Starting phenix.real_space_refine on Thu Jul 24 03:01:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ey5_31378/07_2025/7ey5_31378_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ey5_31378/07_2025/7ey5_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_31378/07_2025/7ey5_31378.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ey5_31378/07_2025/7ey5_31378.map" model { file = "/net/cci-nas-00/data/ceres_data/7ey5_31378/07_2025/7ey5_31378_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ey5_31378/07_2025/7ey5_31378_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.39, per 1000 atoms: 1.65 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: 2.01 Conformation dependent library (CDL) restraints added in 721.3 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: 1.04 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: 1.96 Time building geometry restraints manager: 2.34 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: 7.260 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.090 Process input model: 26.840 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.410 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.046 0.003 TRP B 110 HIS 0.002 0.001 HIS B 82 PHE 0.019 0.001 PHE H 11 TYR 0.037 0.002 TYR L 91 ARG 0.012 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.28291 ( 129) hydrogen bonds : angle 11.18532 ( 303) SS BOND : bond 0.00451 ( 7) SS BOND : angle 1.50214 ( 14) covalent geometry : bond 0.00508 ( 5209) covalent geometry : angle 0.80667 ( 7075) *********************** 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 : 1.445 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8657 (p0) cc_final: 0.8263 (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: 0.6942 (pp30) REVERT: H 116 TYR cc_start: 0.8166 (p90) cc_final: 0.7934 (p90) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2214 time to fit residues: 31.8708 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 : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 0.0570 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.102199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.082467 restraints weight = 13478.158| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.22 r_work: 0.3266 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1642 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= 0.125 Angle : 0.693 8.954 7089 Z= 0.368 Chirality : 0.047 0.144 747 Planarity : 0.005 0.050 906 Dihedral : 6.086 29.012 712 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.36 % Allowed : 9.82 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.30), residues: 638 helix: -3.85 (0.50), residues: 32 sheet: -0.80 (0.36), residues: 222 loop : -2.76 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 106 HIS 0.001 0.001 HIS B 82 PHE 0.010 0.001 PHE B 64 TYR 0.021 0.001 TYR L 91 ARG 0.004 0.000 ARG H 107 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 129) hydrogen bonds : angle 6.85580 ( 303) SS BOND : bond 0.00300 ( 7) SS BOND : angle 0.93527 ( 14) covalent geometry : bond 0.00282 ( 5209) covalent geometry : angle 0.69245 ( 7075) *********************** 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 125 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8929 (p0) cc_final: 0.8563 (p0) REVERT: B 3 GLN cc_start: 0.8333 (pp30) cc_final: 0.7781 (pp30) REVERT: B 83 TRP cc_start: 0.7989 (p90) cc_final: 0.7755 (p90) REVERT: C 18 ARG cc_start: 0.7171 (ttp80) cc_final: 0.6824 (ttp80) REVERT: H 3 GLN cc_start: 0.8538 (pm20) cc_final: 0.8139 (pp30) outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.2670 time to fit residues: 40.3165 Evaluate side-chains 109 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 3 optimal weight: 0.0570 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.4502 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.099257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.078714 restraints weight = 13467.068| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.23 r_work: 0.3194 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5216 Z= 0.210 Angle : 0.738 9.320 7089 Z= 0.388 Chirality : 0.047 0.191 747 Planarity : 0.005 0.047 906 Dihedral : 6.248 32.008 712 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.91 % Favored : 88.09 % Rotamer: Outliers : 1.82 % Allowed : 12.91 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.30), residues: 638 helix: -3.70 (0.56), residues: 32 sheet: -0.85 (0.36), residues: 223 loop : -2.78 (0.26), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 106 HIS 0.001 0.001 HIS B 82 PHE 0.015 0.001 PHE L 71 TYR 0.016 0.002 TYR L 91 ARG 0.008 0.001 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 129) hydrogen bonds : angle 6.64520 ( 303) SS BOND : bond 0.00400 ( 7) SS BOND : angle 1.23268 ( 14) covalent geometry : bond 0.00492 ( 5209) covalent geometry : angle 0.73655 ( 7075) *********************** 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 121 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8938 (p0) cc_final: 0.8562 (p0) REVERT: A 442 ASP cc_start: 0.8599 (m-30) cc_final: 0.8336 (m-30) REVERT: B 3 GLN cc_start: 0.8403 (pp30) cc_final: 0.7943 (pp30) REVERT: B 83 TRP cc_start: 0.8017 (p90) cc_final: 0.7710 (p90) REVERT: C 18 ARG cc_start: 0.7162 (ttp80) cc_final: 0.6812 (ttp80) REVERT: H 116 TYR cc_start: 0.8918 (p90) cc_final: 0.8571 (p90) REVERT: L 103 LYS cc_start: 0.8267 (pptt) cc_final: 0.8037 (pptt) outliers start: 10 outliers final: 5 residues processed: 116 average time/residue: 0.3339 time to fit residues: 48.0070 Evaluate side-chains 104 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain H residue 31 ASP 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 35 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.099826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.079383 restraints weight = 13661.095| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.25 r_work: 0.3205 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5216 Z= 0.180 Angle : 0.727 11.411 7089 Z= 0.380 Chirality : 0.046 0.197 747 Planarity : 0.005 0.047 906 Dihedral : 6.084 29.489 712 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 2.00 % Allowed : 16.00 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.30), residues: 638 helix: -3.67 (0.70), residues: 26 sheet: -0.76 (0.36), residues: 223 loop : -2.61 (0.27), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 106 HIS 0.002 0.001 HIS B 82 PHE 0.012 0.001 PHE L 71 TYR 0.017 0.001 TYR L 91 ARG 0.006 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 129) hydrogen bonds : angle 6.23177 ( 303) SS BOND : bond 0.00379 ( 7) SS BOND : angle 1.06524 ( 14) covalent geometry : bond 0.00419 ( 5209) covalent geometry : angle 0.72597 ( 7075) *********************** 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 118 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8952 (p0) cc_final: 0.8591 (p0) REVERT: A 442 ASP cc_start: 0.8552 (m-30) cc_final: 0.8241 (m-30) REVERT: B 3 GLN cc_start: 0.8425 (pp30) cc_final: 0.7998 (pp30) REVERT: B 83 TRP cc_start: 0.8052 (p90) cc_final: 0.7586 (p90) REVERT: C 18 ARG cc_start: 0.7119 (ttp80) cc_final: 0.6790 (ttp80) REVERT: H 78 LYS cc_start: 0.8945 (ptpp) cc_final: 0.8702 (ptpp) REVERT: L 103 LYS cc_start: 0.8354 (pptt) cc_final: 0.8075 (pptt) outliers start: 11 outliers final: 9 residues processed: 112 average time/residue: 0.3221 time to fit residues: 45.0945 Evaluate side-chains 111 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 55 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 10 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 88 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.098864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.081171 restraints weight = 13399.056| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.67 r_work: 0.3143 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2063 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= 0.227 Angle : 0.763 12.708 7089 Z= 0.398 Chirality : 0.047 0.166 747 Planarity : 0.005 0.047 906 Dihedral : 6.283 32.544 712 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.23 % Favored : 87.77 % Rotamer: Outliers : 2.91 % Allowed : 16.55 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.30), residues: 638 helix: -3.62 (0.73), residues: 26 sheet: -0.83 (0.35), residues: 229 loop : -2.61 (0.27), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.002 0.001 HIS B 82 PHE 0.016 0.001 PHE L 71 TYR 0.020 0.002 TYR L 91 ARG 0.005 0.001 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 129) hydrogen bonds : angle 6.27140 ( 303) SS BOND : bond 0.00401 ( 7) SS BOND : angle 1.19781 ( 14) covalent geometry : bond 0.00528 ( 5209) covalent geometry : angle 0.76183 ( 7075) *********************** 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 121 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8962 (p0) cc_final: 0.8607 (p0) REVERT: A 442 ASP cc_start: 0.8615 (m-30) cc_final: 0.8307 (m-30) REVERT: B 3 GLN cc_start: 0.8450 (pp30) cc_final: 0.8057 (pp30) REVERT: B 83 TRP cc_start: 0.7940 (p90) cc_final: 0.7607 (p90) REVERT: C 18 ARG cc_start: 0.7122 (ttp80) cc_final: 0.6786 (ttp80) REVERT: L 103 LYS cc_start: 0.8470 (pptt) cc_final: 0.8142 (pptt) outliers start: 16 outliers final: 12 residues processed: 112 average time/residue: 0.2380 time to fit residues: 33.1070 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 : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 55 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 10 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.100677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.082655 restraints weight = 13450.481| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.64 r_work: 0.3193 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5216 Z= 0.157 Angle : 0.731 11.541 7089 Z= 0.380 Chirality : 0.046 0.178 747 Planarity : 0.005 0.047 906 Dihedral : 5.916 27.737 712 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.36 % Allowed : 18.36 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.31), residues: 638 helix: -3.42 (0.78), residues: 26 sheet: -0.83 (0.34), residues: 231 loop : -2.55 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 33 HIS 0.002 0.001 HIS B 82 PHE 0.009 0.001 PHE L 71 TYR 0.018 0.001 TYR L 91 ARG 0.004 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 129) hydrogen bonds : angle 5.88989 ( 303) SS BOND : bond 0.00339 ( 7) SS BOND : angle 0.91111 ( 14) covalent geometry : bond 0.00367 ( 5209) covalent geometry : angle 0.73098 ( 7075) *********************** 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 125 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8957 (p0) cc_final: 0.8614 (p0) REVERT: A 442 ASP cc_start: 0.8528 (m-30) cc_final: 0.8230 (m-30) REVERT: B 3 GLN cc_start: 0.8505 (pp30) cc_final: 0.8097 (pp30) REVERT: B 83 TRP cc_start: 0.8006 (p90) cc_final: 0.7531 (p90) REVERT: C 18 ARG cc_start: 0.7117 (ttp80) cc_final: 0.6842 (ttp80) REVERT: L 103 LYS cc_start: 0.8411 (pptt) cc_final: 0.8060 (pptt) outliers start: 13 outliers final: 11 residues processed: 119 average time/residue: 0.2491 time to fit residues: 36.5616 Evaluate side-chains 116 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 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 10 THR Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 19 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.100139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079478 restraints weight = 13416.923| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.31 r_work: 0.3205 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5216 Z= 0.166 Angle : 0.742 10.823 7089 Z= 0.386 Chirality : 0.046 0.158 747 Planarity : 0.005 0.047 906 Dihedral : 5.909 28.654 712 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.31), residues: 638 helix: -3.43 (0.78), residues: 26 sheet: -0.81 (0.34), residues: 231 loop : -2.52 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 33 HIS 0.002 0.001 HIS B 82 PHE 0.010 0.001 PHE L 71 TYR 0.016 0.001 TYR H 116 ARG 0.004 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03171 ( 129) hydrogen bonds : angle 5.83938 ( 303) SS BOND : bond 0.00336 ( 7) SS BOND : angle 0.94578 ( 14) covalent geometry : bond 0.00392 ( 5209) covalent geometry : angle 0.74107 ( 7075) *********************** 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 121 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8961 (p0) cc_final: 0.8642 (p0) REVERT: A 442 ASP cc_start: 0.8554 (m-30) cc_final: 0.8201 (m-30) REVERT: B 3 GLN cc_start: 0.8522 (pp30) cc_final: 0.8157 (pp30) REVERT: B 83 TRP cc_start: 0.8130 (p90) cc_final: 0.7428 (p90) REVERT: C 18 ARG cc_start: 0.7006 (ttp80) cc_final: 0.6709 (ttp80) REVERT: L 103 LYS cc_start: 0.8459 (pptt) cc_final: 0.8079 (pptt) outliers start: 14 outliers final: 13 residues processed: 116 average time/residue: 0.2511 time to fit residues: 36.1423 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 : 0.720 ------------------------------------------------------------------------------- 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 67 GLN 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 53 THR Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 19 VAL 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 9 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.100080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.081910 restraints weight = 13386.920| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.63 r_work: 0.3171 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5216 Z= 0.174 Angle : 0.742 9.390 7089 Z= 0.387 Chirality : 0.045 0.141 747 Planarity : 0.005 0.047 906 Dihedral : 5.886 27.623 712 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 2.91 % Allowed : 19.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.31), residues: 638 helix: -3.40 (0.79), residues: 26 sheet: -0.73 (0.35), residues: 226 loop : -2.52 (0.27), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS B 82 PHE 0.010 0.001 PHE A 486 TYR 0.012 0.001 TYR C 91 ARG 0.004 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 129) hydrogen bonds : angle 5.82511 ( 303) SS BOND : bond 0.00352 ( 7) SS BOND : angle 0.99725 ( 14) covalent geometry : bond 0.00409 ( 5209) covalent geometry : angle 0.74148 ( 7075) *********************** 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: 16 poor density : 105 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8900 (p0) cc_final: 0.8577 (p0) REVERT: A 442 ASP cc_start: 0.8517 (m-30) cc_final: 0.8235 (m-30) REVERT: B 83 TRP cc_start: 0.8058 (p90) cc_final: 0.7411 (p90) REVERT: C 18 ARG cc_start: 0.7074 (ttp80) cc_final: 0.6815 (ttp80) REVERT: H 75 ASP cc_start: 0.8673 (t0) cc_final: 0.8391 (t0) REVERT: L 103 LYS cc_start: 0.8449 (pptt) cc_final: 0.8105 (pptt) outliers start: 16 outliers final: 13 residues processed: 116 average time/residue: 0.2638 time to fit residues: 38.3364 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 : 0.645 ------------------------------------------------------------------------------- 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 67 GLN 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 53 THR Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain L residue 19 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 0.0270 chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.6440 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.101329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.080776 restraints weight = 13362.498| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.33 r_work: 0.3232 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5216 Z= 0.141 Angle : 0.744 8.565 7089 Z= 0.388 Chirality : 0.045 0.144 747 Planarity : 0.005 0.047 906 Dihedral : 5.749 28.333 712 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 2.18 % Allowed : 20.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.31), residues: 638 helix: -3.08 (0.92), residues: 20 sheet: -0.71 (0.35), residues: 224 loop : -2.33 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 33 HIS 0.002 0.001 HIS B 82 PHE 0.009 0.001 PHE B 64 TYR 0.017 0.001 TYR H 116 ARG 0.004 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02910 ( 129) hydrogen bonds : angle 5.64070 ( 303) SS BOND : bond 0.00304 ( 7) SS BOND : angle 0.80866 ( 14) covalent geometry : bond 0.00334 ( 5209) covalent geometry : angle 0.74407 ( 7075) *********************** 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 119 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8878 (p0) cc_final: 0.8651 (p0) REVERT: A 442 ASP cc_start: 0.8538 (m-30) cc_final: 0.8175 (m-30) REVERT: B 67 GLN cc_start: 0.6821 (mt0) cc_final: 0.6593 (pt0) REVERT: B 83 TRP cc_start: 0.8072 (p90) cc_final: 0.7381 (p90) REVERT: C 18 ARG cc_start: 0.7021 (ttp80) cc_final: 0.6773 (ttp80) REVERT: H 75 ASP cc_start: 0.8509 (t0) cc_final: 0.8110 (t0) REVERT: H 78 LYS cc_start: 0.8891 (pttm) cc_final: 0.8621 (pttm) outliers start: 12 outliers final: 11 residues processed: 116 average time/residue: 0.3860 time to fit residues: 55.9709 Evaluate side-chains 117 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 80 LEU Chi-restraints excluded: chain B residue 110 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 31 ASP 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 12 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.100346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.079499 restraints weight = 13435.984| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.37 r_work: 0.3201 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2643 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= 0.177 Angle : 0.757 12.137 7089 Z= 0.391 Chirality : 0.045 0.140 747 Planarity : 0.005 0.047 906 Dihedral : 5.800 27.698 712 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 2.73 % Allowed : 20.18 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.31), residues: 638 helix: -3.00 (0.92), residues: 20 sheet: -0.64 (0.35), residues: 228 loop : -2.40 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS B 82 PHE 0.009 0.001 PHE B 64 TYR 0.012 0.001 TYR C 91 ARG 0.004 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 129) hydrogen bonds : angle 5.79466 ( 303) SS BOND : bond 0.00344 ( 7) SS BOND : angle 1.04884 ( 14) covalent geometry : bond 0.00419 ( 5209) covalent geometry : angle 0.75586 ( 7075) ********************** 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: 15 poor density : 104 time to evaluate : 1.609 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.8880 (p0) cc_final: 0.8595 (p0) REVERT: A 442 ASP cc_start: 0.8543 (m-30) cc_final: 0.8194 (m-30) REVERT: B 83 TRP cc_start: 0.8084 (p90) cc_final: 0.7386 (p90) REVERT: C 18 ARG cc_start: 0.6968 (ttp80) cc_final: 0.6679 (ttp80) REVERT: H 78 LYS cc_start: 0.8917 (pttm) cc_final: 0.8684 (pttm) outliers start: 15 outliers final: 14 residues processed: 115 average time/residue: 0.4361 time to fit residues: 63.5650 Evaluate side-chains 117 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 67 GLN 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 53 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain H residue 4 LEU 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 54 optimal weight: 0.0370 chunk 44 optimal weight: 0.1980 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 18 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.099142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.077383 restraints weight = 13589.808| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.51 r_work: 0.3131 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5216 Z= 0.135 Angle : 0.747 8.664 7089 Z= 0.389 Chirality : 0.045 0.138 747 Planarity : 0.005 0.048 906 Dihedral : 5.564 26.837 712 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.00 % Allowed : 20.91 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.31), residues: 638 helix: -2.99 (0.90), residues: 20 sheet: -0.64 (0.36), residues: 229 loop : -2.33 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 33 HIS 0.002 0.001 HIS B 82 PHE 0.009 0.001 PHE B 64 TYR 0.017 0.001 TYR H 116 ARG 0.003 0.000 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02705 ( 129) hydrogen bonds : angle 5.48435 ( 303) SS BOND : bond 0.00259 ( 7) SS BOND : angle 0.74400 ( 14) covalent geometry : bond 0.00318 ( 5209) covalent geometry : angle 0.74701 ( 7075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4625.59 seconds wall clock time: 87 minutes 44.70 seconds (5264.70 seconds total)