Starting phenix.real_space_refine on Thu Mar 6 00:34:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r4r_4727/03_2025/6r4r_4727.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r4r_4727/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6r4r_4727/03_2025/6r4r_4727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r4r_4727/03_2025/6r4r_4727.map" model { file = "/net/cci-nas-00/data/ceres_data/6r4r_4727/03_2025/6r4r_4727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r4r_4727/03_2025/6r4r_4727.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= 0.011 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, B, E, D, G, F Time building chain proxies: 2.01, per 1000 atoms: 0.47 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: 0.92 Conformation dependent library (CDL) restraints added in 484.1 milliseconds 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: 0.72 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: 1.08 Time building geometry restraints manager: 1.12 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.620 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- 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= 0.504 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 (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: -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 TRP 0.008 0.002 TRP B 55 HIS 0.018 0.011 HIS A 25 PHE 0.008 0.003 PHE B 69 TYR 0.017 0.004 TYR B 8 ARG 0.003 0.001 ARG G 66 *********************** 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 : 0.483 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: 0.1706 time to fit residues: 42.0096 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 : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 0.0170 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 overall best weight: 3.2024 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.219933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.202255 restraints weight = 8039.817| |-----------------------------------------------------------------------------| r_work (start): 0.4782 rms_B_bonded: 2.76 r_work: 0.4717 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4403 Z= 0.214 Angle : 0.737 9.336 5943 Z= 0.365 Chirality : 0.046 0.185 595 Planarity : 0.005 0.041 791 Dihedral : 5.968 17.953 602 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.17 % Allowed : 12.02 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.87 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 55 HIS 0.004 0.001 HIS F 25 PHE 0.010 0.002 PHE D 69 TYR 0.018 0.002 TYR E 59 ARG 0.010 0.001 ARG C 66 *********************** 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 151 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.469 Fit side-chains REVERT: A 51 GLU cc_start: 0.7157 (tt0) cc_final: 0.6855 (tt0) REVERT: A 55 TRP cc_start: 0.6260 (t60) cc_final: 0.6028 (t60) REVERT: A 66 ARG cc_start: 0.7298 (ttm110) cc_final: 0.4945 (tpt170) REVERT: B 28 ASP cc_start: 0.5116 (t70) cc_final: 0.4066 (t0) REVERT: B 29 ILE cc_start: 0.7447 (mm) cc_final: 0.7246 (pt) REVERT: B 44 ASP cc_start: 0.4431 (m-30) cc_final: 0.3709 (m-30) REVERT: B 63 THR cc_start: 0.8534 (m) cc_final: 0.8297 (t) REVERT: D 8 TYR cc_start: 0.7800 (p90) cc_final: 0.7578 (p90) REVERT: D 44 ASP cc_start: 0.6447 (m-30) cc_final: 0.6065 (m-30) REVERT: D 66 ARG cc_start: 0.7477 (ttm110) cc_final: 0.7044 (ttp-110) REVERT: D 69 PHE cc_start: 0.8461 (m-80) cc_final: 0.8241 (m-80) REVERT: E 44 ASP cc_start: 0.6743 (m-30) cc_final: 0.6130 (m-30) REVERT: E 55 TRP cc_start: 0.7916 (t-100) cc_final: 0.7591 (t-100) REVERT: E 69 PHE cc_start: 0.8655 (m-80) cc_final: 0.8133 (m-80) REVERT: E 75 GLU cc_start: 0.8190 (tt0) cc_final: 0.7923 (tt0) REVERT: F 51 GLU cc_start: 0.6656 (tt0) cc_final: 0.6142 (pm20) REVERT: F 63 THR cc_start: 0.8298 (m) cc_final: 0.7855 (t) REVERT: G 63 THR cc_start: 0.8505 (m) cc_final: 0.8131 (t) outliers start: 14 outliers final: 7 residues processed: 142 average time/residue: 0.1486 time to fit residues: 26.6653 Evaluate side-chains 118 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER 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 53 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain G residue 56 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 40.0000 chunk 27 optimal weight: 30.0000 chunk 8 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.0070 chunk 14 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 overall best weight: 7.8008 ------------------------------------------------------------------------------- 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 = 0.4806 r_free = 0.4806 target = 0.180493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.171750 restraints weight = 8275.774| |-----------------------------------------------------------------------------| r_work (start): 0.4708 rms_B_bonded: 3.02 r_work: 0.4642 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4403 Z= 0.322 Angle : 0.772 11.488 5943 Z= 0.391 Chirality : 0.048 0.163 595 Planarity : 0.006 0.046 791 Dihedral : 5.937 19.442 602 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 4.54 % Allowed : 12.47 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.70 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 55 HIS 0.002 0.001 HIS B 25 PHE 0.026 0.002 PHE A 69 TYR 0.023 0.003 TYR B 8 ARG 0.005 0.001 ARG A 66 *********************** 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 146 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 11 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8662 (pt) REVERT: A 28 ASP cc_start: 0.5968 (t0) cc_final: 0.5469 (t0) REVERT: A 29 ILE cc_start: 0.7556 (mm) cc_final: 0.7120 (pt) REVERT: A 66 ARG cc_start: 0.7919 (ttm110) cc_final: 0.5201 (tpt170) REVERT: B 30 LEU cc_start: 0.8116 (tt) cc_final: 0.7600 (mm) REVERT: B 63 THR cc_start: 0.8388 (m) cc_final: 0.8097 (t) REVERT: D 63 THR cc_start: 0.8598 (m) cc_final: 0.8117 (t) REVERT: D 66 ARG cc_start: 0.7766 (ttm110) cc_final: 0.7527 (ttm-80) REVERT: D 69 PHE cc_start: 0.8498 (m-80) cc_final: 0.8242 (m-80) REVERT: E 44 ASP cc_start: 0.6688 (m-30) cc_final: 0.6406 (m-30) REVERT: E 47 GLU cc_start: 0.5650 (tp30) cc_final: 0.4735 (tp30) REVERT: E 51 GLU cc_start: 0.7126 (tt0) cc_final: 0.6906 (tt0) REVERT: F 51 GLU cc_start: 0.7222 (tt0) cc_final: 0.6556 (pm20) REVERT: F 63 THR cc_start: 0.8436 (m) cc_final: 0.8162 (t) REVERT: G 63 THR cc_start: 0.8440 (m) cc_final: 0.8235 (t) REVERT: G 66 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7648 (ttp-110) outliers start: 20 outliers final: 9 residues processed: 136 average time/residue: 0.1453 time to fit residues: 25.5249 Evaluate side-chains 122 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 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 E residue 46 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 27 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 39 optimal weight: 0.0770 chunk 10 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 4.4144 ------------------------------------------------------------------------------- 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 = 0.4871 r_free = 0.4871 target = 0.185715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.176625 restraints weight = 8198.521| |-----------------------------------------------------------------------------| r_work (start): 0.4826 rms_B_bonded: 3.03 r_work: 0.4867 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.4867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.5455 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= 0.215 Angle : 0.629 9.139 5943 Z= 0.315 Chirality : 0.044 0.167 595 Planarity : 0.004 0.054 791 Dihedral : 5.398 18.654 602 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.54 % Allowed : 14.06 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.62 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 55 HIS 0.001 0.000 HIS E 25 PHE 0.018 0.002 PHE B 69 TYR 0.016 0.002 TYR B 8 ARG 0.004 0.001 ARG C 66 *********************** 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 141 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.5551 (t0) cc_final: 0.5181 (t0) REVERT: A 29 ILE cc_start: 0.7463 (mm) cc_final: 0.7011 (pt) REVERT: B 28 ASP cc_start: 0.4698 (t70) cc_final: 0.3641 (t0) REVERT: B 29 ILE cc_start: 0.7440 (mm) cc_final: 0.6945 (pt) REVERT: B 63 THR cc_start: 0.8203 (m) cc_final: 0.7941 (t) REVERT: C 69 PHE cc_start: 0.8453 (m-80) cc_final: 0.8158 (m-80) REVERT: D 30 LEU cc_start: 0.8042 (tt) cc_final: 0.7838 (tp) REVERT: D 63 THR cc_start: 0.8440 (m) cc_final: 0.8077 (t) REVERT: F 51 GLU cc_start: 0.6769 (tt0) cc_final: 0.6499 (pm20) REVERT: G 66 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7822 (ttp-110) outliers start: 20 outliers final: 12 residues processed: 131 average time/residue: 0.1436 time to fit residues: 23.9123 Evaluate side-chains 117 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 53 ILE 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 11 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 27 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 10 optimal weight: 0.0870 chunk 20 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 overall best weight: 5.8166 ------------------------------------------------------------------------------- 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 = 0.4871 r_free = 0.4871 target = 0.205087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.180747 restraints weight = 8171.176| |-----------------------------------------------------------------------------| r_work (start): 0.4749 rms_B_bonded: 2.86 r_work: 0.4683 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4403 Z= 0.258 Angle : 0.651 6.422 5943 Z= 0.332 Chirality : 0.045 0.170 595 Planarity : 0.004 0.043 791 Dihedral : 5.364 17.927 602 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 6.35 % Allowed : 14.74 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.61 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 55 HIS 0.001 0.000 HIS F 25 PHE 0.021 0.002 PHE E 69 TYR 0.018 0.002 TYR D 8 ARG 0.003 0.001 ARG E 66 *********************** 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 : 0.522 Fit side-chains revert: symmetry clash REVERT: B 28 ASP cc_start: 0.4822 (t70) cc_final: 0.3750 (t0) REVERT: B 29 ILE cc_start: 0.7760 (mm) cc_final: 0.7182 (pt) REVERT: B 63 THR cc_start: 0.8267 (m) cc_final: 0.7976 (t) REVERT: D 30 LEU cc_start: 0.8204 (tt) cc_final: 0.7986 (tp) REVERT: D 63 THR cc_start: 0.8557 (m) cc_final: 0.8191 (t) REVERT: D 66 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.7469 (ttp-110) REVERT: D 69 PHE cc_start: 0.8440 (m-80) cc_final: 0.8114 (m-80) REVERT: E 44 ASP cc_start: 0.6647 (m-30) cc_final: 0.5723 (m-30) REVERT: E 47 GLU cc_start: 0.5362 (tp30) cc_final: 0.5052 (tp30) REVERT: E 55 TRP cc_start: 0.8380 (t-100) cc_final: 0.7328 (t-100) REVERT: F 51 GLU cc_start: 0.7102 (tt0) cc_final: 0.6700 (pm20) REVERT: G 66 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7828 (ttp-170) REVERT: G 69 PHE cc_start: 0.7390 (m-80) cc_final: 0.6000 (m-80) outliers start: 28 outliers final: 20 residues processed: 121 average time/residue: 0.1339 time to fit residues: 21.4399 Evaluate side-chains 125 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 77 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 F residue 40 LEU Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain G residue 2 SER 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 Chi-restraints excluded: chain G residue 66 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 HIS ** C 33 ASN ** 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 = 0.4852 r_free = 0.4852 target = 0.203289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.177950 restraints weight = 8193.867| |-----------------------------------------------------------------------------| r_work (start): 0.4735 rms_B_bonded: 2.80 r_work: 0.4671 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4403 Z= 0.287 Angle : 0.670 7.380 5943 Z= 0.345 Chirality : 0.045 0.160 595 Planarity : 0.005 0.046 791 Dihedral : 5.436 19.780 602 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 7.71 % Allowed : 14.06 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.67 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 55 HIS 0.001 0.001 HIS G 25 PHE 0.010 0.002 PHE E 69 TYR 0.017 0.002 TYR D 8 ARG 0.004 0.001 ARG E 66 *********************** 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 143 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: B 18 ARG cc_start: 0.5865 (mtt180) cc_final: 0.5309 (mtm110) REVERT: B 28 ASP cc_start: 0.4668 (t70) cc_final: 0.3692 (t0) REVERT: B 63 THR cc_start: 0.8352 (m) cc_final: 0.8043 (t) REVERT: D 18 ARG cc_start: 0.6110 (mtt180) cc_final: 0.5471 (mtm110) REVERT: D 63 THR cc_start: 0.8636 (m) cc_final: 0.8300 (t) REVERT: D 69 PHE cc_start: 0.8442 (m-80) cc_final: 0.8120 (m-80) REVERT: E 44 ASP cc_start: 0.6687 (m-30) cc_final: 0.5683 (m-30) REVERT: E 47 GLU cc_start: 0.5258 (tp30) cc_final: 0.4969 (tp30) REVERT: E 55 TRP cc_start: 0.8221 (t-100) cc_final: 0.7654 (t-100) REVERT: E 69 PHE cc_start: 0.8617 (m-80) cc_final: 0.8115 (m-80) REVERT: F 51 GLU cc_start: 0.7152 (tt0) cc_final: 0.6637 (pm20) REVERT: G 51 GLU cc_start: 0.6929 (tt0) cc_final: 0.6535 (pm20) REVERT: G 66 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7713 (ttp-170) REVERT: G 69 PHE cc_start: 0.6867 (m-80) cc_final: 0.6218 (m-80) outliers start: 34 outliers final: 21 residues processed: 126 average time/residue: 0.1655 time to fit residues: 25.9231 Evaluate side-chains 123 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 53 ILE 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 40 LEU 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 E 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 40 LEU Chi-restraints excluded: chain F residue 46 GLN 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 Chi-restraints excluded: chain G residue 66 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 30.0000 chunk 5 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 42 optimal weight: 0.5980 chunk 15 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.209755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.180902 restraints weight = 8047.960| |-----------------------------------------------------------------------------| r_work (start): 0.4764 rms_B_bonded: 2.74 r_work: 0.4696 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.6433 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= 0.251 Angle : 0.662 8.376 5943 Z= 0.336 Chirality : 0.044 0.146 595 Planarity : 0.005 0.042 791 Dihedral : 5.332 18.957 602 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 6.35 % Allowed : 17.91 % 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 (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: -4.67 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 55 HIS 0.001 0.001 HIS F 25 PHE 0.028 0.002 PHE B 69 TYR 0.016 0.002 TYR G 8 ARG 0.010 0.001 ARG F 18 *********************** 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 135 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.7337 (OUTLIER) cc_final: 0.6743 (t0) REVERT: B 28 ASP cc_start: 0.4640 (t70) cc_final: 0.3677 (t0) REVERT: B 63 THR cc_start: 0.8273 (m) cc_final: 0.7994 (t) REVERT: D 18 ARG cc_start: 0.6226 (mtt180) cc_final: 0.5572 (mtm110) REVERT: D 63 THR cc_start: 0.8511 (m) cc_final: 0.8260 (t) REVERT: D 69 PHE cc_start: 0.8449 (m-80) cc_final: 0.8032 (m-80) REVERT: E 24 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8083 (pp) REVERT: E 44 ASP cc_start: 0.6665 (m-30) cc_final: 0.5665 (m-30) REVERT: E 47 GLU cc_start: 0.5295 (tp30) cc_final: 0.5053 (tp30) REVERT: E 55 TRP cc_start: 0.8211 (t-100) cc_final: 0.7687 (t-100) REVERT: E 69 PHE cc_start: 0.8531 (m-80) cc_final: 0.8079 (m-10) REVERT: F 1 MET cc_start: 0.5967 (mtp) cc_final: 0.5737 (mtm) REVERT: F 51 GLU cc_start: 0.7095 (tt0) cc_final: 0.6698 (pm20) REVERT: G 51 GLU cc_start: 0.6842 (tt0) cc_final: 0.6484 (pm20) REVERT: G 66 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7746 (ttp-170) REVERT: G 69 PHE cc_start: 0.6683 (m-80) cc_final: 0.6202 (m-80) outliers start: 28 outliers final: 18 residues processed: 123 average time/residue: 0.1428 time to fit residues: 22.5288 Evaluate side-chains 121 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 53 ILE Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 40 LEU 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 24 LEU Chi-restraints excluded: chain D residue 46 GLN 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 F residue 40 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 Chi-restraints excluded: chain G residue 66 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 14 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 17 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 57 ASN ** C 33 ASN ** 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 = 0.4889 r_free = 0.4889 target = 0.205864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.181961 restraints weight = 8045.709| |-----------------------------------------------------------------------------| r_work (start): 0.4780 rms_B_bonded: 2.79 r_work: 0.4712 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4403 Z= 0.227 Angle : 0.655 8.194 5943 Z= 0.331 Chirality : 0.044 0.150 595 Planarity : 0.004 0.043 791 Dihedral : 5.243 21.131 602 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 7.94 % Allowed : 17.91 % 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 (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: -4.65 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 55 HIS 0.001 0.001 HIS G 25 PHE 0.031 0.002 PHE B 69 TYR 0.016 0.002 TYR G 8 ARG 0.009 0.001 ARG F 18 *********************** 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 138 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 0.592 Fit side-chains REVERT: A 57 ASN cc_start: 0.7338 (OUTLIER) cc_final: 0.6641 (t0) REVERT: B 28 ASP cc_start: 0.4397 (t70) cc_final: 0.3461 (t0) REVERT: B 46 GLN cc_start: 0.4854 (OUTLIER) cc_final: 0.3849 (pp30) REVERT: B 63 THR cc_start: 0.8314 (m) cc_final: 0.8034 (t) REVERT: D 63 THR cc_start: 0.8570 (m) cc_final: 0.8319 (t) REVERT: E 1 MET cc_start: 0.6175 (ttm) cc_final: 0.5882 (ttm) REVERT: E 24 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8060 (pp) REVERT: E 44 ASP cc_start: 0.6620 (m-30) cc_final: 0.5636 (m-30) REVERT: E 55 TRP cc_start: 0.8143 (t-100) cc_final: 0.7655 (t-100) REVERT: E 69 PHE cc_start: 0.8502 (m-80) cc_final: 0.8165 (m-10) REVERT: F 46 GLN cc_start: 0.6318 (mt0) cc_final: 0.6022 (mm-40) REVERT: F 51 GLU cc_start: 0.7187 (tt0) cc_final: 0.6717 (pm20) REVERT: G 51 GLU cc_start: 0.6824 (tt0) cc_final: 0.6451 (pm20) REVERT: G 66 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7721 (ttp-170) REVERT: G 69 PHE cc_start: 0.6600 (m-80) cc_final: 0.6242 (m-80) outliers start: 35 outliers final: 25 residues processed: 122 average time/residue: 0.1485 time to fit residues: 23.5592 Evaluate side-chains 126 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 57 ASN 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 40 LEU Chi-restraints excluded: chain B residue 46 GLN 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 1 MET 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 11 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 11 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 F residue 40 LEU Chi-restraints excluded: chain G residue 2 SER 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 Chi-restraints excluded: chain G residue 66 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 33 optimal weight: 40.0000 chunk 3 optimal weight: 4.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- 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 = 0.4876 r_free = 0.4876 target = 0.201663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.181203 restraints weight = 8195.014| |-----------------------------------------------------------------------------| r_work (start): 0.4754 rms_B_bonded: 2.77 r_work: 0.4690 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4403 Z= 0.273 Angle : 0.690 7.933 5943 Z= 0.351 Chirality : 0.045 0.150 595 Planarity : 0.005 0.041 791 Dihedral : 5.354 21.079 602 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 7.03 % Allowed : 18.82 % 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 (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: -4.66 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 55 HIS 0.001 0.001 HIS B 25 PHE 0.032 0.002 PHE B 69 TYR 0.019 0.002 TYR A 59 ARG 0.009 0.001 ARG F 18 *********************** 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 128 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 GLN cc_start: 0.4838 (OUTLIER) cc_final: 0.3834 (pp30) REVERT: B 63 THR cc_start: 0.8305 (m) cc_final: 0.8045 (t) REVERT: B 68 ASP cc_start: 0.7995 (m-30) cc_final: 0.7692 (t0) REVERT: D 18 ARG cc_start: 0.6002 (mtt180) cc_final: 0.5475 (mtm110) REVERT: D 63 THR cc_start: 0.8559 (m) cc_final: 0.8320 (t) REVERT: E 1 MET cc_start: 0.6560 (ttm) cc_final: 0.6192 (ttm) REVERT: E 15 LYS cc_start: 0.6182 (pttt) cc_final: 0.5823 (ptmt) REVERT: E 44 ASP cc_start: 0.6661 (m-30) cc_final: 0.5889 (m-30) REVERT: E 55 TRP cc_start: 0.8170 (t-100) cc_final: 0.7732 (t-100) REVERT: E 69 PHE cc_start: 0.8555 (m-80) cc_final: 0.8249 (m-10) REVERT: F 51 GLU cc_start: 0.7220 (tt0) cc_final: 0.6784 (pm20) REVERT: G 51 GLU cc_start: 0.6888 (tt0) cc_final: 0.6581 (pm20) REVERT: G 66 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7726 (ttp-170) REVERT: G 69 PHE cc_start: 0.6355 (m-80) cc_final: 0.6084 (m-80) outliers start: 31 outliers final: 20 residues processed: 112 average time/residue: 0.1434 time to fit residues: 20.9363 Evaluate side-chains 118 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 40 LEU Chi-restraints excluded: chain B residue 46 GLN 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 D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU 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 Chi-restraints excluded: chain G residue 66 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 0.3980 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 overall best weight: 6.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN ** C 33 ASN ** 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 = 0.4867 r_free = 0.4867 target = 0.200178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.180035 restraints weight = 8075.476| |-----------------------------------------------------------------------------| r_work (start): 0.4760 rms_B_bonded: 2.77 r_work: 0.4689 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4403 Z= 0.288 Angle : 0.709 8.007 5943 Z= 0.359 Chirality : 0.046 0.151 595 Planarity : 0.005 0.044 791 Dihedral : 5.451 21.543 602 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 5.67 % Allowed : 19.50 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.64 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 55 HIS 0.001 0.001 HIS G 25 PHE 0.032 0.002 PHE B 69 TYR 0.016 0.002 TYR G 8 ARG 0.009 0.001 ARG F 18 ********************** 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 123 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.573 Fit side-chains REVERT: A 57 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.6745 (t0) REVERT: B 46 GLN cc_start: 0.4687 (OUTLIER) cc_final: 0.3905 (pp30) REVERT: B 63 THR cc_start: 0.8327 (m) cc_final: 0.8053 (t) REVERT: B 68 ASP cc_start: 0.7726 (m-30) cc_final: 0.7508 (t0) REVERT: D 18 ARG cc_start: 0.6095 (mtt180) cc_final: 0.5504 (mtm110) REVERT: D 63 THR cc_start: 0.8555 (m) cc_final: 0.8341 (t) REVERT: E 15 LYS cc_start: 0.6069 (pttt) cc_final: 0.5544 (ptmt) REVERT: E 55 TRP cc_start: 0.8153 (t-100) cc_final: 0.7697 (t-100) REVERT: E 69 PHE cc_start: 0.8463 (m-80) cc_final: 0.8214 (m-10) REVERT: F 46 GLN cc_start: 0.6577 (tt0) cc_final: 0.6068 (mm-40) REVERT: F 51 GLU cc_start: 0.7256 (tt0) cc_final: 0.6833 (pm20) REVERT: G 51 GLU cc_start: 0.6938 (tt0) cc_final: 0.6655 (pm20) REVERT: G 66 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7810 (ttp-110) REVERT: G 69 PHE cc_start: 0.6401 (m-80) cc_final: 0.6087 (m-80) outliers start: 25 outliers final: 20 residues processed: 110 average time/residue: 0.1454 time to fit residues: 20.6317 Evaluate side-chains 119 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 57 ASN 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 40 LEU Chi-restraints excluded: chain B residue 46 GLN 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 D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 21 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 30.0000 chunk 48 optimal weight: 8.9990 chunk 10 optimal weight: 30.0000 chunk 2 optimal weight: 0.0670 chunk 14 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4909 r_free = 0.4909 target = 0.206711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.183326 restraints weight = 7886.846| |-----------------------------------------------------------------------------| r_work (start): 0.4816 rms_B_bonded: 2.80 r_work: 0.4810 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.4810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.6942 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= 0.226 Angle : 0.681 8.550 5943 Z= 0.340 Chirality : 0.044 0.152 595 Planarity : 0.004 0.041 791 Dihedral : 5.314 22.986 602 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 6.12 % Allowed : 19.50 % 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 (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: -4.62 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 55 HIS 0.001 0.001 HIS G 25 PHE 0.033 0.002 PHE B 69 TYR 0.016 0.002 TYR G 8 ARG 0.008 0.001 ARG F 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1860.99 seconds wall clock time: 33 minutes 25.99 seconds (2005.99 seconds total)