Starting phenix.real_space_refine on Tue Mar 3 13:19:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ey5_31378/03_2026/7ey5_31378_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ey5_31378/03_2026/7ey5_31378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ey5_31378/03_2026/7ey5_31378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ey5_31378/03_2026/7ey5_31378.map" model { file = "/net/cci-nas-00/data/ceres_data/7ey5_31378/03_2026/7ey5_31378_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ey5_31378/03_2026/7ey5_31378_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.039 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3237 2.51 5 N 845 2.21 5 O 970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5072 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "B" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 933 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 840 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "H" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1014 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Time building chain proxies: 1.28, per 1000 atoms: 0.25 Number of scatterers: 5072 At special positions: 0 Unit cell: (95.92, 92.65, 109, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 970 8.00 N 845 7.00 C 3237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 362.1 milliseconds 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1174 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 12 sheets defined 7.3% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.624A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.854A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.733A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.528A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.908A pdb=" N ALA H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.503A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 16 through 20 removed outlier: 5.449A pdb=" N GLU B 16 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.951A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE B 34 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 115 " --> pdb=" O TYR B 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 7 removed outlier: 3.598A pdb=" N SER C 22 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS C 23 " --> pdb=" O PHE C 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR C 72 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.872A pdb=" N LEU C 11 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU C 106 " --> pdb=" O LEU C 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 34 through 37 removed outlier: 6.677A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 60 through 62 removed outlier: 6.217A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 103 through 105 Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.564A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR L 69 " --> pdb=" O THR L 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.247A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 303 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.68 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1598 1.34 - 1.46: 1411 1.46 - 1.58: 2175 1.58 - 1.70: 0 1.70 - 1.82: 25 Bond restraints: 5209 Sorted by residual: bond pdb=" CD2 TYR L 91 " pdb=" CE2 TYR L 91 " ideal model delta sigma weight residual 1.382 1.347 0.035 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CB MET B 48 " pdb=" CG MET B 48 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CB VAL H 48 " pdb=" CG1 VAL H 48 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.03e+00 bond pdb=" CB TYR L 91 " pdb=" CG TYR L 91 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.20e-02 2.07e+03 9.47e-01 bond pdb=" CA ASN B 105 " pdb=" CB ASN B 105 " ideal model delta sigma weight residual 1.530 1.545 -0.014 1.54e-02 4.22e+03 8.81e-01 ... (remaining 5204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 6948 2.50 - 5.00: 113 5.00 - 7.49: 10 7.49 - 9.99: 1 9.99 - 12.49: 3 Bond angle restraints: 7075 Sorted by residual: angle pdb=" N GLY B 113 " pdb=" CA GLY B 113 " pdb=" C GLY B 113 " ideal model delta sigma weight residual 113.18 102.33 10.85 2.37e+00 1.78e-01 2.09e+01 angle pdb=" CA LEU B 115 " pdb=" CB LEU B 115 " pdb=" CG LEU B 115 " ideal model delta sigma weight residual 116.30 103.81 12.49 3.50e+00 8.16e-02 1.27e+01 angle pdb=" C VAL C 13 " pdb=" N SER C 14 " pdb=" CA SER C 14 " ideal model delta sigma weight residual 120.97 130.81 -9.84 2.84e+00 1.24e-01 1.20e+01 angle pdb=" CA TYR L 91 " pdb=" CB TYR L 91 " pdb=" CG TYR L 91 " ideal model delta sigma weight residual 113.90 119.58 -5.68 1.80e+00 3.09e-01 9.95e+00 angle pdb=" C VAL H 12 " pdb=" N LYS H 13 " pdb=" CA LYS H 13 " ideal model delta sigma weight residual 121.95 133.22 -11.27 3.74e+00 7.15e-02 9.08e+00 ... (remaining 7070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 2701 16.91 - 33.81: 283 33.81 - 50.72: 38 50.72 - 67.63: 12 67.63 - 84.53: 6 Dihedral angle restraints: 3040 sinusoidal: 1181 harmonic: 1859 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -153.03 67.03 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CA THR B 114 " pdb=" C THR B 114 " pdb=" N LEU B 115 " pdb=" CA LEU B 115 " ideal model delta harmonic sigma weight residual -180.00 -147.39 -32.61 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA ASN B 31 " pdb=" C ASN B 31 " pdb=" N PHE B 32 " pdb=" CA PHE B 32 " ideal model delta harmonic sigma weight residual -180.00 -148.73 -31.27 0 5.00e+00 4.00e-02 3.91e+01 ... (remaining 3037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 628 0.066 - 0.131: 111 0.131 - 0.197: 6 0.197 - 0.263: 1 0.263 - 0.329: 1 Chirality restraints: 747 Sorted by residual: chirality pdb=" CG LEU B 115 " pdb=" CB LEU B 115 " pdb=" CD1 LEU B 115 " pdb=" CD2 LEU B 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CB THR A 430 " pdb=" CA THR A 430 " pdb=" OG1 THR A 430 " pdb=" CG2 THR A 430 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" CB VAL H 48 " pdb=" CA VAL H 48 " pdb=" CG1 VAL H 48 " pdb=" CG2 VAL H 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 744 not shown) Planarity restraints: 906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 110 " -0.019 2.00e-02 2.50e+03 1.76e-02 7.74e+00 pdb=" CG TRP B 110 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 110 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 110 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 110 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 110 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 110 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 110 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 110 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 110 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 106 " -0.028 2.00e-02 2.50e+03 1.66e-02 6.86e+00 pdb=" CG TRP B 106 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 106 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP B 106 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 106 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 106 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 106 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 106 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 106 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 106 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 29 " 0.039 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO B 30 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.033 5.00e-02 4.00e+02 ... (remaining 903 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 241 2.71 - 3.26: 5068 3.26 - 3.80: 7726 3.80 - 4.35: 9597 4.35 - 4.90: 16730 Nonbonded interactions: 39362 Sorted by model distance: nonbonded pdb=" NE2 GLN L 6 " pdb=" O TYR L 86 " model vdw 2.161 3.120 nonbonded pdb=" OG SER C 26 " pdb=" OE1 GLN C 27 " model vdw 2.194 3.040 nonbonded pdb=" NH1 ARG H 38 " pdb=" OE2 GLU H 46 " model vdw 2.199 3.120 nonbonded pdb=" OG SER A 359 " pdb=" OD1 ASN A 394 " model vdw 2.200 3.040 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.208 3.040 ... (remaining 39357 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: 5.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.340 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5216 Z= 0.222 Angle : 0.809 12.490 7089 Z= 0.432 Chirality : 0.050 0.329 747 Planarity : 0.005 0.060 906 Dihedral : 13.838 84.534 1845 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.85 % Favored : 87.15 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.29), residues: 638 helix: -4.24 (0.41), residues: 32 sheet: -1.61 (0.35), residues: 227 loop : -2.87 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 18 TYR 0.037 0.002 TYR L 91 PHE 0.019 0.001 PHE H 11 TRP 0.046 0.003 TRP B 110 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 5209) covalent geometry : angle 0.80667 ( 7075) SS BOND : bond 0.00451 ( 7) SS BOND : angle 1.50214 ( 14) hydrogen bonds : bond 0.28291 ( 129) hydrogen bonds : angle 11.18532 ( 303) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8657 (p0) cc_final: 0.8262 (p0) REVERT: C 18 ARG cc_start: 0.7110 (ttp80) cc_final: 0.6855 (ttp80) REVERT: C 42 GLN cc_start: 0.7144 (pp30) cc_final: 0.6941 (pp30) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0857 time to fit residues: 12.2983 Evaluate side-chains 96 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.100517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.080452 restraints weight = 13496.652| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.22 r_work: 0.3236 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5216 Z= 0.146 Angle : 0.715 9.660 7089 Z= 0.380 Chirality : 0.047 0.143 747 Planarity : 0.005 0.053 906 Dihedral : 6.279 31.398 712 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.91 % Allowed : 9.64 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.30), residues: 638 helix: -3.91 (0.48), residues: 32 sheet: -0.83 (0.36), residues: 217 loop : -2.78 (0.26), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 107 TYR 0.020 0.001 TYR L 91 PHE 0.016 0.001 PHE A 486 TRP 0.021 0.002 TRP B 106 HIS 0.001 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5209) covalent geometry : angle 0.71386 ( 7075) SS BOND : bond 0.00357 ( 7) SS BOND : angle 1.08514 ( 14) hydrogen bonds : bond 0.04060 ( 129) hydrogen bonds : angle 7.06414 ( 303) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8926 (p0) cc_final: 0.8557 (p0) REVERT: B 3 GLN cc_start: 0.8338 (pp30) cc_final: 0.7790 (pp30) REVERT: B 83 TRP cc_start: 0.7997 (p90) cc_final: 0.7741 (p90) REVERT: C 18 ARG cc_start: 0.7163 (ttp80) cc_final: 0.6822 (ttp80) REVERT: H 3 GLN cc_start: 0.8556 (pm20) cc_final: 0.8151 (pp30) REVERT: H 116 TYR cc_start: 0.8754 (p90) cc_final: 0.8386 (p90) outliers start: 5 outliers final: 3 residues processed: 119 average time/residue: 0.0916 time to fit residues: 13.4622 Evaluate side-chains 106 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 110 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 34 optimal weight: 0.0030 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** 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 = 0.3754 r_free = 0.3754 target = 0.101185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081179 restraints weight = 13374.411| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.21 r_work: 0.3245 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5216 Z= 0.139 Angle : 0.693 9.605 7089 Z= 0.362 Chirality : 0.046 0.187 747 Planarity : 0.005 0.048 906 Dihedral : 5.949 28.882 712 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 1.45 % Allowed : 11.64 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.30), residues: 638 helix: -3.86 (0.52), residues: 32 sheet: -0.83 (0.35), residues: 231 loop : -2.74 (0.26), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 107 TYR 0.019 0.001 TYR A 369 PHE 0.010 0.001 PHE A 486 TRP 0.014 0.001 TRP B 106 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5209) covalent geometry : angle 0.69251 ( 7075) SS BOND : bond 0.00317 ( 7) SS BOND : angle 0.90455 ( 14) hydrogen bonds : bond 0.03527 ( 129) hydrogen bonds : angle 6.31567 ( 303) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8962 (p0) cc_final: 0.8590 (p0) REVERT: A 442 ASP cc_start: 0.8540 (m-30) cc_final: 0.8267 (m-30) REVERT: B 3 GLN cc_start: 0.8377 (pp30) cc_final: 0.7920 (pp30) REVERT: B 83 TRP cc_start: 0.7997 (p90) cc_final: 0.7706 (p90) REVERT: C 18 ARG cc_start: 0.7095 (ttp80) cc_final: 0.6764 (ttp80) REVERT: L 91 TYR cc_start: 0.6650 (t80) cc_final: 0.6238 (t80) outliers start: 8 outliers final: 6 residues processed: 123 average time/residue: 0.0892 time to fit residues: 13.5506 Evaluate side-chains 113 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 43 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 57 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.101127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.080970 restraints weight = 13486.090| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.25 r_work: 0.3240 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5216 Z= 0.145 Angle : 0.694 10.252 7089 Z= 0.360 Chirality : 0.045 0.188 747 Planarity : 0.005 0.045 906 Dihedral : 5.794 28.129 712 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.00 % Allowed : 14.18 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.30), residues: 638 helix: -3.88 (0.64), residues: 26 sheet: -0.73 (0.35), residues: 231 loop : -2.55 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.019 0.001 TYR L 91 PHE 0.009 0.001 PHE L 71 TRP 0.009 0.001 TRP B 106 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5209) covalent geometry : angle 0.69317 ( 7075) SS BOND : bond 0.00344 ( 7) SS BOND : angle 0.95303 ( 14) hydrogen bonds : bond 0.03226 ( 129) hydrogen bonds : angle 6.01577 ( 303) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8912 (p0) cc_final: 0.8525 (p0) REVERT: A 442 ASP cc_start: 0.8510 (m-30) cc_final: 0.8210 (m-30) REVERT: B 3 GLN cc_start: 0.8400 (pp30) cc_final: 0.7991 (pp30) REVERT: B 83 TRP cc_start: 0.8103 (p90) cc_final: 0.7475 (p90) REVERT: C 18 ARG cc_start: 0.7091 (ttp80) cc_final: 0.6759 (ttp80) REVERT: L 91 TYR cc_start: 0.6696 (t80) cc_final: 0.6271 (t80) REVERT: L 103 LYS cc_start: 0.8238 (pptt) cc_final: 0.7994 (pptt) outliers start: 11 outliers final: 7 residues processed: 124 average time/residue: 0.0867 time to fit residues: 13.4556 Evaluate side-chains 112 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 43 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 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 = 0.3727 r_free = 0.3727 target = 0.099586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.078954 restraints weight = 13719.944| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.29 r_work: 0.3193 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5216 Z= 0.203 Angle : 0.741 10.998 7089 Z= 0.387 Chirality : 0.046 0.189 747 Planarity : 0.005 0.045 906 Dihedral : 6.012 30.228 712 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.91 % Favored : 88.09 % Rotamer: Outliers : 2.55 % Allowed : 16.55 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.30), residues: 638 helix: -3.75 (0.69), residues: 26 sheet: -0.82 (0.34), residues: 237 loop : -2.56 (0.27), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.020 0.002 TYR L 91 PHE 0.014 0.001 PHE L 71 TRP 0.011 0.002 TRP H 47 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 5209) covalent geometry : angle 0.74006 ( 7075) SS BOND : bond 0.00389 ( 7) SS BOND : angle 1.15388 ( 14) hydrogen bonds : bond 0.03449 ( 129) hydrogen bonds : angle 6.09940 ( 303) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8926 (p0) cc_final: 0.8558 (p0) REVERT: A 442 ASP cc_start: 0.8541 (m-30) cc_final: 0.8233 (m-30) REVERT: B 3 GLN cc_start: 0.8442 (pp30) cc_final: 0.8049 (pp30) REVERT: B 83 TRP cc_start: 0.8139 (p90) cc_final: 0.7547 (p90) REVERT: C 18 ARG cc_start: 0.7051 (ttp80) cc_final: 0.6738 (ttp80) REVERT: L 103 LYS cc_start: 0.8417 (pptt) cc_final: 0.8117 (pptt) outliers start: 14 outliers final: 10 residues processed: 113 average time/residue: 0.0937 time to fit residues: 13.1425 Evaluate side-chains 112 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 83 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 0.0040 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.101372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081095 restraints weight = 13718.178| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.29 r_work: 0.3241 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5216 Z= 0.139 Angle : 0.706 11.125 7089 Z= 0.365 Chirality : 0.045 0.163 747 Planarity : 0.005 0.045 906 Dihedral : 5.723 26.895 712 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 1.64 % Allowed : 18.55 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.31), residues: 638 helix: -3.53 (0.74), residues: 26 sheet: -0.68 (0.35), residues: 230 loop : -2.46 (0.27), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.018 0.001 TYR L 91 PHE 0.009 0.001 PHE A 486 TRP 0.010 0.001 TRP B 33 HIS 0.003 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5209) covalent geometry : angle 0.70532 ( 7075) SS BOND : bond 0.00336 ( 7) SS BOND : angle 0.89287 ( 14) hydrogen bonds : bond 0.02977 ( 129) hydrogen bonds : angle 5.71197 ( 303) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8906 (p0) cc_final: 0.8557 (p0) REVERT: A 442 ASP cc_start: 0.8463 (m-30) cc_final: 0.8164 (m-30) REVERT: B 3 GLN cc_start: 0.8430 (pp30) cc_final: 0.8046 (pp30) REVERT: B 83 TRP cc_start: 0.8028 (p90) cc_final: 0.7389 (p90) REVERT: C 18 ARG cc_start: 0.7028 (ttp80) cc_final: 0.6741 (ttp80) REVERT: H 75 ASP cc_start: 0.8605 (t0) cc_final: 0.8383 (t0) REVERT: H 78 LYS cc_start: 0.8947 (ptpp) cc_final: 0.8744 (pttm) REVERT: L 103 LYS cc_start: 0.8383 (pptt) cc_final: 0.8066 (pptt) outliers start: 9 outliers final: 8 residues processed: 115 average time/residue: 0.0839 time to fit residues: 11.9645 Evaluate side-chains 114 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 8 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.098652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.080563 restraints weight = 13592.945| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.79 r_work: 0.3135 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 5216 Z= 0.250 Angle : 0.781 11.959 7089 Z= 0.409 Chirality : 0.047 0.151 747 Planarity : 0.005 0.045 906 Dihedral : 6.196 31.123 712 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 3.27 % Allowed : 18.73 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.30), residues: 638 helix: -3.36 (0.79), residues: 26 sheet: -0.72 (0.34), residues: 228 loop : -2.53 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 19 TYR 0.020 0.002 TYR C 91 PHE 0.016 0.001 PHE L 71 TRP 0.015 0.002 TRP H 47 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00584 ( 5209) covalent geometry : angle 0.77947 ( 7075) SS BOND : bond 0.00417 ( 7) SS BOND : angle 1.27288 ( 14) hydrogen bonds : bond 0.03635 ( 129) hydrogen bonds : angle 6.22389 ( 303) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8914 (p0) cc_final: 0.8582 (p0) REVERT: A 442 ASP cc_start: 0.8578 (m-30) cc_final: 0.8287 (m-30) REVERT: B 3 GLN cc_start: 0.8582 (pp30) cc_final: 0.8222 (pp30) REVERT: B 70 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8509 (pp) REVERT: B 83 TRP cc_start: 0.8011 (p90) cc_final: 0.7522 (p90) REVERT: H 78 LYS cc_start: 0.8993 (ptpp) cc_final: 0.8745 (ptpt) REVERT: L 103 LYS cc_start: 0.8492 (pptt) cc_final: 0.8173 (pptt) outliers start: 18 outliers final: 13 residues processed: 112 average time/residue: 0.0834 time to fit residues: 11.6782 Evaluate side-chains 115 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 0.0870 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.0050 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.102036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.081901 restraints weight = 13447.705| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.25 r_work: 0.3272 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5216 Z= 0.130 Angle : 0.710 11.414 7089 Z= 0.369 Chirality : 0.045 0.140 747 Planarity : 0.005 0.046 906 Dihedral : 5.606 27.185 712 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 2.55 % Allowed : 19.45 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.31), residues: 638 helix: -2.72 (0.99), residues: 20 sheet: -0.70 (0.35), residues: 229 loop : -2.38 (0.27), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 18 TYR 0.017 0.001 TYR A 369 PHE 0.008 0.001 PHE B 64 TRP 0.013 0.001 TRP B 33 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 5209) covalent geometry : angle 0.71007 ( 7075) SS BOND : bond 0.00281 ( 7) SS BOND : angle 0.69982 ( 14) hydrogen bonds : bond 0.02793 ( 129) hydrogen bonds : angle 5.52664 ( 303) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8797 (p0) cc_final: 0.8503 (p0) REVERT: A 442 ASP cc_start: 0.8451 (m-30) cc_final: 0.8153 (m-30) REVERT: B 3 GLN cc_start: 0.8461 (pp30) cc_final: 0.8121 (pp30) REVERT: B 70 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8384 (pp) REVERT: B 83 TRP cc_start: 0.8030 (p90) cc_final: 0.7393 (p90) REVERT: H 78 LYS cc_start: 0.8898 (ptpp) cc_final: 0.8681 (ptpt) REVERT: L 103 LYS cc_start: 0.8384 (pptt) cc_final: 0.8063 (pptt) outliers start: 14 outliers final: 12 residues processed: 115 average time/residue: 0.0873 time to fit residues: 12.4207 Evaluate side-chains 116 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 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 = 0.3763 r_free = 0.3763 target = 0.101633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.080976 restraints weight = 13492.857| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.37 r_work: 0.3238 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5216 Z= 0.143 Angle : 0.723 11.605 7089 Z= 0.376 Chirality : 0.045 0.136 747 Planarity : 0.005 0.046 906 Dihedral : 5.591 26.294 712 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 2.55 % Allowed : 19.82 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.31), residues: 638 helix: -2.59 (0.99), residues: 20 sheet: -0.67 (0.35), residues: 229 loop : -2.34 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 18 TYR 0.018 0.001 TYR A 369 PHE 0.008 0.001 PHE A 486 TRP 0.009 0.001 TRP B 33 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5209) covalent geometry : angle 0.72306 ( 7075) SS BOND : bond 0.00307 ( 7) SS BOND : angle 0.83001 ( 14) hydrogen bonds : bond 0.02866 ( 129) hydrogen bonds : angle 5.52764 ( 303) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8826 (p0) cc_final: 0.8553 (p0) REVERT: A 442 ASP cc_start: 0.8510 (m-30) cc_final: 0.8158 (m-30) REVERT: B 70 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8487 (pp) REVERT: B 83 TRP cc_start: 0.8055 (p90) cc_final: 0.7363 (p90) REVERT: H 78 LYS cc_start: 0.8921 (ptpp) cc_final: 0.8698 (ptpt) REVERT: L 103 LYS cc_start: 0.8390 (pptt) cc_final: 0.8029 (pptt) outliers start: 14 outliers final: 11 residues processed: 120 average time/residue: 0.0907 time to fit residues: 13.3715 Evaluate side-chains 115 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** 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 = 0.3760 r_free = 0.3760 target = 0.101474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081321 restraints weight = 13560.913| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.25 r_work: 0.3249 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5216 Z= 0.150 Angle : 0.756 12.026 7089 Z= 0.392 Chirality : 0.045 0.139 747 Planarity : 0.005 0.046 906 Dihedral : 5.602 26.417 712 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.36 % Allowed : 19.82 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.31), residues: 638 helix: -2.48 (1.02), residues: 20 sheet: -0.65 (0.35), residues: 229 loop : -2.31 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 19 TYR 0.017 0.001 TYR A 369 PHE 0.009 0.001 PHE A 486 TRP 0.009 0.001 TRP B 33 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 5209) covalent geometry : angle 0.75589 ( 7075) SS BOND : bond 0.00303 ( 7) SS BOND : angle 0.85306 ( 14) hydrogen bonds : bond 0.02821 ( 129) hydrogen bonds : angle 5.49188 ( 303) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8768 (p0) cc_final: 0.8505 (p0) REVERT: A 442 ASP cc_start: 0.8394 (m-30) cc_final: 0.8080 (m-30) REVERT: B 3 GLN cc_start: 0.8873 (pm20) cc_final: 0.8614 (pt0) REVERT: B 70 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8468 (pp) REVERT: B 83 TRP cc_start: 0.7934 (p90) cc_final: 0.7303 (p90) REVERT: L 81 GLU cc_start: 0.8282 (pm20) cc_final: 0.7656 (pm20) REVERT: L 103 LYS cc_start: 0.8361 (pptt) cc_final: 0.8043 (pptt) outliers start: 13 outliers final: 12 residues processed: 114 average time/residue: 0.0855 time to fit residues: 12.0692 Evaluate side-chains 117 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.0060 chunk 15 optimal weight: 0.2980 chunk 30 optimal weight: 0.0970 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.100464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.078575 restraints weight = 13650.852| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.54 r_work: 0.3146 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5216 Z= 0.129 Angle : 0.727 8.192 7089 Z= 0.378 Chirality : 0.044 0.137 747 Planarity : 0.005 0.046 906 Dihedral : 5.342 27.140 712 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 2.36 % Allowed : 20.18 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.31), residues: 638 helix: -2.67 (0.96), residues: 20 sheet: -0.52 (0.36), residues: 220 loop : -2.28 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 18 TYR 0.017 0.001 TYR H 116 PHE 0.008 0.001 PHE B 64 TRP 0.012 0.001 TRP B 33 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5209) covalent geometry : angle 0.72710 ( 7075) SS BOND : bond 0.00251 ( 7) SS BOND : angle 0.65829 ( 14) hydrogen bonds : bond 0.02537 ( 129) hydrogen bonds : angle 5.21944 ( 303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1356.48 seconds wall clock time: 23 minutes 57.20 seconds (1437.20 seconds total)