Starting phenix.real_space_refine on Fri Aug 22 14:34:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r4r_4727/08_2025/6r4r_4727.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r4r_4727/08_2025/6r4r_4727.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 { model { file = "/net/cci-nas-00/data/ceres_data/6r4r_4727/08_2025/6r4r_4727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r4r_4727/08_2025/6r4r_4727.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6r4r_4727/08_2025/6r4r_4727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r4r_4727/08_2025/6r4r_4727.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.467 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 7 5.16 5 C 2723 2.51 5 N 686 2.21 5 O 896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4312 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 0.56, per 1000 atoms: 0.13 Number of scatterers: 4312 At special positions: 0 Unit cell: (90.695, 115.005, 44.88, 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 7 16.00 O 896 8.00 N 686 7.00 C 2723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 169.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.618A pdb=" N LYS A 16 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLU C 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG A 18 " --> pdb=" O GLU C 19 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS C 16 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU E 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG C 18 " --> pdb=" O GLU E 19 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS E 16 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU G 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG E 18 " --> pdb=" O GLU G 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 25 removed outlier: 6.538A pdb=" N ASP A 23 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP C 23 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP E 23 " --> pdb=" O LEU G 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 37 through 41 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 56 removed outlier: 6.149A pdb=" N GLU A 51 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLY C 54 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE A 53 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU C 56 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TRP A 55 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU C 51 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY E 54 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 53 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU E 56 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N TRP C 55 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU E 51 " --> pdb=" O GLU G 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY G 54 " --> pdb=" O GLU E 51 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE E 53 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU G 56 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TRP E 55 " --> pdb=" O LEU G 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 61 through 68 Processing sheet with id=AA8, first strand: chain 'A' and resid 71 through 76 Processing sheet with id=AA9, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.617A pdb=" N LYS B 16 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU D 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 18 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS D 16 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU F 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG D 18 " --> pdb=" O GLU F 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 23 through 25 removed outlier: 6.538A pdb=" N ASP B 23 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP D 23 " --> pdb=" O LEU F 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 29 through 34 Processing sheet with id=AB4, first strand: chain 'B' and resid 37 through 41 Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.151A pdb=" N GLU B 51 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY D 54 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 53 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU D 56 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N TRP B 55 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU D 51 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY F 54 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 53 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU F 56 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TRP D 55 " --> pdb=" O LEU F 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 61 through 68 Processing sheet with id=AB7, first strand: chain 'B' and resid 71 through 76 110 hydrogen bonds defined for protein. 330 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: 0.51 Time building geometry restraints manager: 0.33 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: 1415 1.34 - 1.45: 707 1.45 - 1.57: 2267 1.57 - 1.69: 0 1.69 - 1.80: 14 Bond restraints: 4403 Sorted by residual: bond pdb=" CG LEU C 30 " pdb=" CD1 LEU C 30 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.98e+00 bond pdb=" CG LEU G 30 " pdb=" CD1 LEU G 30 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.94e+00 bond pdb=" CG LEU E 30 " pdb=" CD1 LEU E 30 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CG LEU A 30 " pdb=" CD1 LEU A 30 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CG LEU D 30 " pdb=" CD1 LEU D 30 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.89e+00 ... (remaining 4398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 5708 3.12 - 6.23: 207 6.23 - 9.35: 7 9.35 - 12.47: 14 12.47 - 15.58: 7 Bond angle restraints: 5943 Sorted by residual: angle pdb=" C GLU C 20 " pdb=" N ASP C 21 " pdb=" CA ASP C 21 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C GLU F 20 " pdb=" N ASP F 21 " pdb=" CA ASP F 21 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C GLU E 20 " pdb=" N ASP E 21 " pdb=" CA ASP E 21 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C GLU G 20 " pdb=" N ASP G 21 " pdb=" CA ASP G 21 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C GLU D 20 " pdb=" N ASP D 21 " pdb=" CA ASP D 21 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 ... (remaining 5938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.72: 1867 7.72 - 15.43: 499 15.43 - 23.15: 119 23.15 - 30.87: 35 30.87 - 38.59: 35 Dihedral angle restraints: 2555 sinusoidal: 1036 harmonic: 1519 Sorted by residual: dihedral pdb=" CA GLY E 5 " pdb=" C GLY E 5 " pdb=" N TYR E 6 " pdb=" CA TYR E 6 " ideal model delta harmonic sigma weight residual -180.00 -159.56 -20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLY G 5 " pdb=" C GLY G 5 " pdb=" N TYR G 6 " pdb=" CA TYR G 6 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLY C 5 " pdb=" C GLY C 5 " pdb=" N TYR C 6 " pdb=" CA TYR C 6 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 2552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 405 0.069 - 0.137: 162 0.137 - 0.206: 21 0.206 - 0.275: 0 0.275 - 0.344: 7 Chirality restraints: 595 Sorted by residual: chirality pdb=" CA ASP F 21 " pdb=" N ASP F 21 " pdb=" C ASP F 21 " pdb=" CB ASP F 21 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ASP D 21 " pdb=" N ASP D 21 " pdb=" C ASP D 21 " pdb=" CB ASP D 21 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ASP A 21 " pdb=" N ASP A 21 " pdb=" C ASP A 21 " pdb=" CB ASP A 21 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 592 not shown) Planarity restraints: 791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 48 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C ALA C 48 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA C 48 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS C 49 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 48 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C ALA E 48 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA E 48 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS E 49 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 48 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C ALA G 48 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA G 48 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS G 49 " -0.018 2.00e-02 2.50e+03 ... (remaining 788 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1211 2.83 - 3.34: 3397 3.34 - 3.86: 7837 3.86 - 4.38: 8251 4.38 - 4.90: 15637 Nonbonded interactions: 36333 Sorted by model distance: nonbonded pdb=" OE2 GLU A 47 " pdb=" NZ LYS A 49 " model vdw 2.308 3.120 nonbonded pdb=" OE2 GLU B 47 " pdb=" NZ LYS B 49 " model vdw 2.309 3.120 nonbonded pdb=" OE2 GLU F 47 " pdb=" NZ LYS F 49 " model vdw 2.310 3.120 nonbonded pdb=" OE2 GLU E 47 " pdb=" NZ LYS E 49 " model vdw 2.310 3.120 nonbonded pdb=" OE2 GLU C 47 " pdb=" NZ LYS C 49 " model vdw 2.310 3.120 ... (remaining 36328 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.140 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 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 : 0.008 0.057 4403 Z= 0.332 Angle : 1.430 15.584 5943 Z= 0.726 Chirality : 0.075 0.344 595 Planarity : 0.008 0.054 791 Dihedral : 10.872 38.585 1617 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.16 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 66 TYR 0.017 0.004 TYR B 8 PHE 0.008 0.003 PHE B 69 TRP 0.008 0.002 TRP B 55 HIS 0.018 0.011 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00758 ( 4403) covalent geometry : angle 1.43040 ( 5943) hydrogen bonds : bond 0.12628 ( 110) hydrogen bonds : angle 8.19636 ( 330) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.158 Fit side-chains REVERT: A 66 ARG cc_start: 0.7176 (ttm110) cc_final: 0.5303 (tpt170) REVERT: B 66 ARG cc_start: 0.7045 (ttm110) cc_final: 0.5719 (tpt170) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.0649 time to fit residues: 16.2262 Evaluate side-chains 116 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS ** E 46 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 = 0.4832 r_free = 0.4832 target = 0.187601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.178032 restraints weight = 8115.132| |-----------------------------------------------------------------------------| r_work (start): 0.4739 rms_B_bonded: 3.18 r_work: 0.4658 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4403 Z= 0.186 Angle : 0.793 10.849 5943 Z= 0.395 Chirality : 0.048 0.199 595 Planarity : 0.005 0.045 791 Dihedral : 6.029 17.066 602 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.17 % Allowed : 11.56 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.88 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 66 TYR 0.024 0.002 TYR E 59 PHE 0.012 0.002 PHE D 69 TRP 0.017 0.002 TRP B 55 HIS 0.004 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 4403) covalent geometry : angle 0.79333 ( 5943) hydrogen bonds : bond 0.03023 ( 110) hydrogen bonds : angle 5.17824 ( 330) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.114 Fit side-chains REVERT: A 51 GLU cc_start: 0.7314 (tt0) cc_final: 0.7037 (tt0) REVERT: A 55 TRP cc_start: 0.6435 (t60) cc_final: 0.5836 (t60) REVERT: A 66 ARG cc_start: 0.7535 (ttm110) cc_final: 0.5083 (tpt170) REVERT: B 63 THR cc_start: 0.8479 (m) cc_final: 0.8219 (t) REVERT: D 8 TYR cc_start: 0.7858 (p90) cc_final: 0.7640 (p90) REVERT: E 44 ASP cc_start: 0.6859 (m-30) cc_final: 0.6594 (m-30) REVERT: E 55 TRP cc_start: 0.8075 (t-100) cc_final: 0.7756 (t-100) REVERT: F 63 THR cc_start: 0.8307 (m) cc_final: 0.7930 (t) REVERT: G 63 THR cc_start: 0.8512 (m) cc_final: 0.8205 (t) outliers start: 14 outliers final: 5 residues processed: 139 average time/residue: 0.0602 time to fit residues: 10.5671 Evaluate side-chains 117 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 77 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 2 optimal weight: 40.0000 chunk 48 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 33 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 = 0.4824 r_free = 0.4824 target = 0.182523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.173827 restraints weight = 8288.028| |-----------------------------------------------------------------------------| r_work (start): 0.4733 rms_B_bonded: 3.02 r_work: 0.4656 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4403 Z= 0.180 Angle : 0.705 10.661 5943 Z= 0.358 Chirality : 0.046 0.141 595 Planarity : 0.005 0.042 791 Dihedral : 5.686 14.898 602 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 2.95 % Allowed : 14.97 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.80 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 66 TYR 0.020 0.002 TYR B 8 PHE 0.010 0.002 PHE A 69 TRP 0.017 0.002 TRP B 55 HIS 0.002 0.000 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 4403) covalent geometry : angle 0.70488 ( 5943) hydrogen bonds : bond 0.02959 ( 110) hydrogen bonds : angle 4.88976 ( 330) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.124 Fit side-chains REVERT: A 11 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8602 (pt) REVERT: A 28 ASP cc_start: 0.5992 (t0) cc_final: 0.5389 (t0) REVERT: B 28 ASP cc_start: 0.5140 (t0) cc_final: 0.4323 (t70) REVERT: B 63 THR cc_start: 0.8414 (m) cc_final: 0.8130 (t) REVERT: D 63 THR cc_start: 0.8585 (m) cc_final: 0.8172 (t) REVERT: D 69 PHE cc_start: 0.8399 (m-80) cc_final: 0.8076 (m-80) REVERT: E 47 GLU cc_start: 0.5841 (tp30) cc_final: 0.5311 (tp30) REVERT: E 51 GLU cc_start: 0.7179 (tt0) cc_final: 0.6848 (tt0) REVERT: E 75 GLU cc_start: 0.8099 (tt0) cc_final: 0.7632 (tt0) REVERT: F 51 GLU cc_start: 0.7113 (tt0) cc_final: 0.6505 (pm20) REVERT: F 63 THR cc_start: 0.8508 (m) cc_final: 0.8266 (t) REVERT: G 66 ARG cc_start: 0.7469 (ttp-110) cc_final: 0.6560 (ttp-170) outliers start: 13 outliers final: 6 residues processed: 127 average time/residue: 0.0562 time to fit residues: 9.3105 Evaluate side-chains 114 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain F residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 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 = 0.4880 r_free = 0.4880 target = 0.210090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.191663 restraints weight = 8422.685| |-----------------------------------------------------------------------------| r_work (start): 0.4753 rms_B_bonded: 2.74 r_work: 0.4688 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4403 Z= 0.173 Angle : 0.676 9.815 5943 Z= 0.343 Chirality : 0.044 0.147 595 Planarity : 0.005 0.051 791 Dihedral : 5.589 18.366 602 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 5.44 % Allowed : 14.06 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.75 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 66 TYR 0.019 0.002 TYR D 8 PHE 0.026 0.002 PHE A 69 TRP 0.013 0.001 TRP A 55 HIS 0.001 0.000 HIS G 25 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 4403) covalent geometry : angle 0.67637 ( 5943) hydrogen bonds : bond 0.02850 ( 110) hydrogen bonds : angle 4.87101 ( 330) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.154 Fit side-chains REVERT: A 11 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8572 (pt) REVERT: B 28 ASP cc_start: 0.4780 (t0) cc_final: 0.3896 (t70) REVERT: B 63 THR cc_start: 0.8424 (m) cc_final: 0.8096 (t) REVERT: C 47 GLU cc_start: 0.6177 (tp30) cc_final: 0.5800 (mm-30) REVERT: D 63 THR cc_start: 0.8636 (m) cc_final: 0.8249 (t) REVERT: D 66 ARG cc_start: 0.7485 (ttp-110) cc_final: 0.6505 (ttp-110) REVERT: E 51 GLU cc_start: 0.7253 (tt0) cc_final: 0.7043 (tt0) REVERT: E 75 GLU cc_start: 0.8105 (tt0) cc_final: 0.7647 (tt0) REVERT: F 51 GLU cc_start: 0.7307 (tt0) cc_final: 0.6695 (pm20) REVERT: G 66 ARG cc_start: 0.7655 (ttp-110) cc_final: 0.6536 (ttp-170) outliers start: 24 outliers final: 14 residues processed: 121 average time/residue: 0.0548 time to fit residues: 8.7180 Evaluate side-chains 113 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 16 optimal weight: 30.0000 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 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 = 0.4851 r_free = 0.4851 target = 0.200077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.178293 restraints weight = 8293.671| |-----------------------------------------------------------------------------| r_work (start): 0.4733 rms_B_bonded: 2.88 r_work: 0.4662 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4403 Z= 0.180 Angle : 0.691 10.151 5943 Z= 0.347 Chirality : 0.045 0.145 595 Planarity : 0.005 0.041 791 Dihedral : 5.464 16.533 602 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 6.35 % Allowed : 15.87 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.75 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 66 TYR 0.019 0.002 TYR D 8 PHE 0.023 0.002 PHE A 69 TRP 0.007 0.001 TRP E 55 HIS 0.001 0.001 HIS G 25 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 4403) covalent geometry : angle 0.69120 ( 5943) hydrogen bonds : bond 0.02896 ( 110) hydrogen bonds : angle 4.94651 ( 330) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.164 Fit side-chains REVERT: A 11 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8613 (pt) REVERT: A 51 GLU cc_start: 0.7235 (tt0) cc_final: 0.6946 (tt0) REVERT: B 18 ARG cc_start: 0.6172 (mtt180) cc_final: 0.5524 (mtm110) REVERT: B 28 ASP cc_start: 0.5063 (t0) cc_final: 0.4155 (t0) REVERT: B 63 THR cc_start: 0.8297 (m) cc_final: 0.7978 (t) REVERT: C 47 GLU cc_start: 0.6261 (tp30) cc_final: 0.5555 (tp30) REVERT: D 63 THR cc_start: 0.8587 (m) cc_final: 0.8227 (t) REVERT: D 69 PHE cc_start: 0.8430 (m-80) cc_final: 0.8067 (m-80) REVERT: E 44 ASP cc_start: 0.6818 (m-30) cc_final: 0.6618 (m-30) REVERT: E 75 GLU cc_start: 0.8023 (tt0) cc_final: 0.7592 (tt0) REVERT: F 51 GLU cc_start: 0.7186 (tt0) cc_final: 0.6817 (pm20) REVERT: G 66 ARG cc_start: 0.7602 (ttp-110) cc_final: 0.6579 (ttp-170) outliers start: 28 outliers final: 14 residues processed: 124 average time/residue: 0.0693 time to fit residues: 10.9686 Evaluate side-chains 115 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 23 optimal weight: 30.0000 chunk 11 optimal weight: 7.9990 chunk 5 optimal weight: 0.0270 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 38 optimal weight: 30.0000 overall best weight: 4.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.206554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.181909 restraints weight = 8137.215| |-----------------------------------------------------------------------------| r_work (start): 0.4750 rms_B_bonded: 2.85 r_work: 0.4680 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.6154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4403 Z= 0.152 Angle : 0.652 8.606 5943 Z= 0.330 Chirality : 0.044 0.150 595 Planarity : 0.004 0.041 791 Dihedral : 5.287 18.888 602 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 7.26 % Allowed : 16.78 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.76 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 66 TYR 0.018 0.002 TYR B 8 PHE 0.026 0.003 PHE B 69 TRP 0.012 0.001 TRP C 55 HIS 0.001 0.001 HIS G 25 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4403) covalent geometry : angle 0.65161 ( 5943) hydrogen bonds : bond 0.02797 ( 110) hydrogen bonds : angle 4.86688 ( 330) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7238 (tt0) cc_final: 0.6958 (tt0) REVERT: B 18 ARG cc_start: 0.5947 (mtt180) cc_final: 0.5343 (mtm110) REVERT: B 28 ASP cc_start: 0.4637 (t0) cc_final: 0.3850 (t0) REVERT: B 63 THR cc_start: 0.8275 (m) cc_final: 0.7984 (t) REVERT: C 47 GLU cc_start: 0.6495 (tp30) cc_final: 0.5762 (tp30) REVERT: D 63 THR cc_start: 0.8586 (m) cc_final: 0.8259 (t) REVERT: D 69 PHE cc_start: 0.8461 (m-80) cc_final: 0.8134 (m-80) REVERT: E 55 TRP cc_start: 0.8329 (t-100) cc_final: 0.7630 (t-100) REVERT: E 75 GLU cc_start: 0.7968 (tt0) cc_final: 0.7652 (tt0) REVERT: F 18 ARG cc_start: 0.6636 (mtt180) cc_final: 0.6014 (mtm110) REVERT: F 51 GLU cc_start: 0.7164 (tt0) cc_final: 0.6750 (pm20) REVERT: G 1 MET cc_start: 0.6325 (ttm) cc_final: 0.5896 (ttm) REVERT: G 51 GLU cc_start: 0.6854 (tt0) cc_final: 0.6504 (pm20) outliers start: 32 outliers final: 16 residues processed: 125 average time/residue: 0.0613 time to fit residues: 9.7859 Evaluate side-chains 111 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN F 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.244572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.5087 r_free = 0.5087 target = 0.221161 restraints weight = 9365.911| |-----------------------------------------------------------------------------| r_work (start): 0.4840 rms_B_bonded: 1.20 r_work: 0.4864 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.4816 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.4816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4403 Z= 0.167 Angle : 0.685 8.818 5943 Z= 0.345 Chirality : 0.045 0.155 595 Planarity : 0.004 0.043 791 Dihedral : 5.313 21.093 602 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 7.26 % Allowed : 17.01 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.75 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 66 TYR 0.016 0.002 TYR B 8 PHE 0.029 0.003 PHE B 69 TRP 0.022 0.002 TRP C 55 HIS 0.002 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 4403) covalent geometry : angle 0.68451 ( 5943) hydrogen bonds : bond 0.02822 ( 110) hydrogen bonds : angle 4.93403 ( 330) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 11 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8586 (pt) REVERT: A 51 GLU cc_start: 0.7219 (tt0) cc_final: 0.6944 (tt0) REVERT: B 28 ASP cc_start: 0.4596 (t0) cc_final: 0.3839 (t0) REVERT: B 63 THR cc_start: 0.8292 (m) cc_final: 0.7993 (t) REVERT: C 47 GLU cc_start: 0.6162 (tp30) cc_final: 0.5416 (tp30) REVERT: D 18 ARG cc_start: 0.6289 (mtt180) cc_final: 0.5703 (mtm110) REVERT: D 63 THR cc_start: 0.8593 (m) cc_final: 0.8322 (t) REVERT: D 69 PHE cc_start: 0.8404 (m-80) cc_final: 0.8018 (m-80) REVERT: E 24 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8046 (pp) REVERT: E 55 TRP cc_start: 0.8068 (t-100) cc_final: 0.7575 (t-100) REVERT: E 75 GLU cc_start: 0.7948 (tt0) cc_final: 0.7598 (tt0) REVERT: F 18 ARG cc_start: 0.6616 (mtt180) cc_final: 0.6078 (mtm110) REVERT: F 51 GLU cc_start: 0.7136 (tt0) cc_final: 0.6894 (pm20) REVERT: G 69 PHE cc_start: 0.6757 (m-80) cc_final: 0.5928 (m-80) outliers start: 32 outliers final: 19 residues processed: 121 average time/residue: 0.0586 time to fit residues: 9.2387 Evaluate side-chains 116 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 30.0000 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 5 optimal weight: 0.3980 chunk 12 optimal weight: 30.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.209314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.187140 restraints weight = 7882.925| |-----------------------------------------------------------------------------| r_work (start): 0.4832 rms_B_bonded: 2.80 r_work: 0.4828 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4403 Z= 0.125 Angle : 0.650 8.641 5943 Z= 0.325 Chirality : 0.043 0.148 595 Planarity : 0.004 0.041 791 Dihedral : 5.120 21.567 602 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 5.67 % Allowed : 20.18 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.73 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 66 TYR 0.016 0.002 TYR F 8 PHE 0.029 0.002 PHE B 69 TRP 0.019 0.001 TRP C 55 HIS 0.002 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4403) covalent geometry : angle 0.64950 ( 5943) hydrogen bonds : bond 0.02710 ( 110) hydrogen bonds : angle 4.79292 ( 330) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6508 (t0) cc_final: 0.6284 (t0) REVERT: A 51 GLU cc_start: 0.7331 (tt0) cc_final: 0.7065 (tt0) REVERT: B 28 ASP cc_start: 0.4660 (t0) cc_final: 0.4037 (t0) REVERT: B 63 THR cc_start: 0.8269 (m) cc_final: 0.7996 (t) REVERT: C 47 GLU cc_start: 0.6008 (tp30) cc_final: 0.5273 (tp30) REVERT: D 43 SER cc_start: 0.8704 (p) cc_final: 0.8365 (m) REVERT: D 63 THR cc_start: 0.8670 (m) cc_final: 0.8436 (t) REVERT: E 24 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8081 (pp) REVERT: E 47 GLU cc_start: 0.5299 (tp30) cc_final: 0.5069 (tp30) REVERT: E 55 TRP cc_start: 0.8058 (t-100) cc_final: 0.7696 (t-100) REVERT: E 69 PHE cc_start: 0.8577 (m-80) cc_final: 0.8243 (m-80) REVERT: E 75 GLU cc_start: 0.7819 (tt0) cc_final: 0.7525 (tt0) REVERT: F 51 GLU cc_start: 0.7134 (tt0) cc_final: 0.6849 (pm20) REVERT: G 69 PHE cc_start: 0.6474 (m-80) cc_final: 0.6255 (m-80) outliers start: 25 outliers final: 18 residues processed: 123 average time/residue: 0.0485 time to fit residues: 7.8398 Evaluate side-chains 115 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 18 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 36 optimal weight: 30.0000 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 40.0000 overall best weight: 7.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.241898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5082 r_free = 0.5082 target = 0.219771 restraints weight = 9480.649| |-----------------------------------------------------------------------------| r_work (start): 0.4819 rms_B_bonded: 1.21 r_work: 0.4843 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.4794 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.4794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4403 Z= 0.197 Angle : 0.734 9.770 5943 Z= 0.373 Chirality : 0.047 0.156 595 Planarity : 0.005 0.044 791 Dihedral : 5.491 21.351 602 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 5.90 % Allowed : 19.95 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.78 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 66 TYR 0.023 0.002 TYR B 14 PHE 0.032 0.003 PHE B 69 TRP 0.015 0.001 TRP C 55 HIS 0.002 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 4403) covalent geometry : angle 0.73408 ( 5943) hydrogen bonds : bond 0.02863 ( 110) hydrogen bonds : angle 5.17738 ( 330) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6537 (t0) cc_final: 0.6277 (t0) REVERT: A 51 GLU cc_start: 0.7286 (tt0) cc_final: 0.7063 (tt0) REVERT: B 28 ASP cc_start: 0.4600 (t0) cc_final: 0.4004 (t0) REVERT: B 63 THR cc_start: 0.8276 (m) cc_final: 0.8000 (t) REVERT: C 43 SER cc_start: 0.8605 (p) cc_final: 0.8170 (m) REVERT: C 57 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.7175 (t0) REVERT: D 18 ARG cc_start: 0.6005 (mtt180) cc_final: 0.5544 (mtm110) REVERT: D 43 SER cc_start: 0.8666 (p) cc_final: 0.8361 (m) REVERT: D 63 THR cc_start: 0.8628 (m) cc_final: 0.8389 (t) REVERT: E 55 TRP cc_start: 0.8092 (t-100) cc_final: 0.7683 (t-100) REVERT: E 75 GLU cc_start: 0.7878 (tt0) cc_final: 0.7572 (tt0) REVERT: F 18 ARG cc_start: 0.6627 (mtt180) cc_final: 0.5991 (mtm110) REVERT: G 69 PHE cc_start: 0.6628 (m-80) cc_final: 0.5792 (m-80) outliers start: 26 outliers final: 22 residues processed: 112 average time/residue: 0.0620 time to fit residues: 9.0693 Evaluate side-chains 118 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 22 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 HIS ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 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 = 0.4978 r_free = 0.4978 target = 0.245502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5118 r_free = 0.5118 target = 0.222383 restraints weight = 9256.031| |-----------------------------------------------------------------------------| r_work (start): 0.4857 rms_B_bonded: 1.18 r_work: 0.4888 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.4837 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.4837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.6800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4403 Z= 0.167 Angle : 0.708 9.069 5943 Z= 0.358 Chirality : 0.045 0.149 595 Planarity : 0.004 0.043 791 Dihedral : 5.401 21.439 602 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.54 % Allowed : 21.32 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.77 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 66 TYR 0.024 0.002 TYR B 14 PHE 0.031 0.003 PHE B 69 TRP 0.013 0.001 TRP B 55 HIS 0.002 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 4403) covalent geometry : angle 0.70826 ( 5943) hydrogen bonds : bond 0.02841 ( 110) hydrogen bonds : angle 5.05541 ( 330) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7229 (tt0) cc_final: 0.6995 (tt0) REVERT: B 28 ASP cc_start: 0.4678 (t0) cc_final: 0.4050 (t0) REVERT: B 63 THR cc_start: 0.8265 (m) cc_final: 0.7981 (t) REVERT: B 68 ASP cc_start: 0.7892 (m-30) cc_final: 0.7683 (t0) REVERT: C 43 SER cc_start: 0.8621 (p) cc_final: 0.8186 (m) REVERT: D 15 LYS cc_start: 0.5880 (ptmt) cc_final: 0.5676 (ptmt) REVERT: D 18 ARG cc_start: 0.6018 (mtt180) cc_final: 0.5517 (mtm110) REVERT: D 43 SER cc_start: 0.8625 (p) cc_final: 0.8365 (m) REVERT: D 63 THR cc_start: 0.8677 (m) cc_final: 0.8472 (t) REVERT: E 55 TRP cc_start: 0.8042 (t-100) cc_final: 0.7760 (t-100) REVERT: E 69 PHE cc_start: 0.8408 (m-80) cc_final: 0.8101 (m-10) REVERT: E 75 GLU cc_start: 0.7845 (tt0) cc_final: 0.7540 (tt0) REVERT: F 18 ARG cc_start: 0.6581 (mtt180) cc_final: 0.5957 (mtm110) REVERT: G 69 PHE cc_start: 0.6522 (m-80) cc_final: 0.6024 (m-80) outliers start: 20 outliers final: 16 residues processed: 110 average time/residue: 0.0589 time to fit residues: 8.4169 Evaluate side-chains 110 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.244355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5110 r_free = 0.5110 target = 0.221209 restraints weight = 9283.639| |-----------------------------------------------------------------------------| r_work (start): 0.4862 rms_B_bonded: 1.18 r_work: 0.4895 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.4846 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.4846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.6927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4403 Z= 0.182 Angle : 0.740 9.445 5943 Z= 0.369 Chirality : 0.045 0.150 595 Planarity : 0.005 0.045 791 Dihedral : 5.451 21.204 602 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.76 % Allowed : 20.86 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.76 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 66 TYR 0.022 0.002 TYR B 14 PHE 0.032 0.003 PHE B 69 TRP 0.009 0.001 TRP C 55 HIS 0.002 0.001 HIS B 25 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 4403) covalent geometry : angle 0.74020 ( 5943) hydrogen bonds : bond 0.02857 ( 110) hydrogen bonds : angle 5.11073 ( 330) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 891.77 seconds wall clock time: 16 minutes 0.01 seconds (960.01 seconds total)