Starting phenix.real_space_refine on Thu Dec 7 20:17:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/12_2023/6r4r_4727.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/12_2023/6r4r_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/12_2023/6r4r_4727.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/12_2023/6r4r_4727.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/12_2023/6r4r_4727.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4r_4727/12_2023/6r4r_4727.pdb" } 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 Residue "A TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4312 Number of models: 1 Model: "" Number of chains: 7 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} Chain: "B" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "C" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "D" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "E" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "G" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Time building chain proxies: 2.71, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 1.96 Conformation dependent library (CDL) restraints added in 839.3 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: 0.56 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: 1.04 Time building geometry restraints manager: 1.97 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: 100.19 - 106.91: 99 106.91 - 113.64: 2147 113.64 - 120.36: 1875 120.36 - 127.09: 1766 127.09 - 133.82: 56 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 2.520 nonbonded pdb=" OE2 GLU B 47 " pdb=" NZ LYS B 49 " model vdw 2.309 2.520 nonbonded pdb=" OE2 GLU F 47 " pdb=" NZ LYS F 49 " model vdw 2.310 2.520 nonbonded pdb=" OE2 GLU E 47 " pdb=" NZ LYS E 49 " model vdw 2.310 2.520 nonbonded pdb=" OE2 GLU C 47 " pdb=" NZ LYS C 49 " model vdw 2.310 2.520 ... (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 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 2.480 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.470 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.640 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.534 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1575 time to fit residues: 38.7356 Evaluate side-chains 114 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.512 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6752 ------------------------------------------------------------------------------- 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: 30.0000 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4403 Z= 0.199 Angle : 0.741 10.187 5943 Z= 0.362 Chirality : 0.047 0.192 595 Planarity : 0.005 0.038 791 Dihedral : 5.932 16.093 602 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.95 % Allowed : 12.93 % Favored : 84.13 % 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: -4.90 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 55 HIS 0.003 0.001 HIS F 25 PHE 0.011 0.002 PHE D 69 TYR 0.021 0.002 TYR E 59 ARG 0.006 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 146 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 0.580 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 137 average time/residue: 0.1522 time to fit residues: 26.4063 Evaluate side-chains 114 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.545 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0438 time to fit residues: 1.1836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 30.0000 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 30 optimal weight: 30.0000 chunk 12 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 35 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4403 Z= 0.196 Angle : 0.659 10.674 5943 Z= 0.328 Chirality : 0.044 0.155 595 Planarity : 0.004 0.033 791 Dihedral : 5.335 18.203 602 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.40 % Allowed : 15.19 % 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: -4.77 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 55 HIS 0.001 0.001 HIS B 25 PHE 0.013 0.002 PHE B 69 TYR 0.018 0.002 TYR E 8 ARG 0.003 0.001 ARG E 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 132 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 117 time to evaluate : 0.512 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 128 average time/residue: 0.1632 time to fit residues: 26.0167 Evaluate side-chains 110 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.540 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0459 time to fit residues: 1.3600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 30.0000 chunk 4 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 44 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 12 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 overall best weight: 5.8186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.5505 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= 0.254 Angle : 0.688 10.194 5943 Z= 0.347 Chirality : 0.046 0.139 595 Planarity : 0.004 0.029 791 Dihedral : 5.380 17.025 602 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 4.08 % Allowed : 17.46 % Favored : 78.46 % 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 (0.26), 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 0.012 0.002 TRP A 55 HIS 0.001 0.001 HIS G 25 PHE 0.017 0.002 PHE E 69 TYR 0.019 0.002 TYR E 8 ARG 0.009 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 131 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.546 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 120 average time/residue: 0.1561 time to fit residues: 23.7366 Evaluate side-chains 110 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0448 time to fit residues: 1.4060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 30.0000 chunk 9 optimal weight: 40.0000 chunk 27 optimal weight: 30.0000 overall best weight: 14.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN A 57 ASN B 46 GLN C 25 HIS ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 4403 Z= 0.526 Angle : 0.896 10.782 5943 Z= 0.467 Chirality : 0.054 0.153 595 Planarity : 0.006 0.048 791 Dihedral : 6.480 20.454 602 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 5.67 % Allowed : 17.91 % Favored : 76.42 % 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: -4.81 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 55 HIS 0.002 0.001 HIS G 25 PHE 0.027 0.004 PHE E 69 TYR 0.022 0.004 TYR G 76 ARG 0.010 0.002 ARG G 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 112 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 0.552 Fit side-chains outliers start: 25 outliers final: 15 residues processed: 102 average time/residue: 0.1388 time to fit residues: 18.4460 Evaluate side-chains 99 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.523 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0479 time to fit residues: 1.9022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 overall best weight: 5.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN B 46 GLN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.6548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4403 Z= 0.258 Angle : 0.669 7.320 5943 Z= 0.342 Chirality : 0.045 0.145 595 Planarity : 0.004 0.048 791 Dihedral : 5.591 16.575 602 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.40 % Allowed : 19.05 % Favored : 77.55 % 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: -4.84 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 55 HIS 0.002 0.001 HIS F 25 PHE 0.019 0.002 PHE B 69 TYR 0.021 0.002 TYR D 8 ARG 0.006 0.001 ARG G 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 118 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.506 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 108 average time/residue: 0.1939 time to fit residues: 25.8411 Evaluate side-chains 96 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0403 time to fit residues: 1.0664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 40.0000 chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 29 optimal weight: 30.0000 chunk 28 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 30 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4403 Z= 0.382 Angle : 0.786 7.968 5943 Z= 0.402 Chirality : 0.050 0.155 595 Planarity : 0.006 0.051 791 Dihedral : 5.889 16.205 602 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 2.95 % Allowed : 20.63 % Favored : 76.42 % 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: -4.94 (0.23), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 55 HIS 0.003 0.001 HIS B 25 PHE 0.014 0.003 PHE E 69 TYR 0.018 0.003 TYR D 8 ARG 0.009 0.001 ARG C 66 *********************** 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 107 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.542 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 101 average time/residue: 0.1638 time to fit residues: 20.8378 Evaluate side-chains 101 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0446 time to fit residues: 1.4206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 9.9990 chunk 4 optimal weight: 0.0770 chunk 37 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 30.0000 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.7084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4403 Z= 0.213 Angle : 0.658 8.661 5943 Z= 0.324 Chirality : 0.044 0.142 595 Planarity : 0.004 0.048 791 Dihedral : 5.248 18.664 602 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.59 % Allowed : 22.00 % Favored : 76.42 % 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: -4.90 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 55 HIS 0.002 0.001 HIS G 25 PHE 0.010 0.002 PHE C 69 TYR 0.018 0.002 TYR D 8 ARG 0.006 0.001 ARG C 66 *********************** 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 109 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.553 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 108 average time/residue: 0.1607 time to fit residues: 21.9970 Evaluate side-chains 99 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.523 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0431 time to fit residues: 0.8583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.7227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4403 Z= 0.291 Angle : 0.721 9.254 5943 Z= 0.359 Chirality : 0.047 0.154 595 Planarity : 0.005 0.045 791 Dihedral : 5.440 18.828 602 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 2.95 % Allowed : 22.22 % 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: -4.90 (0.23), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 55 HIS 0.002 0.001 HIS B 25 PHE 0.032 0.003 PHE B 69 TYR 0.018 0.002 TYR E 59 ARG 0.005 0.001 ARG G 66 *********************** 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 111 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.543 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 102 average time/residue: 0.1666 time to fit residues: 21.4066 Evaluate side-chains 99 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.475 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0444 time to fit residues: 1.3244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 40.0000 chunk 41 optimal weight: 30.0000 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 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 46 GLN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.7307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4403 Z= 0.277 Angle : 0.715 8.949 5943 Z= 0.356 Chirality : 0.047 0.155 595 Planarity : 0.004 0.048 791 Dihedral : 5.409 19.953 602 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.59 % Allowed : 22.68 % 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: -4.88 (0.23), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 55 HIS 0.002 0.001 HIS E 25 PHE 0.022 0.003 PHE C 69 TYR 0.017 0.002 TYR D 8 ARG 0.005 0.001 ARG G 66 ********************** 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 97 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.484 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 93 average time/residue: 0.1707 time to fit residues: 20.0502 Evaluate side-chains 92 residues out of total 441 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.531 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0388 time to fit residues: 0.8219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** 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 = 0.4855 r_free = 0.4855 target = 0.200907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.180934 restraints weight = 8249.574| |-----------------------------------------------------------------------------| r_work (start): 0.4769 rms_B_bonded: 2.64 r_work: 0.4776 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4688 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.4688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.7376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4403 Z= 0.287 Angle : 0.713 9.184 5943 Z= 0.357 Chirality : 0.047 0.145 595 Planarity : 0.004 0.046 791 Dihedral : 5.420 20.331 602 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 1.13 % Allowed : 23.13 % 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: -4.84 (0.23), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 55 HIS 0.002 0.001 HIS E 25 PHE 0.024 0.003 PHE C 69 TYR 0.016 0.002 TYR D 8 ARG 0.005 0.001 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1234.67 seconds wall clock time: 23 minutes 4.86 seconds (1384.86 seconds total)