Starting phenix.real_space_refine on Fri Aug 22 17:07:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qg0_18386/08_2025/8qg0_18386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qg0_18386/08_2025/8qg0_18386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qg0_18386/08_2025/8qg0_18386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qg0_18386/08_2025/8qg0_18386.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qg0_18386/08_2025/8qg0_18386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qg0_18386/08_2025/8qg0_18386.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 33 5.49 5 S 13 5.16 5 C 3811 2.51 5 N 1012 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.00s 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: 6080 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3478 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 403} Chain: "B" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1894 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "Q" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 363 Classifications: {'RNA': 17} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 15} Time building chain proxies: 1.88, per 1000 atoms: 0.31 Number of scatterers: 6080 At special positions: 0 Unit cell: (67.1, 91.3, 104.5, 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 13 16.00 P 33 15.00 O 1211 8.00 N 1012 7.00 C 3811 6.00 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: 0.72 Conformation dependent library (CDL) restraints added in 373.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1236 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 11 sheets defined 33.5% alpha, 13.7% beta 6 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 58 through 73 Processing helix chain 'A' and resid 92 through 107 removed outlier: 3.583A pdb=" N ASN A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.972A pdb=" N TYR A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 removed outlier: 3.808A pdb=" N ASN A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 3.948A pdb=" N ASN A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.534A pdb=" N VAL A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 359 through 376 removed outlier: 3.516A pdb=" N HIS A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 407 Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 417 through 421 removed outlier: 3.660A pdb=" N GLN A 421 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 93 removed outlier: 4.078A pdb=" N GLY B 81 " --> pdb=" O ASN B 77 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.829A pdb=" N VAL B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 216 removed outlier: 3.531A pdb=" N PHE B 205 " --> pdb=" O MET B 201 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 184 removed outlier: 6.841A pdb=" N ILE A 183 " --> pdb=" O HIS A 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 189 removed outlier: 3.557A pdb=" N CYS A 197 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 195 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.874A pdb=" N GLU A 212 " --> pdb=" O MET A 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 291 through 293 Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.608A pdb=" N ARG B 110 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB1, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.705A pdb=" N ASN B 30 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 234 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS B 223 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 41 removed outlier: 3.716A pdb=" N SER B 38 " --> pdb=" O LEU B 61 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1447 1.33 - 1.45: 1410 1.45 - 1.57: 3348 1.57 - 1.69: 65 1.69 - 1.80: 25 Bond restraints: 6295 Sorted by residual: bond pdb=" N LEU A 249 " pdb=" CA LEU A 249 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.52e-02 4.33e+03 9.71e+00 bond pdb=" N ARG A 383 " pdb=" CA ARG A 383 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.21e-02 6.83e+03 9.59e+00 bond pdb=" N SER B 163 " pdb=" CA SER B 163 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.43e+00 bond pdb=" N ILE B 167 " pdb=" CA ILE B 167 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 8.26e+00 bond pdb=" N SER A 384 " pdb=" CA SER A 384 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 7.84e+00 ... (remaining 6290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 8424 1.91 - 3.82: 223 3.82 - 5.72: 30 5.72 - 7.63: 5 7.63 - 9.54: 2 Bond angle restraints: 8684 Sorted by residual: angle pdb=" C LYS B 168 " pdb=" CA LYS B 168 " pdb=" CB LYS B 168 " ideal model delta sigma weight residual 116.54 110.28 6.26 1.15e+00 7.56e-01 2.97e+01 angle pdb=" N LEU A 249 " pdb=" CA LEU A 249 " pdb=" CB LEU A 249 " ideal model delta sigma weight residual 111.65 104.47 7.18 1.40e+00 5.10e-01 2.63e+01 angle pdb=" N LEU A 249 " pdb=" CA LEU A 249 " pdb=" C LEU A 249 " ideal model delta sigma weight residual 110.61 105.67 4.94 1.25e+00 6.40e-01 1.56e+01 angle pdb=" CA ILE B 167 " pdb=" C ILE B 167 " pdb=" O ILE B 167 " ideal model delta sigma weight residual 121.05 116.93 4.12 1.11e+00 8.12e-01 1.38e+01 angle pdb=" N TYR B 171 " pdb=" CA TYR B 171 " pdb=" C TYR B 171 " ideal model delta sigma weight residual 113.38 109.05 4.33 1.17e+00 7.31e-01 1.37e+01 ... (remaining 8679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3219 17.93 - 35.85: 360 35.85 - 53.78: 108 53.78 - 71.70: 38 71.70 - 89.63: 12 Dihedral angle restraints: 3737 sinusoidal: 1807 harmonic: 1930 Sorted by residual: dihedral pdb=" N LEU A 249 " pdb=" C LEU A 249 " pdb=" CA LEU A 249 " pdb=" CB LEU A 249 " ideal model delta harmonic sigma weight residual 122.80 111.66 11.14 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" CA VAL A 300 " pdb=" C VAL A 300 " pdb=" N MET A 301 " pdb=" CA MET A 301 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA TYR B 22 " pdb=" C TYR B 22 " pdb=" N ILE B 23 " pdb=" CA ILE B 23 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 3734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 930 0.103 - 0.205: 40 0.205 - 0.308: 1 0.308 - 0.411: 0 0.411 - 0.514: 1 Chirality restraints: 972 Sorted by residual: 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 3.02 -0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" CB ILE B 167 " pdb=" CA ILE B 167 " pdb=" CG1 ILE B 167 " pdb=" CG2 ILE B 167 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA TYR B 164 " pdb=" N TYR B 164 " pdb=" C TYR B 164 " pdb=" CB TYR B 164 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.16e-01 ... (remaining 969 not shown) Planarity restraints: 974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 40 " 0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO B 41 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 41 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 41 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 355 " 0.011 2.00e-02 2.50e+03 9.58e-03 2.29e+00 pdb=" CG TRP A 355 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 355 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 355 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 355 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 355 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 355 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 355 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 355 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 355 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 341 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO A 342 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 342 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 342 " 0.021 5.00e-02 4.00e+02 ... (remaining 971 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 543 2.74 - 3.28: 6374 3.28 - 3.82: 10696 3.82 - 4.36: 13200 4.36 - 4.90: 21656 Nonbonded interactions: 52469 Sorted by model distance: nonbonded pdb=" O6 DG P 11 " pdb=" N6 A Q 6 " model vdw 2.198 3.120 nonbonded pdb=" NE ARG A 257 " pdb=" O2' A Q 15 " model vdw 2.208 3.120 nonbonded pdb=" O2 DC P 8 " pdb=" N2 G Q 11 " model vdw 2.220 3.120 nonbonded pdb=" OG1 THR A 250 " pdb=" O ALA A 288 " model vdw 2.239 3.040 nonbonded pdb=" O ILE A 87 " pdb=" NE2 GLN A 99 " model vdw 2.246 3.120 ... (remaining 52464 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.980 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6295 Z= 0.231 Angle : 0.728 9.538 8684 Z= 0.439 Chirality : 0.049 0.514 972 Planarity : 0.005 0.079 974 Dihedral : 17.660 89.630 2501 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.50 % Allowed : 0.50 % Favored : 99.00 % Cbeta Deviations : 0.32 % 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 aren not related in a simple way. whole: -1.84 (0.33), residues: 652 helix: 0.39 (0.39), residues: 179 sheet: -2.31 (0.46), residues: 132 loop : -1.62 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 202 TYR 0.014 0.002 TYR A 323 PHE 0.018 0.002 PHE A 382 TRP 0.025 0.002 TRP A 355 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 6295) covalent geometry : angle 0.72768 ( 8684) hydrogen bonds : bond 0.22439 ( 195) hydrogen bonds : angle 8.76424 ( 548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.231 Fit side-chains REVERT: B 21 LEU cc_start: 0.7830 (mp) cc_final: 0.7626 (mp) outliers start: 3 outliers final: 1 residues processed: 116 average time/residue: 0.0799 time to fit residues: 12.4814 Evaluate side-chains 99 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN A 378 ASN B 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.218839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.198104 restraints weight = 8060.130| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 2.39 r_work: 0.4384 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6295 Z= 0.179 Angle : 0.659 9.105 8684 Z= 0.348 Chirality : 0.047 0.203 972 Planarity : 0.005 0.060 974 Dihedral : 18.079 92.077 1155 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.32 % Allowed : 11.11 % Favored : 86.57 % 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 aren not related in a simple way. whole: -1.90 (0.33), residues: 652 helix: 0.28 (0.38), residues: 197 sheet: -2.21 (0.45), residues: 138 loop : -1.78 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 85 TYR 0.012 0.001 TYR A 287 PHE 0.010 0.002 PHE B 205 TRP 0.014 0.002 TRP A 355 HIS 0.004 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 6295) covalent geometry : angle 0.65902 ( 8684) hydrogen bonds : bond 0.05097 ( 195) hydrogen bonds : angle 5.81219 ( 548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.226 Fit side-chains REVERT: A 355 TRP cc_start: 0.7086 (m-10) cc_final: 0.6591 (m-90) REVERT: B 110 ARG cc_start: 0.6056 (mmm160) cc_final: 0.5441 (mmm160) outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 0.0724 time to fit residues: 10.7928 Evaluate side-chains 103 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 165 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 54 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN A 211 ASN A 354 ASN A 378 ASN A 417 ASN B 158 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.221030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.200096 restraints weight = 8019.763| |-----------------------------------------------------------------------------| r_work (start): 0.4604 rms_B_bonded: 2.39 r_work: 0.4434 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6295 Z= 0.132 Angle : 0.598 7.975 8684 Z= 0.314 Chirality : 0.046 0.193 972 Planarity : 0.005 0.072 974 Dihedral : 18.068 91.161 1155 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.82 % Allowed : 13.60 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.33), residues: 652 helix: 0.37 (0.38), residues: 198 sheet: -2.01 (0.48), residues: 131 loop : -1.55 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 110 TYR 0.011 0.001 TYR B 31 PHE 0.011 0.001 PHE B 205 TRP 0.012 0.001 TRP A 379 HIS 0.002 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6295) covalent geometry : angle 0.59774 ( 8684) hydrogen bonds : bond 0.04288 ( 195) hydrogen bonds : angle 5.16431 ( 548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.231 Fit side-chains REVERT: A 139 MET cc_start: 0.6190 (ptt) cc_final: 0.5953 (ptt) REVERT: A 355 TRP cc_start: 0.7007 (m-10) cc_final: 0.6591 (m-10) REVERT: B 170 LYS cc_start: 0.6742 (OUTLIER) cc_final: 0.6325 (pttt) outliers start: 17 outliers final: 13 residues processed: 108 average time/residue: 0.0763 time to fit residues: 11.1733 Evaluate side-chains 108 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.214372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.194126 restraints weight = 7772.221| |-----------------------------------------------------------------------------| r_work (start): 0.4600 rms_B_bonded: 2.21 r_work: 0.4435 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6295 Z= 0.138 Angle : 0.596 9.879 8684 Z= 0.311 Chirality : 0.044 0.172 972 Planarity : 0.005 0.062 974 Dihedral : 18.105 92.564 1155 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.48 % Allowed : 15.75 % Favored : 80.76 % 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 aren not related in a simple way. whole: -1.53 (0.33), residues: 652 helix: 0.42 (0.38), residues: 198 sheet: -1.89 (0.48), residues: 131 loop : -1.52 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 110 TYR 0.014 0.001 TYR B 31 PHE 0.008 0.001 PHE B 205 TRP 0.011 0.001 TRP A 76 HIS 0.003 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 6295) covalent geometry : angle 0.59562 ( 8684) hydrogen bonds : bond 0.04183 ( 195) hydrogen bonds : angle 4.89639 ( 548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.217 Fit side-chains REVERT: A 147 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6795 (ptp-170) REVERT: A 355 TRP cc_start: 0.6986 (m-10) cc_final: 0.6676 (m-10) REVERT: A 363 ASN cc_start: 0.6728 (OUTLIER) cc_final: 0.6249 (t0) REVERT: B 145 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6665 (tt) REVERT: B 151 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7309 (mt) REVERT: B 187 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.6123 (t-170) outliers start: 21 outliers final: 13 residues processed: 110 average time/residue: 0.0717 time to fit residues: 10.8891 Evaluate side-chains 115 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN B 184 GLN B 187 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.218228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.196498 restraints weight = 8179.031| |-----------------------------------------------------------------------------| r_work (start): 0.4564 rms_B_bonded: 2.49 r_work: 0.4380 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6295 Z= 0.202 Angle : 0.671 10.940 8684 Z= 0.344 Chirality : 0.047 0.204 972 Planarity : 0.005 0.060 974 Dihedral : 18.274 95.919 1155 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.48 % Allowed : 16.42 % Favored : 79.10 % 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 aren not related in a simple way. whole: -1.63 (0.33), residues: 652 helix: 0.25 (0.37), residues: 200 sheet: -1.79 (0.49), residues: 129 loop : -1.61 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 110 TYR 0.018 0.002 TYR A 323 PHE 0.012 0.002 PHE A 202 TRP 0.011 0.001 TRP A 76 HIS 0.006 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 6295) covalent geometry : angle 0.67078 ( 8684) hydrogen bonds : bond 0.04599 ( 195) hydrogen bonds : angle 5.06151 ( 548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.215 Fit side-chains REVERT: A 363 ASN cc_start: 0.6857 (OUTLIER) cc_final: 0.6364 (t0) REVERT: B 145 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6841 (tt) REVERT: B 170 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.6263 (pttt) REVERT: B 187 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.6210 (t70) outliers start: 27 outliers final: 21 residues processed: 110 average time/residue: 0.0783 time to fit residues: 11.5658 Evaluate side-chains 118 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 62 optimal weight: 0.0570 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.0040 overall best weight: 0.2710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.218098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.198214 restraints weight = 7722.574| |-----------------------------------------------------------------------------| r_work (start): 0.4637 rms_B_bonded: 2.20 r_work: 0.4466 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6295 Z= 0.116 Angle : 0.592 9.494 8684 Z= 0.306 Chirality : 0.044 0.161 972 Planarity : 0.004 0.056 974 Dihedral : 18.188 94.599 1155 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.82 % Allowed : 18.91 % Favored : 78.28 % 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 aren not related in a simple way. whole: -1.34 (0.34), residues: 652 helix: 0.55 (0.38), residues: 197 sheet: -1.70 (0.48), residues: 129 loop : -1.42 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 110 TYR 0.012 0.001 TYR A 152 PHE 0.007 0.001 PHE A 138 TRP 0.012 0.001 TRP A 76 HIS 0.003 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6295) covalent geometry : angle 0.59212 ( 8684) hydrogen bonds : bond 0.03930 ( 195) hydrogen bonds : angle 4.75110 ( 548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.231 Fit side-chains REVERT: A 355 TRP cc_start: 0.6933 (m-10) cc_final: 0.6474 (m-10) REVERT: A 377 MET cc_start: 0.6571 (tpt) cc_final: 0.6212 (tpp) REVERT: B 145 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6450 (tt) REVERT: B 170 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6268 (pttt) outliers start: 17 outliers final: 11 residues processed: 104 average time/residue: 0.0746 time to fit residues: 10.8135 Evaluate side-chains 105 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 170 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.217011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.196549 restraints weight = 8124.051| |-----------------------------------------------------------------------------| r_work (start): 0.4558 rms_B_bonded: 2.31 r_work: 0.4380 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6295 Z= 0.166 Angle : 0.628 11.214 8684 Z= 0.324 Chirality : 0.045 0.159 972 Planarity : 0.005 0.056 974 Dihedral : 18.346 96.750 1154 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.32 % Allowed : 19.57 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.33), residues: 652 helix: 0.47 (0.37), residues: 198 sheet: -1.67 (0.49), residues: 129 loop : -1.46 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 257 TYR 0.013 0.001 TYR B 31 PHE 0.011 0.001 PHE A 426 TRP 0.011 0.001 TRP A 76 HIS 0.004 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6295) covalent geometry : angle 0.62813 ( 8684) hydrogen bonds : bond 0.04299 ( 195) hydrogen bonds : angle 4.84069 ( 548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.234 Fit side-chains REVERT: A 131 ILE cc_start: 0.4680 (OUTLIER) cc_final: 0.4157 (tt) REVERT: A 290 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6575 (mp) REVERT: A 363 ASN cc_start: 0.6774 (OUTLIER) cc_final: 0.6382 (t0) REVERT: B 145 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6689 (tt) REVERT: B 170 LYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6331 (pttt) outliers start: 20 outliers final: 14 residues processed: 104 average time/residue: 0.0773 time to fit residues: 10.9679 Evaluate side-chains 107 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN B 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.212831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.192472 restraints weight = 7789.924| |-----------------------------------------------------------------------------| r_work (start): 0.4575 rms_B_bonded: 2.22 r_work: 0.4394 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6295 Z= 0.151 Angle : 0.616 9.616 8684 Z= 0.320 Chirality : 0.044 0.158 972 Planarity : 0.005 0.056 974 Dihedral : 18.352 97.609 1154 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.15 % Allowed : 20.73 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.33), residues: 652 helix: 0.49 (0.37), residues: 198 sheet: -1.69 (0.49), residues: 129 loop : -1.49 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 110 TYR 0.010 0.001 TYR B 31 PHE 0.008 0.001 PHE A 426 TRP 0.020 0.001 TRP A 355 HIS 0.003 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6295) covalent geometry : angle 0.61573 ( 8684) hydrogen bonds : bond 0.04152 ( 195) hydrogen bonds : angle 4.80781 ( 548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.241 Fit side-chains REVERT: A 131 ILE cc_start: 0.4982 (OUTLIER) cc_final: 0.4478 (tt) REVERT: A 355 TRP cc_start: 0.7071 (m-10) cc_final: 0.6602 (m-90) REVERT: B 145 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6643 (tt) REVERT: B 170 LYS cc_start: 0.6627 (OUTLIER) cc_final: 0.6157 (pttt) outliers start: 19 outliers final: 13 residues processed: 104 average time/residue: 0.0695 time to fit residues: 10.0942 Evaluate side-chains 106 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 170 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 329 GLN A 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.222174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.201904 restraints weight = 8135.429| |-----------------------------------------------------------------------------| r_work (start): 0.4620 rms_B_bonded: 2.31 r_work: 0.4450 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6295 Z= 0.130 Angle : 0.625 12.823 8684 Z= 0.319 Chirality : 0.045 0.222 972 Planarity : 0.004 0.055 974 Dihedral : 18.398 97.402 1154 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.65 % Allowed : 20.73 % Favored : 76.62 % 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 aren not related in a simple way. whole: -1.28 (0.34), residues: 652 helix: 0.66 (0.38), residues: 197 sheet: -1.70 (0.48), residues: 129 loop : -1.41 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 110 TYR 0.015 0.001 TYR A 152 PHE 0.012 0.001 PHE A 202 TRP 0.017 0.001 TRP A 355 HIS 0.002 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6295) covalent geometry : angle 0.62472 ( 8684) hydrogen bonds : bond 0.03865 ( 195) hydrogen bonds : angle 4.69584 ( 548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.240 Fit side-chains REVERT: A 131 ILE cc_start: 0.5014 (OUTLIER) cc_final: 0.4730 (tt) REVERT: A 355 TRP cc_start: 0.6970 (m-10) cc_final: 0.6474 (m-90) REVERT: B 145 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6657 (tt) REVERT: B 170 LYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6134 (pttt) outliers start: 16 outliers final: 13 residues processed: 97 average time/residue: 0.0722 time to fit residues: 9.8199 Evaluate side-chains 102 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 170 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 65 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 365 HIS A 378 ASN B 158 ASN B 187 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.208127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.187547 restraints weight = 7866.901| |-----------------------------------------------------------------------------| r_work (start): 0.4513 rms_B_bonded: 2.25 r_work: 0.4333 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6295 Z= 0.224 Angle : 0.715 12.512 8684 Z= 0.365 Chirality : 0.048 0.192 972 Planarity : 0.005 0.059 974 Dihedral : 18.598 100.641 1154 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.48 % Allowed : 20.73 % Favored : 75.79 % 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 aren not related in a simple way. whole: -1.53 (0.33), residues: 652 helix: 0.33 (0.37), residues: 200 sheet: -1.66 (0.50), residues: 129 loop : -1.58 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 257 TYR 0.014 0.002 TYR A 360 PHE 0.009 0.002 PHE B 216 TRP 0.018 0.002 TRP A 355 HIS 0.005 0.001 HIS A 252 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 6295) covalent geometry : angle 0.71504 ( 8684) hydrogen bonds : bond 0.04568 ( 195) hydrogen bonds : angle 5.00489 ( 548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.263 Fit side-chains REVERT: A 225 TYR cc_start: 0.8035 (t80) cc_final: 0.7718 (t80) REVERT: A 355 TRP cc_start: 0.7107 (m-10) cc_final: 0.6465 (m-10) REVERT: B 145 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.6884 (tt) REVERT: B 170 LYS cc_start: 0.6418 (OUTLIER) cc_final: 0.5913 (pttt) REVERT: B 187 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.5548 (t-170) outliers start: 21 outliers final: 17 residues processed: 99 average time/residue: 0.0723 time to fit residues: 10.0192 Evaluate side-chains 104 residues out of total 603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 187 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 2 optimal weight: 0.0770 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN A 365 HIS A 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.215925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.195951 restraints weight = 7738.495| |-----------------------------------------------------------------------------| r_work (start): 0.4608 rms_B_bonded: 2.18 r_work: 0.4432 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6295 Z= 0.137 Angle : 0.642 11.383 8684 Z= 0.330 Chirality : 0.045 0.204 972 Planarity : 0.005 0.056 974 Dihedral : 18.554 99.627 1154 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.82 % Allowed : 22.22 % Favored : 74.96 % 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 aren not related in a simple way. whole: -1.36 (0.33), residues: 652 helix: 0.58 (0.37), residues: 197 sheet: -1.62 (0.50), residues: 129 loop : -1.51 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 202 TYR 0.013 0.001 TYR A 152 PHE 0.010 0.001 PHE A 426 TRP 0.016 0.001 TRP A 355 HIS 0.005 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6295) covalent geometry : angle 0.64237 ( 8684) hydrogen bonds : bond 0.04010 ( 195) hydrogen bonds : angle 4.77233 ( 548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1443.51 seconds wall clock time: 25 minutes 40.38 seconds (1540.38 seconds total)