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: 2.24 (0.36), residues: 513 helix: 2.32 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.64 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 156 TYR 0.020 0.002 TYR A 162 PHE 0.020 0.001 PHE B 51 TRP 0.015 0.001 TRP A 295 HIS 0.002 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 ( 4217) covalent geometry : angle 0.88531 / 0.44 ( 5721) SS BOND : bond 0.00058 / 0.03 ( 1) SS BOND : angle 0.24331 / 0.12 ( 2) hydrogen bonds : bond 0.04251 / 2.78 ( 323) hydrogen bonds : angle 4.00068 / 3.00 ( 969) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8726 (tppt) cc_final: 0.8507 (tppt) REVERT: A 66 LYS cc_start: 0.8478 (tttt) cc_final: 0.7582 (ttmm) REVERT: A 70 GLN cc_start: 0.8442 (mm110) cc_final: 0.8007 (mm110) REVERT: A 79 ARG cc_start: 0.8651 (ttm110) cc_final: 0.8065 (ptp-110) REVERT: A 82 GLN cc_start: 0.8602 (pt0) cc_final: 0.7808 (pp30) REVERT: A 83 GLU cc_start: 0.8606 (tp30) cc_final: 0.8255 (tp30) REVERT: A 86 ASP cc_start: 0.8574 (m-30) cc_final: 0.8089 (m-30) REVERT: A 158 PHE cc_start: 0.9196 (t80) cc_final: 0.8975 (t80) REVERT: A 174 LEU cc_start: 0.8498 (tp) cc_final: 0.8083 (tp) REVERT: A 187 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7834 (pttt) REVERT: A 207 ARG cc_start: 0.8986 (mtm180) cc_final: 0.8726 (mtm180) REVERT: A 263 GLU cc_start: 0.8813 (tt0) cc_final: 0.8412 (tm-30) REVERT: A 268 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7758 (p0) REVERT: A 282 LEU cc_start: 0.8589 (mt) cc_final: 0.8311 (mt) REVERT: A 284 TYR cc_start: 0.8776 (t80) cc_final: 0.8512 (t80) REVERT: B 43 LYS cc_start: 0.8146 (tptt) cc_final: 0.7633 (tptt) REVERT: B 45 LYS cc_start: 0.8706 (mtmm) cc_final: 0.8222 (pttp) REVERT: B 48 LEU cc_start: 0.8941 (mt) cc_final: 0.8639 (mt) REVERT: B 66 LYS cc_start: 0.8909 (ttpt) cc_final: 0.8175 (ttmt) REVERT: B 70 GLN cc_start: 0.8966 (mt0) cc_final: 0.8628 (mm-40) REVERT: B 73 GLU cc_start: 0.9019 (pt0) cc_final: 0.8683 (pt0) REVERT: B 84 LYS cc_start: 0.9183 (pttp) cc_final: 0.8918 (pttm) REVERT: B 86 ASP cc_start: 0.9013 (p0) cc_final: 0.8661 (p0) REVERT: B 104 LYS cc_start: 0.9332 (ttmm) cc_final: 0.9093 (mtmm) REVERT: B 240 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8310 (mt-10) REVERT: B 291 MET cc_start: 0.8738 (tmm) cc_final: 0.7648 (mmp) outliers start: 15 outliers final: 9 residues processed: 198 average time/residue: 0.0585 time to fit residues: 14.2390 Evaluate side-chains 206 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.0070 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.154796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.119485 restraints weight = 7392.327| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.78 r_work: 0.3389 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4218 Z= 0.175 Angle : 0.909 12.417 5723 Z= 0.454 Chirality : 0.046 0.198 667 Planarity : 0.004 0.034 685 Dihedral : 7.788 59.668 575 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.66 % Allowed : 30.66 % Favored : 65.68 % 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 (0.37), residues: 513 helix: 2.25 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -1.73 (0.54), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.020 0.002 TYR A 57 PHE 0.023 0.001 PHE B 51 TRP 0.027 0.001 TRP A 199 HIS 0.001 0.000 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 4217) covalent geometry : angle 0.90922 / 0.45 ( 5721) SS BOND : bond 0.00006 / 0.00 ( 1) SS BOND : angle 0.20016 / 0.09 ( 2) hydrogen bonds : bond 0.04409 / 2.88 ( 323) hydrogen bonds : angle 3.97910 / 2.96 ( 969) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8821 (tppt) cc_final: 0.8452 (tppt) REVERT: A 66 LYS cc_start: 0.8719 (tttt) cc_final: 0.7862 (ttmm) REVERT: A 70 GLN cc_start: 0.8721 (mm110) cc_final: 0.8314 (mm110) REVERT: A 79 ARG cc_start: 0.8712 (ttm110) cc_final: 0.8159 (ptp-110) REVERT: A 82 GLN cc_start: 0.8698 (pt0) cc_final: 0.7877 (pp30) REVERT: A 83 GLU cc_start: 0.8598 (tp30) cc_final: 0.8213 (tp30) REVERT: A 86 ASP cc_start: 0.8534 (m-30) cc_final: 0.8098 (m-30) REVERT: A 187 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7713 (pttt) REVERT: A 207 ARG cc_start: 0.8985 (mtm180) cc_final: 0.8727 (mtm180) REVERT: A 263 GLU cc_start: 0.8854 (tt0) cc_final: 0.8370 (tm-30) REVERT: A 284 TYR cc_start: 0.9142 (t80) cc_final: 0.8902 (t80) REVERT: B 43 LYS cc_start: 0.8171 (tptt) cc_final: 0.7556 (tptt) REVERT: B 45 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8273 (pttp) REVERT: B 48 LEU cc_start: 0.9003 (mt) cc_final: 0.8758 (mt) REVERT: B 58 LEU cc_start: 0.9054 (mt) cc_final: 0.8813 (mt) REVERT: B 66 LYS cc_start: 0.8996 (ttpt) cc_final: 0.8275 (ttmt) REVERT: B 70 GLN cc_start: 0.9112 (mt0) cc_final: 0.8853 (mm-40) REVERT: B 73 GLU cc_start: 0.8989 (pt0) cc_final: 0.8681 (pt0) REVERT: B 86 ASP cc_start: 0.8924 (p0) cc_final: 0.8549 (p0) REVERT: B 104 LYS cc_start: 0.9357 (ttmm) cc_final: 0.9145 (mtmm) REVERT: B 222 PHE cc_start: 0.8238 (m-10) cc_final: 0.7900 (m-10) REVERT: B 240 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8599 (mt-10) REVERT: B 291 MET cc_start: 0.8742 (tmm) cc_final: 0.7669 (mmp) outliers start: 16 outliers final: 10 residues processed: 197 average time/residue: 0.0655 time to fit residues: 15.7789 Evaluate side-chains 200 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 221 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.152543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.116363 restraints weight = 7471.790| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.92 r_work: 0.3363 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4218 Z= 0.182 Angle : 0.966 14.709 5723 Z= 0.477 Chirality : 0.046 0.197 667 Planarity : 0.004 0.036 685 Dihedral : 7.675 58.002 575 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.20 % Allowed : 32.27 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.37), residues: 513 helix: 2.16 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.69 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.015 0.002 TYR A 162 PHE 0.025 0.002 PHE A 158 TRP 0.019 0.001 TRP A 199 HIS 0.002 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 ( 4217) covalent geometry : angle 0.96655 / 0.48 ( 5721) SS BOND : bond 0.00069 / 0.04 ( 1) SS BOND : angle 0.22678 / 0.12 ( 2) hydrogen bonds : bond 0.04430 / 2.91 ( 323) hydrogen bonds : angle 4.02832 / 3.00 ( 969) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8772 (tppt) cc_final: 0.8416 (tppt) REVERT: A 66 LYS cc_start: 0.8785 (tttt) cc_final: 0.8026 (ttmt) REVERT: A 70 GLN cc_start: 0.8793 (mm110) cc_final: 0.8379 (mm110) REVERT: A 79 ARG cc_start: 0.8687 (ttm110) cc_final: 0.8148 (ptp-110) REVERT: A 82 GLN cc_start: 0.8722 (pt0) cc_final: 0.7869 (pp30) REVERT: A 83 GLU cc_start: 0.8567 (tp30) cc_final: 0.8189 (tp30) REVERT: A 86 ASP cc_start: 0.8497 (m-30) cc_final: 0.8074 (m-30) REVERT: A 187 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7639 (pttt) REVERT: A 207 ARG cc_start: 0.8932 (mtm180) cc_final: 0.8677 (mtm180) REVERT: A 263 GLU cc_start: 0.8740 (tt0) cc_final: 0.8449 (tm-30) REVERT: A 271 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8542 (mmmt) REVERT: A 284 TYR cc_start: 0.9169 (t80) cc_final: 0.8951 (t80) REVERT: B 43 LYS cc_start: 0.8163 (tptt) cc_final: 0.7562 (tptt) REVERT: B 45 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8273 (pttp) REVERT: B 48 LEU cc_start: 0.9019 (mt) cc_final: 0.8708 (mt) REVERT: B 66 LYS cc_start: 0.9050 (ttpt) cc_final: 0.8202 (ttmt) REVERT: B 70 GLN cc_start: 0.9085 (mt0) cc_final: 0.8793 (mm-40) REVERT: B 83 GLU cc_start: 0.8635 (pp20) cc_final: 0.8322 (pp20) REVERT: B 84 LYS cc_start: 0.9167 (pttp) cc_final: 0.8802 (ptpp) REVERT: B 86 ASP cc_start: 0.8795 (p0) cc_final: 0.8349 (p0) REVERT: B 240 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8580 (mt-10) REVERT: B 282 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8615 (tp) REVERT: B 291 MET cc_start: 0.8719 (tmm) cc_final: 0.7988 (mmp) outliers start: 14 outliers final: 11 residues processed: 188 average time/residue: 0.0656 time to fit residues: 14.9988 Evaluate side-chains 188 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.152335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.116254 restraints weight = 7208.903| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.80 r_work: 0.3385 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4218 Z= 0.185 Angle : 0.977 12.687 5723 Z= 0.489 Chirality : 0.048 0.190 667 Planarity : 0.004 0.036 685 Dihedral : 7.647 56.937 575 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.43 % Allowed : 32.95 % Favored : 63.62 % 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: 2.01 (0.37), residues: 513 helix: 2.23 (0.25), residues: 394 sheet: None (None), residues: 0 loop : -1.87 (0.53), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.023 0.002 TYR B 57 PHE 0.024 0.002 PHE A 158 TRP 0.017 0.001 TRP A 199 HIS 0.002 0.001 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 4217) covalent geometry : angle 0.97750 / 0.49 ( 5721) SS BOND : bond 0.00025 / 0.01 ( 1) SS BOND : angle 0.14679 / 0.07 ( 2) hydrogen bonds : bond 0.04440 / 2.89 ( 323) hydrogen bonds : angle 4.05298 / 3.01 ( 969) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 176 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8729 (tppt) cc_final: 0.8401 (tppt) REVERT: A 66 LYS cc_start: 0.8786 (tttt) cc_final: 0.8041 (ttmt) REVERT: A 70 GLN cc_start: 0.8803 (mm110) cc_final: 0.8390 (mm110) REVERT: A 82 GLN cc_start: 0.8735 (pt0) cc_final: 0.7927 (pp30) REVERT: A 83 GLU cc_start: 0.8589 (tp30) cc_final: 0.8311 (tp30) REVERT: A 86 ASP cc_start: 0.8528 (m-30) cc_final: 0.7895 (m-30) REVERT: A 187 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7731 (pttt) REVERT: A 207 ARG cc_start: 0.8924 (mtm180) cc_final: 0.8673 (mtm180) REVERT: A 263 GLU cc_start: 0.8802 (tt0) cc_final: 0.8511 (tm-30) REVERT: A 284 TYR cc_start: 0.9234 (t80) cc_final: 0.9002 (t80) REVERT: B 43 LYS cc_start: 0.8164 (tptt) cc_final: 0.7556 (tptt) REVERT: B 45 LYS cc_start: 0.8643 (mtmm) cc_final: 0.8274 (pttp) REVERT: B 48 LEU cc_start: 0.9049 (mt) cc_final: 0.8744 (mt) REVERT: B 66 LYS cc_start: 0.9113 (ttpt) cc_final: 0.8334 (ttmt) REVERT: B 70 GLN cc_start: 0.9096 (mt0) cc_final: 0.8893 (mm-40) REVERT: B 84 LYS cc_start: 0.9148 (pttp) cc_final: 0.8824 (ptpp) REVERT: B 86 ASP cc_start: 0.8791 (p0) cc_final: 0.8458 (p0) REVERT: B 222 PHE cc_start: 0.8258 (m-10) cc_final: 0.8025 (m-10) REVERT: B 240 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8552 (mt-10) REVERT: B 282 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8624 (tp) REVERT: B 291 MET cc_start: 0.8680 (tmm) cc_final: 0.7883 (mmp) outliers start: 15 outliers final: 9 residues processed: 181 average time/residue: 0.0682 time to fit residues: 15.0320 Evaluate side-chains 185 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 0.0030 chunk 10 optimal weight: 0.4980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.152117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.116742 restraints weight = 7465.375| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.83 r_work: 0.3364 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4218 Z= 0.183 Angle : 0.959 12.699 5723 Z= 0.479 Chirality : 0.047 0.190 667 Planarity : 0.004 0.038 685 Dihedral : 7.528 56.364 575 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.97 % Allowed : 32.72 % Favored : 64.30 % 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: 1.95 (0.37), residues: 513 helix: 2.12 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.78 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 79 TYR 0.022 0.002 TYR B 57 PHE 0.023 0.001 PHE B 51 TRP 0.017 0.001 TRP A 295 HIS 0.002 0.001 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 4217) covalent geometry : angle 0.95929 / 0.48 ( 5721) SS BOND : bond 0.00015 / 0.01 ( 1) SS BOND : angle 0.12845 / 0.07 ( 2) hydrogen bonds : bond 0.04446 / 2.87 ( 323) hydrogen bonds : angle 4.02438 / 2.98 ( 969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1013.67 seconds wall clock time: 18 minutes 8.05 seconds (1088.05 seconds total)