Starting phenix.real_space_refine on Mon Aug 25 15:46:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h3n_0136/08_2025/6h3n_0136.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h3n_0136/08_2025/6h3n_0136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6h3n_0136/08_2025/6h3n_0136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h3n_0136/08_2025/6h3n_0136.map" model { file = "/net/cci-nas-00/data/ceres_data/6h3n_0136/08_2025/6h3n_0136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h3n_0136/08_2025/6h3n_0136.cif" } resolution = 3.25 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: 5 Type Number sf(0) Gaussians S 45 5.16 5 C 9339 2.51 5 N 2730 2.21 5 O 2817 1.98 5 H 14388 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29319 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9773 Classifications: {'peptide': 627} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 591} Chain breaks: 1 Chain: "B" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9773 Classifications: {'peptide': 627} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 31, 'TRANS': 591} Chain breaks: 1 Chain: "C" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9773 Classifications: {'peptide': 627} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 591} Chain breaks: 1 Time building chain proxies: 4.87, per 1000 atoms: 0.17 Number of scatterers: 29319 At special positions: 0 Unit cell: (91.3, 93.5, 182.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 O 2817 8.00 N 2730 7.00 C 9339 6.00 H 14388 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.32 Conformation dependent library (CDL) restraints added in 739.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 14.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 151 through 163 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 264 through 281 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 625 through 635 Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 151 through 163 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 264 through 281 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 114 through 125 Processing helix chain 'C' and resid 151 through 163 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 264 through 281 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 625 through 637 155 hydrogen bonds defined for protein. 348 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: 5.33 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 14367 1.13 - 1.30: 2550 1.30 - 1.47: 6356 1.47 - 1.64: 6331 1.64 - 1.81: 69 Bond restraints: 29673 Sorted by residual: bond pdb=" CD2 PHE B 152 " pdb=" HD2 PHE B 152 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" CZ2 TRP C 98 " pdb=" HZ2 TRP C 98 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" CD1 PHE A 127 " pdb=" HD1 PHE A 127 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" CZ3 TRP A 141 " pdb=" HZ3 TRP A 141 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" CD1 PHE C 392 " pdb=" HD1 PHE C 392 " ideal model delta sigma weight residual 0.930 1.091 -0.161 2.00e-02 2.50e+03 6.51e+01 ... (remaining 29668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 48791 3.31 - 6.62: 4094 6.62 - 9.92: 400 9.92 - 13.23: 24 13.23 - 16.54: 4 Bond angle restraints: 53313 Sorted by residual: angle pdb=" C PRO A 638 " pdb=" N PRO A 639 " pdb=" CA PRO A 639 " ideal model delta sigma weight residual 119.66 127.34 -7.68 7.20e-01 1.93e+00 1.14e+02 angle pdb=" C PHE A 637 " pdb=" N PRO A 638 " pdb=" CA PRO A 638 " ideal model delta sigma weight residual 119.66 126.66 -7.00 7.20e-01 1.93e+00 9.46e+01 angle pdb=" C PHE B 637 " pdb=" N PRO B 638 " pdb=" CA PRO B 638 " ideal model delta sigma weight residual 119.66 126.49 -6.83 7.20e-01 1.93e+00 9.00e+01 angle pdb=" C GLY B 374 " pdb=" N PRO B 375 " pdb=" CA PRO B 375 " ideal model delta sigma weight residual 119.78 128.65 -8.87 1.03e+00 9.43e-01 7.41e+01 angle pdb=" C GLY C 374 " pdb=" N PRO C 375 " pdb=" CA PRO C 375 " ideal model delta sigma weight residual 119.78 128.62 -8.84 1.03e+00 9.43e-01 7.36e+01 ... (remaining 53308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 13210 16.78 - 33.57: 478 33.57 - 50.35: 194 50.35 - 67.14: 108 67.14 - 83.92: 26 Dihedral angle restraints: 14016 sinusoidal: 7665 harmonic: 6351 Sorted by residual: dihedral pdb=" CD2 HIS B 175 " pdb=" CG HIS B 175 " pdb=" ND1 HIS B 175 " pdb=" HD1 HIS B 175 " ideal model delta harmonic sigma weight residual 180.00 -147.20 -32.80 0 5.00e+00 4.00e-02 4.30e+01 dihedral pdb=" CD2 HIS B 209 " pdb=" CG HIS B 209 " pdb=" ND1 HIS B 209 " pdb=" HD1 HIS B 209 " ideal model delta harmonic sigma weight residual 180.00 156.25 23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CD2 HIS B 71 " pdb=" CG HIS B 71 " pdb=" ND1 HIS B 71 " pdb=" HD1 HIS B 71 " ideal model delta harmonic sigma weight residual -180.00 -156.58 -23.42 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 14013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1099 0.054 - 0.107: 738 0.107 - 0.161: 244 0.161 - 0.215: 54 0.215 - 0.268: 7 Chirality restraints: 2142 Sorted by residual: chirality pdb=" CA TRP C 96 " pdb=" N TRP C 96 " pdb=" C TRP C 96 " pdb=" CB TRP C 96 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ARG C 502 " pdb=" N ARG C 502 " pdb=" C ARG C 502 " pdb=" CB ARG C 502 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA TRP A 96 " pdb=" N TRP A 96 " pdb=" C TRP A 96 " pdb=" CB TRP A 96 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2139 not shown) Planarity restraints: 4569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 175 " -0.096 2.00e-02 2.50e+03 1.18e-01 3.12e+02 pdb=" CG HIS B 175 " -0.076 2.00e-02 2.50e+03 pdb=" ND1 HIS B 175 " -0.120 2.00e-02 2.50e+03 pdb=" CD2 HIS B 175 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 HIS B 175 " -0.057 2.00e-02 2.50e+03 pdb=" NE2 HIS B 175 " 0.035 2.00e-02 2.50e+03 pdb=" HD1 HIS B 175 " 0.274 2.00e-02 2.50e+03 pdb=" HD2 HIS B 175 " 0.095 2.00e-02 2.50e+03 pdb=" HE1 HIS B 175 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 209 " -0.088 2.00e-02 2.50e+03 9.05e-02 1.84e+02 pdb=" CG HIS B 209 " -0.050 2.00e-02 2.50e+03 pdb=" ND1 HIS B 209 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 HIS B 209 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 HIS B 209 " -0.048 2.00e-02 2.50e+03 pdb=" NE2 HIS B 209 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS B 209 " 0.210 2.00e-02 2.50e+03 pdb=" HD2 HIS B 209 " 0.074 2.00e-02 2.50e+03 pdb=" HE1 HIS B 209 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 209 " -0.086 2.00e-02 2.50e+03 8.71e-02 1.71e+02 pdb=" CG HIS A 209 " -0.048 2.00e-02 2.50e+03 pdb=" ND1 HIS A 209 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 HIS A 209 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 HIS A 209 " -0.045 2.00e-02 2.50e+03 pdb=" NE2 HIS A 209 " 0.022 2.00e-02 2.50e+03 pdb=" HD1 HIS A 209 " 0.202 2.00e-02 2.50e+03 pdb=" HD2 HIS A 209 " 0.071 2.00e-02 2.50e+03 pdb=" HE1 HIS A 209 " -0.066 2.00e-02 2.50e+03 ... (remaining 4566 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 3911 2.19 - 2.79: 57698 2.79 - 3.39: 81498 3.39 - 4.00: 117025 4.00 - 4.60: 172218 Nonbonded interactions: 432350 Sorted by model distance: nonbonded pdb=" O TRP C 98 " pdb=" HG1 THR C 101 " model vdw 1.587 2.450 nonbonded pdb=" O TRP B 98 " pdb=" HG1 THR B 101 " model vdw 1.591 2.450 nonbonded pdb=" O TRP A 98 " pdb=" HG1 THR A 101 " model vdw 1.593 2.450 nonbonded pdb=" OE1 GLU B 494 " pdb=" H GLU B 494 " model vdw 1.597 2.450 nonbonded pdb=" OE1 GLU C 402 " pdb=" H GLU C 402 " model vdw 1.598 2.450 ... (remaining 432345 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' selection = chain 'B' selection = chain 'C' } 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: 2.930 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: 0.190 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 23.190 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:1.330 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.015 0.067 15285 Z= 0.911 Angle : 1.517 16.538 20715 Z= 1.030 Chirality : 0.074 0.268 2142 Planarity : 0.010 0.162 2796 Dihedral : 10.777 83.921 5700 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.70 % Allowed : 4.65 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.43 (0.18), residues: 1869 helix: 0.60 (0.36), residues: 192 sheet: 0.31 (0.21), residues: 528 loop : -0.72 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 396 TYR 0.056 0.007 TYR A 138 PHE 0.019 0.004 PHE A 33 TRP 0.045 0.006 TRP B 414 HIS 0.007 0.002 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.01472 (15285) covalent geometry : angle 1.51686 (20715) hydrogen bonds : bond 0.13052 ( 155) hydrogen bonds : angle 4.59031 ( 348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 0.750 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 SER cc_start: 0.7932 (t) cc_final: 0.7210 (t) REVERT: A 132 ASP cc_start: 0.7244 (t0) cc_final: 0.6971 (p0) REVERT: A 246 ARG cc_start: 0.7439 (mmt180) cc_final: 0.7097 (mmp-170) REVERT: A 280 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7363 (tm-30) REVERT: A 356 LEU cc_start: 0.8802 (mt) cc_final: 0.8412 (mm) REVERT: B 33 PHE cc_start: 0.5004 (m-10) cc_final: 0.4735 (m-10) REVERT: B 80 VAL cc_start: 0.7290 (m) cc_final: 0.7031 (m) REVERT: B 378 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8043 (mm-30) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.3488 time to fit residues: 204.9383 Evaluate side-chains 219 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN B 454 GLN B 510 ASN C 510 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.153140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.120383 restraints weight = 46155.940| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.18 r_work: 0.3607 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15285 Z= 0.183 Angle : 0.585 5.682 20715 Z= 0.321 Chirality : 0.046 0.146 2142 Planarity : 0.006 0.049 2796 Dihedral : 4.658 18.692 2109 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.84 % Allowed : 7.98 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.09 (0.19), residues: 1869 helix: 1.56 (0.37), residues: 189 sheet: -0.11 (0.21), residues: 513 loop : -0.25 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 302 TYR 0.013 0.002 TYR A 143 PHE 0.017 0.002 PHE A 154 TRP 0.006 0.001 TRP C 96 HIS 0.006 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00402 (15285) covalent geometry : angle 0.58490 (20715) hydrogen bonds : bond 0.05147 ( 155) hydrogen bonds : angle 4.27196 ( 348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.825 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7457 (t0) cc_final: 0.7153 (p0) REVERT: A 215 MET cc_start: 0.8044 (ttt) cc_final: 0.7843 (ttt) REVERT: A 246 ARG cc_start: 0.7958 (mmt180) cc_final: 0.7289 (mmp-170) REVERT: A 280 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7021 (tm-30) REVERT: A 309 ASP cc_start: 0.8582 (p0) cc_final: 0.8307 (p0) REVERT: A 356 LEU cc_start: 0.8567 (mt) cc_final: 0.8055 (mm) REVERT: A 637 PHE cc_start: 0.7959 (m-80) cc_final: 0.7712 (m-10) REVERT: B 378 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8160 (mm-30) REVERT: B 469 MET cc_start: 0.7896 (ttt) cc_final: 0.7633 (ttp) REVERT: B 502 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.7273 (ttt90) REVERT: C 56 MET cc_start: 0.7640 (ttm) cc_final: 0.7411 (ttm) REVERT: C 246 ARG cc_start: 0.8081 (mmt180) cc_final: 0.7817 (mmm160) REVERT: C 253 TYR cc_start: 0.7791 (m-80) cc_final: 0.7528 (m-80) REVERT: C 270 GLN cc_start: 0.7272 (mm-40) cc_final: 0.6990 (mm-40) REVERT: C 488 GLU cc_start: 0.7897 (tp30) cc_final: 0.7546 (tp30) outliers start: 29 outliers final: 22 residues processed: 255 average time/residue: 0.3474 time to fit residues: 123.1850 Evaluate side-chains 214 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 519 ASP Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 612 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 104 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 264 GLN C 243 ASN C 264 GLN C 283 HIS C 368 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.147688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.115475 restraints weight = 47652.909| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.18 r_work: 0.3541 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15285 Z= 0.211 Angle : 0.548 8.189 20715 Z= 0.290 Chirality : 0.044 0.146 2142 Planarity : 0.005 0.045 2796 Dihedral : 4.613 18.060 2109 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.90 % Allowed : 8.94 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.39 (0.19), residues: 1869 helix: 1.91 (0.38), residues: 192 sheet: -0.70 (0.21), residues: 519 loop : -0.35 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 217 TYR 0.019 0.002 TYR C 138 PHE 0.016 0.002 PHE A 154 TRP 0.009 0.001 TRP C 96 HIS 0.006 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00455 (15285) covalent geometry : angle 0.54754 (20715) hydrogen bonds : bond 0.04442 ( 155) hydrogen bonds : angle 4.20807 ( 348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.792 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: 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 132 ASP cc_start: 0.7491 (t0) cc_final: 0.7244 (p0) REVERT: A 172 GLN cc_start: 0.8356 (pm20) cc_final: 0.7660 (tt0) REVERT: A 212 ASP cc_start: 0.7568 (t0) cc_final: 0.6620 (t0) REVERT: A 246 ARG cc_start: 0.7953 (mmt180) cc_final: 0.7250 (mmm160) REVERT: A 280 GLN cc_start: 0.7860 (mm-40) cc_final: 0.7166 (tm-30) REVERT: A 356 LEU cc_start: 0.8727 (mt) cc_final: 0.8148 (mm) REVERT: A 636 MET cc_start: 0.8759 (mmp) cc_final: 0.8448 (tpp) REVERT: B 27 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6829 (mt-10) REVERT: B 46 LEU cc_start: 0.8180 (tp) cc_final: 0.7834 (tt) REVERT: B 253 TYR cc_start: 0.7700 (m-80) cc_final: 0.7436 (m-80) REVERT: B 469 MET cc_start: 0.8219 (ttt) cc_final: 0.7934 (ttp) REVERT: B 487 MET cc_start: 0.8548 (mtt) cc_final: 0.8285 (mtm) REVERT: C 246 ARG cc_start: 0.8212 (mmt180) cc_final: 0.7887 (mmm160) REVERT: C 253 TYR cc_start: 0.7885 (m-80) cc_final: 0.7612 (m-80) REVERT: C 488 GLU cc_start: 0.8011 (tp30) cc_final: 0.7645 (tp30) outliers start: 30 outliers final: 22 residues processed: 213 average time/residue: 0.3445 time to fit residues: 103.8005 Evaluate side-chains 192 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 527 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 9 optimal weight: 0.0970 chunk 99 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 368 GLN C 243 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.137830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.105309 restraints weight = 48869.177| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.35 r_work: 0.3357 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15285 Z= 0.178 Angle : 0.505 6.032 20715 Z= 0.265 Chirality : 0.044 0.147 2142 Planarity : 0.004 0.039 2796 Dihedral : 4.527 18.413 2109 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.90 % Allowed : 10.84 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.47 (0.19), residues: 1869 helix: 2.01 (0.38), residues: 192 sheet: -0.93 (0.21), residues: 519 loop : -0.34 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 308 TYR 0.012 0.001 TYR C 143 PHE 0.013 0.001 PHE A 211 TRP 0.008 0.001 TRP C 96 HIS 0.005 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00391 (15285) covalent geometry : angle 0.50487 (20715) hydrogen bonds : bond 0.04143 ( 155) hydrogen bonds : angle 4.05722 ( 348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.786 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ASP cc_start: 0.7604 (t0) cc_final: 0.7276 (p0) REVERT: A 172 GLN cc_start: 0.8385 (pm20) cc_final: 0.7727 (tt0) REVERT: A 246 ARG cc_start: 0.8075 (mmt180) cc_final: 0.7412 (mmp-170) REVERT: A 280 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7121 (tm-30) REVERT: A 636 MET cc_start: 0.8818 (mmp) cc_final: 0.8533 (tpp) REVERT: B 46 LEU cc_start: 0.8263 (tp) cc_final: 0.7873 (tt) REVERT: B 253 TYR cc_start: 0.7705 (m-80) cc_final: 0.7417 (m-80) REVERT: B 379 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: B 469 MET cc_start: 0.8440 (ttt) cc_final: 0.8153 (ttp) REVERT: B 483 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8405 (m110) REVERT: C 253 TYR cc_start: 0.7919 (m-80) cc_final: 0.7582 (m-80) REVERT: C 441 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: C 488 GLU cc_start: 0.7915 (tp30) cc_final: 0.7638 (tp30) outliers start: 30 outliers final: 22 residues processed: 193 average time/residue: 0.3073 time to fit residues: 86.3787 Evaluate side-chains 181 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 527 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 88 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.2980 chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 0.0170 chunk 62 optimal weight: 3.9990 chunk 102 optimal weight: 0.0670 chunk 77 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN C 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.139368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.106882 restraints weight = 48548.770| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.35 r_work: 0.3472 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15285 Z= 0.095 Angle : 0.467 5.874 20715 Z= 0.242 Chirality : 0.044 0.146 2142 Planarity : 0.004 0.035 2796 Dihedral : 4.309 18.664 2109 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.33 % Allowed : 11.28 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.28 (0.19), residues: 1869 helix: 2.30 (0.38), residues: 192 sheet: -0.84 (0.21), residues: 513 loop : -0.23 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 217 TYR 0.008 0.001 TYR A 322 PHE 0.019 0.001 PHE B 33 TRP 0.007 0.001 TRP C 96 HIS 0.004 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00212 (15285) covalent geometry : angle 0.46668 (20715) hydrogen bonds : bond 0.03755 ( 155) hydrogen bonds : angle 3.81612 ( 348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.836 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: 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 132 ASP cc_start: 0.7566 (t0) cc_final: 0.7265 (p0) REVERT: A 153 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7420 (t0) REVERT: A 172 GLN cc_start: 0.8344 (pm20) cc_final: 0.7697 (tt0) REVERT: A 246 ARG cc_start: 0.8054 (mmt180) cc_final: 0.7159 (mmm160) REVERT: A 280 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7113 (tm-30) REVERT: A 636 MET cc_start: 0.8800 (mmp) cc_final: 0.8518 (tpp) REVERT: B 27 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6550 (mm-30) REVERT: B 46 LEU cc_start: 0.8143 (tp) cc_final: 0.7763 (tt) REVERT: B 253 TYR cc_start: 0.7711 (m-80) cc_final: 0.7461 (m-80) REVERT: B 379 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7327 (tp30) REVERT: B 469 MET cc_start: 0.8392 (ttt) cc_final: 0.8110 (ttp) REVERT: C 253 TYR cc_start: 0.7893 (m-80) cc_final: 0.7602 (m-80) REVERT: C 446 THR cc_start: 0.8826 (m) cc_final: 0.8543 (p) outliers start: 21 outliers final: 14 residues processed: 186 average time/residue: 0.3153 time to fit residues: 85.8008 Evaluate side-chains 169 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 99 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 534 ASN C 45 ASN C 526 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.102428 restraints weight = 50507.860| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.35 r_work: 0.3321 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.005 0.049 15285 Z= 0.215 Angle : 0.509 6.175 20715 Z= 0.268 Chirality : 0.043 0.150 2142 Planarity : 0.004 0.042 2796 Dihedral : 4.469 18.762 2109 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.90 % Allowed : 10.65 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.64 (0.19), residues: 1869 helix: 2.05 (0.38), residues: 192 sheet: -1.08 (0.21), residues: 519 loop : -0.48 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 187 TYR 0.012 0.001 TYR C 138 PHE 0.020 0.002 PHE B 33 TRP 0.007 0.001 TRP A 96 HIS 0.007 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00471 (15285) covalent geometry : angle 0.50919 (20715) hydrogen bonds : bond 0.04119 ( 155) hydrogen bonds : angle 4.05040 ( 348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.877 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: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7490 (t0) REVERT: A 172 GLN cc_start: 0.8427 (pm20) cc_final: 0.7809 (tt0) REVERT: A 246 ARG cc_start: 0.8070 (mmt180) cc_final: 0.7455 (mmp-170) REVERT: A 280 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7277 (tm-30) REVERT: A 519 ASP cc_start: 0.8330 (t0) cc_final: 0.7469 (m-30) REVERT: A 607 ARG cc_start: 0.4771 (ttt90) cc_final: 0.4038 (tpt90) REVERT: A 636 MET cc_start: 0.8843 (mmp) cc_final: 0.8572 (tpp) REVERT: B 27 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7428 (mp0) REVERT: B 46 LEU cc_start: 0.8164 (tp) cc_final: 0.7873 (tt) REVERT: B 253 TYR cc_start: 0.7803 (m-80) cc_final: 0.7523 (m-80) REVERT: B 379 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: B 469 MET cc_start: 0.8522 (ttt) cc_final: 0.8219 (ttp) REVERT: C 246 ARG cc_start: 0.8196 (mmt180) cc_final: 0.7945 (mmm160) REVERT: C 253 TYR cc_start: 0.7876 (m-80) cc_final: 0.7590 (m-80) REVERT: C 369 THR cc_start: 0.9271 (p) cc_final: 0.8964 (p) REVERT: C 446 THR cc_start: 0.8798 (m) cc_final: 0.8515 (p) outliers start: 30 outliers final: 23 residues processed: 172 average time/residue: 0.2962 time to fit residues: 76.1345 Evaluate side-chains 173 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 53 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 133 optimal weight: 0.3980 chunk 97 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.136753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.104925 restraints weight = 50600.020| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.33 r_work: 0.3418 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15285 Z= 0.146 Angle : 0.478 5.991 20715 Z= 0.248 Chirality : 0.044 0.148 2142 Planarity : 0.004 0.033 2796 Dihedral : 4.335 18.986 2109 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.58 % Allowed : 11.41 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.62 (0.19), residues: 1869 helix: 2.18 (0.38), residues: 192 sheet: -1.10 (0.21), residues: 519 loop : -0.47 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 187 TYR 0.008 0.001 TYR B 497 PHE 0.010 0.001 PHE B 592 TRP 0.007 0.001 TRP C 96 HIS 0.003 0.001 HIS C 186 Details of bonding type rmsd covalent geometry : bond 0.00323 (15285) covalent geometry : angle 0.47784 (20715) hydrogen bonds : bond 0.03789 ( 155) hydrogen bonds : angle 3.89863 ( 348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.788 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7461 (t0) REVERT: A 172 GLN cc_start: 0.8462 (pm20) cc_final: 0.7562 (tm-30) REVERT: A 246 ARG cc_start: 0.8141 (mmt180) cc_final: 0.7425 (mmp-170) REVERT: A 280 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7308 (tm-30) REVERT: A 301 PHE cc_start: 0.8592 (p90) cc_final: 0.8222 (p90) REVERT: A 488 GLU cc_start: 0.8079 (tp30) cc_final: 0.7871 (tt0) REVERT: A 519 ASP cc_start: 0.8377 (t0) cc_final: 0.7591 (m-30) REVERT: A 607 ARG cc_start: 0.5227 (ttt90) cc_final: 0.4279 (tpt90) REVERT: A 636 MET cc_start: 0.8837 (mmp) cc_final: 0.8573 (tpp) REVERT: B 9 VAL cc_start: 0.7938 (t) cc_final: 0.7693 (t) REVERT: B 253 TYR cc_start: 0.7844 (m-80) cc_final: 0.7585 (m-80) REVERT: B 379 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7529 (tp30) REVERT: B 469 MET cc_start: 0.8559 (ttt) cc_final: 0.8323 (ttp) REVERT: C 253 TYR cc_start: 0.7898 (m-80) cc_final: 0.7640 (m-80) REVERT: C 369 THR cc_start: 0.9267 (p) cc_final: 0.8950 (p) REVERT: C 446 THR cc_start: 0.8780 (m) cc_final: 0.8532 (p) outliers start: 25 outliers final: 21 residues processed: 170 average time/residue: 0.2880 time to fit residues: 73.6889 Evaluate side-chains 173 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 ASN Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 162 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 177 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 96 optimal weight: 0.0770 chunk 174 optimal weight: 0.6980 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 503 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.132290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.100938 restraints weight = 51425.374| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.38 r_work: 0.3367 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15285 Z= 0.191 Angle : 0.493 6.086 20715 Z= 0.257 Chirality : 0.043 0.144 2142 Planarity : 0.004 0.037 2796 Dihedral : 4.382 18.749 2109 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.65 % Allowed : 11.47 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.79 (0.19), residues: 1869 helix: 2.08 (0.38), residues: 192 sheet: -1.17 (0.22), residues: 486 loop : -0.64 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 569 TYR 0.010 0.001 TYR B 497 PHE 0.012 0.001 PHE C 592 TRP 0.007 0.001 TRP A 96 HIS 0.006 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00423 (15285) covalent geometry : angle 0.49305 (20715) hydrogen bonds : bond 0.03897 ( 155) hydrogen bonds : angle 3.98279 ( 348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.576 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7480 (t0) REVERT: A 172 GLN cc_start: 0.8459 (pm20) cc_final: 0.7481 (tm-30) REVERT: A 301 PHE cc_start: 0.8582 (p90) cc_final: 0.8349 (p90) REVERT: A 519 ASP cc_start: 0.8262 (t0) cc_final: 0.7500 (m-30) REVERT: A 607 ARG cc_start: 0.5035 (ttt90) cc_final: 0.3625 (tpt90) REVERT: A 636 MET cc_start: 0.8847 (mmp) cc_final: 0.8589 (tpp) REVERT: B 9 VAL cc_start: 0.7868 (t) cc_final: 0.7634 (t) REVERT: B 246 ARG cc_start: 0.8094 (mmt180) cc_final: 0.7443 (mmp-170) REVERT: B 253 TYR cc_start: 0.7949 (m-80) cc_final: 0.7617 (m-80) REVERT: B 280 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7134 (tm-30) REVERT: B 379 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: B 469 MET cc_start: 0.8602 (ttt) cc_final: 0.8293 (ttp) REVERT: C 253 TYR cc_start: 0.7885 (m-80) cc_final: 0.7610 (m-80) REVERT: C 369 THR cc_start: 0.9280 (p) cc_final: 0.8940 (p) REVERT: C 446 THR cc_start: 0.8774 (m) cc_final: 0.8522 (p) outliers start: 26 outliers final: 21 residues processed: 172 average time/residue: 0.2570 time to fit residues: 66.0847 Evaluate side-chains 176 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 18 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.132589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.101590 restraints weight = 51038.078| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.34 r_work: 0.3399 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15285 Z= 0.158 Angle : 0.484 6.003 20715 Z= 0.251 Chirality : 0.044 0.143 2142 Planarity : 0.004 0.033 2796 Dihedral : 4.309 18.878 2109 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.58 % Allowed : 11.72 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.80 (0.19), residues: 1869 helix: 2.15 (0.38), residues: 192 sheet: -1.21 (0.22), residues: 492 loop : -0.65 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 308 TYR 0.008 0.001 TYR C 138 PHE 0.010 0.001 PHE B 592 TRP 0.007 0.001 TRP A 96 HIS 0.005 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00351 (15285) covalent geometry : angle 0.48442 (20715) hydrogen bonds : bond 0.03800 ( 155) hydrogen bonds : angle 3.89330 ( 348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.600 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7500 (t0) REVERT: A 172 GLN cc_start: 0.8502 (pm20) cc_final: 0.7564 (tm-30) REVERT: A 301 PHE cc_start: 0.8595 (p90) cc_final: 0.8348 (p90) REVERT: A 519 ASP cc_start: 0.8266 (t0) cc_final: 0.7578 (m-30) REVERT: A 555 SER cc_start: 0.8621 (t) cc_final: 0.8299 (m) REVERT: A 607 ARG cc_start: 0.5140 (ttt90) cc_final: 0.3708 (tpt90) REVERT: A 636 MET cc_start: 0.8856 (mmp) cc_final: 0.8610 (tpp) REVERT: B 9 VAL cc_start: 0.7851 (t) cc_final: 0.7633 (t) REVERT: B 246 ARG cc_start: 0.8100 (mmt180) cc_final: 0.7398 (mmp-170) REVERT: B 253 TYR cc_start: 0.7918 (m-80) cc_final: 0.7597 (m-80) REVERT: B 280 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7136 (tm-30) REVERT: B 379 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7567 (tp30) REVERT: B 469 MET cc_start: 0.8600 (ttt) cc_final: 0.8301 (ttp) REVERT: C 253 TYR cc_start: 0.7890 (m-80) cc_final: 0.7038 (m-80) REVERT: C 369 THR cc_start: 0.9290 (p) cc_final: 0.8948 (p) REVERT: C 446 THR cc_start: 0.8760 (m) cc_final: 0.8530 (p) outliers start: 25 outliers final: 22 residues processed: 168 average time/residue: 0.2596 time to fit residues: 65.2238 Evaluate side-chains 179 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 441 ASP Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 133 optimal weight: 0.3980 chunk 104 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 153 optimal weight: 0.3980 chunk 32 optimal weight: 0.0170 chunk 34 optimal weight: 0.6980 chunk 174 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 567 GLN C 580 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.136998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.105421 restraints weight = 50111.180| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.36 r_work: 0.3408 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15285 Z= 0.095 Angle : 0.467 7.023 20715 Z= 0.237 Chirality : 0.044 0.147 2142 Planarity : 0.003 0.030 2796 Dihedral : 4.083 18.558 2109 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.39 % Allowed : 11.85 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -0.58 (0.19), residues: 1869 helix: 2.43 (0.38), residues: 192 sheet: -1.04 (0.22), residues: 486 loop : -0.53 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 308 TYR 0.007 0.001 TYR C 138 PHE 0.011 0.001 PHE C 592 TRP 0.008 0.001 TRP A 96 HIS 0.005 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00218 (15285) covalent geometry : angle 0.46738 (20715) hydrogen bonds : bond 0.03514 ( 155) hydrogen bonds : angle 3.69212 ( 348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.838 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: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7484 (t0) REVERT: A 172 GLN cc_start: 0.8553 (pm20) cc_final: 0.7671 (tm-30) REVERT: A 519 ASP cc_start: 0.8229 (t0) cc_final: 0.7566 (m-30) REVERT: A 555 SER cc_start: 0.8642 (t) cc_final: 0.8334 (m) REVERT: A 607 ARG cc_start: 0.5051 (ttt90) cc_final: 0.3629 (tpt90) REVERT: A 636 MET cc_start: 0.8835 (mmp) cc_final: 0.8580 (tpp) REVERT: B 9 VAL cc_start: 0.7843 (t) cc_final: 0.7627 (t) REVERT: B 246 ARG cc_start: 0.8101 (mmt180) cc_final: 0.7437 (mmm160) REVERT: B 253 TYR cc_start: 0.7900 (m-80) cc_final: 0.7653 (m-80) REVERT: B 280 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7133 (tm-30) REVERT: B 379 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7532 (tp30) REVERT: B 469 MET cc_start: 0.8571 (ttt) cc_final: 0.8199 (ttp) REVERT: B 632 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8337 (mt0) REVERT: C 246 ARG cc_start: 0.8256 (mmt180) cc_final: 0.7852 (mmp-170) REVERT: C 369 THR cc_start: 0.9249 (p) cc_final: 0.8938 (p) REVERT: C 446 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8574 (p) REVERT: C 487 MET cc_start: 0.8472 (mtt) cc_final: 0.8152 (mtm) outliers start: 22 outliers final: 16 residues processed: 171 average time/residue: 0.2972 time to fit residues: 76.4951 Evaluate side-chains 169 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 503 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS C 45 ASN ** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 GLN C 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.129643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.099288 restraints weight = 52769.277| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.34 r_work: 0.3366 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15285 Z= 0.241 Angle : 0.531 6.169 20715 Z= 0.279 Chirality : 0.044 0.139 2142 Planarity : 0.004 0.048 2796 Dihedral : 4.440 18.598 2109 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.46 % Allowed : 12.23 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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 aren not related in a simple way. whole: -1.01 (0.19), residues: 1869 helix: 2.07 (0.38), residues: 192 sheet: -1.20 (0.22), residues: 486 loop : -0.89 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 569 TYR 0.015 0.002 TYR C 385 PHE 0.031 0.002 PHE A 301 TRP 0.009 0.001 TRP A 96 HIS 0.008 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00539 (15285) covalent geometry : angle 0.53124 (20715) hydrogen bonds : bond 0.03999 ( 155) hydrogen bonds : angle 4.00908 ( 348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7848.20 seconds wall clock time: 133 minutes 43.05 seconds (8023.05 seconds total)