Starting phenix.real_space_refine on Wed Oct 9 18:02:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7o_38105/10_2024/8x7o_38105.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7o_38105/10_2024/8x7o_38105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7o_38105/10_2024/8x7o_38105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7o_38105/10_2024/8x7o_38105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7o_38105/10_2024/8x7o_38105.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x7o_38105/10_2024/8x7o_38105.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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 12 5.16 5 C 2518 2.51 5 N 704 2.21 5 O 762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 3996 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "B" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "D" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "E" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "F" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "G" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "H" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "I" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "J" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'IZV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'IZV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'IZV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'IZV': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'IZV': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'IZV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'IZV': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'IZV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.11, per 1000 atoms: 0.78 Number of scatterers: 3996 At special positions: 0 Unit cell: (75.53, 110.39, 44.82, 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 12 16.00 O 762 8.00 N 704 7.00 C 2518 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: 1.36 Conformation dependent library (CDL) restraints added in 508.5 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 48 removed outlier: 6.725A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY I 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.422A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL I 63 " --> pdb=" O THR J 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.511A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL I 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.361A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR E 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ALA J 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL E 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA I 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 93 removed outlier: 8.873A pdb=" N ALA A 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N GLY B 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR A 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA A 91 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR E 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA E 91 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR J 92 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ALA I 90 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N GLY J 93 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N THR I 92 " --> pdb=" O GLY J 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 46 through 48 removed outlier: 6.723A pdb=" N GLY C 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY F 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 64 removed outlier: 6.422A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL F 63 " --> pdb=" O THR G 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.511A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL F 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 78 removed outlier: 6.360A pdb=" N ALA C 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA F 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 90 through 93 removed outlier: 8.873A pdb=" N ALA C 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N GLY D 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR C 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA C 91 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR G 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N ALA F 90 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLY G 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR F 92 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA F 91 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR H 92 " --> pdb=" O ALA F 91 " (cutoff:3.500A) 33 hydrogen bonds defined for protein. 99 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.30: 670 1.30 - 1.38: 715 1.38 - 1.47: 858 1.47 - 1.56: 1759 1.56 - 1.65: 28 Bond restraints: 4030 Sorted by residual: bond pdb=" C07 IZV J 202 " pdb=" S16 IZV J 202 " ideal model delta sigma weight residual 1.766 1.607 0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" C07 IZV A 202 " pdb=" S16 IZV A 202 " ideal model delta sigma weight residual 1.766 1.608 0.158 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C07 IZV I 201 " pdb=" S16 IZV I 201 " ideal model delta sigma weight residual 1.766 1.608 0.158 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C07 IZV C 201 " pdb=" S16 IZV C 201 " ideal model delta sigma weight residual 1.766 1.608 0.158 2.00e-02 2.50e+03 6.25e+01 bond pdb=" C07 IZV E 201 " pdb=" S16 IZV E 201 " ideal model delta sigma weight residual 1.766 1.608 0.158 2.00e-02 2.50e+03 6.25e+01 ... (remaining 4025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 4830 2.31 - 4.62: 533 4.62 - 6.93: 71 6.93 - 9.24: 0 9.24 - 11.55: 12 Bond angle restraints: 5446 Sorted by residual: angle pdb=" C07 IZV F 201 " pdb=" S16 IZV F 201 " pdb=" C17 IZV F 201 " ideal model delta sigma weight residual 89.25 100.80 -11.55 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C07 IZV G 202 " pdb=" S16 IZV G 202 " pdb=" C17 IZV G 202 " ideal model delta sigma weight residual 89.25 100.79 -11.54 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C07 IZV J 202 " pdb=" S16 IZV J 202 " pdb=" C17 IZV J 202 " ideal model delta sigma weight residual 89.25 100.79 -11.54 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C07 IZV I 201 " pdb=" S16 IZV I 201 " pdb=" C17 IZV I 201 " ideal model delta sigma weight residual 89.25 100.78 -11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C07 IZV G 201 " pdb=" S16 IZV G 201 " pdb=" C17 IZV G 201 " ideal model delta sigma weight residual 89.25 100.78 -11.53 3.00e+00 1.11e-01 1.48e+01 ... (remaining 5441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.34: 1825 10.34 - 20.68: 335 20.68 - 31.02: 60 31.02 - 41.36: 0 41.36 - 51.69: 20 Dihedral angle restraints: 2240 sinusoidal: 760 harmonic: 1480 Sorted by residual: dihedral pdb=" CA GLY D 67 " pdb=" C GLY D 67 " pdb=" N GLY D 68 " pdb=" CA GLY D 68 " ideal model delta harmonic sigma weight residual 0.00 25.07 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLY F 67 " pdb=" C GLY F 67 " pdb=" N GLY F 68 " pdb=" CA GLY F 68 " ideal model delta harmonic sigma weight residual 0.00 25.04 -25.04 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLY I 67 " pdb=" C GLY I 67 " pdb=" N GLY I 68 " pdb=" CA GLY I 68 " ideal model delta harmonic sigma weight residual 0.00 25.02 -25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 2237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 365 0.052 - 0.104: 169 0.104 - 0.156: 96 0.156 - 0.208: 20 0.208 - 0.260: 20 Chirality restraints: 670 Sorted by residual: chirality pdb=" CA ILE E 88 " pdb=" N ILE E 88 " pdb=" C ILE E 88 " pdb=" CB ILE E 88 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ILE J 88 " pdb=" N ILE J 88 " pdb=" C ILE J 88 " pdb=" CB ILE J 88 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 667 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 52 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C VAL B 52 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL B 52 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA B 53 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 52 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C VAL H 52 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL H 52 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA H 53 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 52 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C VAL D 52 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL D 52 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA D 53 " 0.013 2.00e-02 2.50e+03 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 971 2.80 - 3.33: 3192 3.33 - 3.85: 6252 3.85 - 4.38: 7329 4.38 - 4.90: 14297 Nonbonded interactions: 32041 Sorted by model distance: nonbonded pdb=" CE1 HIS C 50 " pdb=" O01 IZV C 201 " model vdw 2.280 3.260 nonbonded pdb=" CE1 HIS A 50 " pdb=" O01 IZV A 201 " model vdw 2.315 3.260 nonbonded pdb=" CE1 HIS E 50 " pdb=" O01 IZV E 201 " model vdw 2.363 3.260 nonbonded pdb=" CE1 HIS G 50 " pdb=" O01 IZV G 201 " model vdw 2.417 3.260 nonbonded pdb=" OG1 THR F 64 " pdb=" OG1 THR H 54 " model vdw 2.514 3.040 ... (remaining 32036 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 45 through 99) selection = chain 'B' selection = (chain 'C' and resid 45 through 99) selection = (chain 'D' and resid 45 through 99) selection = (chain 'E' and resid 45 through 99) selection = (chain 'F' and resid 45 through 99) selection = (chain 'G' and resid 45 through 99) selection = chain 'H' selection = (chain 'I' and resid 45 through 99) selection = (chain 'J' and resid 45 through 99) } 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 group one per residue 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: 0.800 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.580 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5694 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 : 0.019 0.159 4030 Z= 1.144 Angle : 1.484 11.548 5446 Z= 0.791 Chirality : 0.081 0.260 670 Planarity : 0.006 0.023 664 Dihedral : 11.598 51.694 1300 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.07 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.21), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.016 0.008 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: B 80 LYS cc_start: 0.7941 (tppp) cc_final: 0.6263 (pttm) REVERT: B 83 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8134 (mt-10) REVERT: D 83 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8219 (mt-10) REVERT: E 98 ASP cc_start: 0.6421 (m-30) cc_final: 0.5262 (m-30) REVERT: F 98 ASP cc_start: 0.6278 (m-30) cc_final: 0.5816 (m-30) REVERT: G 98 ASP cc_start: 0.6963 (m-30) cc_final: 0.6533 (m-30) REVERT: I 96 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7698 (tttt) REVERT: J 96 LYS cc_start: 0.7185 (mtpt) cc_final: 0.6971 (tttp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2492 time to fit residues: 26.9524 Evaluate side-chains 74 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN I 62 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.5642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4030 Z= 0.298 Angle : 0.664 4.733 5446 Z= 0.352 Chirality : 0.055 0.167 670 Planarity : 0.003 0.015 664 Dihedral : 5.927 18.491 540 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.21 % Allowed : 17.89 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 50 PHE 0.021 0.004 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.397 Fit side-chains REVERT: B 83 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8364 (mt-10) REVERT: D 46 LYS cc_start: 0.7662 (tttt) cc_final: 0.7243 (tppt) REVERT: E 61 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7351 (mt-10) REVERT: G 79 GLN cc_start: 0.8890 (tt0) cc_final: 0.8652 (mt0) REVERT: H 96 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7301 (tttm) REVERT: I 79 GLN cc_start: 0.9278 (tt0) cc_final: 0.9073 (tt0) REVERT: J 79 GLN cc_start: 0.8984 (tt0) cc_final: 0.8743 (mt0) outliers start: 16 outliers final: 5 residues processed: 86 average time/residue: 0.1993 time to fit residues: 20.7504 Evaluate side-chains 74 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 96 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 49 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN I 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.7300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 4030 Z= 0.470 Angle : 0.675 5.287 5446 Z= 0.363 Chirality : 0.055 0.166 670 Planarity : 0.003 0.012 664 Dihedral : 6.100 17.261 540 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 6.58 % Allowed : 13.95 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.11 (0.27), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.21), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 50 PHE 0.013 0.003 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 78 time to evaluate : 0.422 Fit side-chains REVERT: A 83 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7749 (mp0) REVERT: A 99 GLN cc_start: 0.6773 (mt0) cc_final: 0.6521 (mt0) REVERT: B 83 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8353 (mp0) REVERT: B 97 LYS cc_start: 0.8082 (mttt) cc_final: 0.7092 (mmtt) REVERT: C 83 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7531 (mp0) REVERT: D 46 LYS cc_start: 0.7765 (tttt) cc_final: 0.7292 (tppt) REVERT: D 83 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8164 (mp0) REVERT: D 97 LYS cc_start: 0.8000 (mmtt) cc_final: 0.6973 (mmtt) outliers start: 25 outliers final: 11 residues processed: 99 average time/residue: 0.2072 time to fit residues: 24.6076 Evaluate side-chains 86 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain J residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.7602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4030 Z= 0.199 Angle : 0.517 4.185 5446 Z= 0.279 Chirality : 0.051 0.151 670 Planarity : 0.002 0.013 664 Dihedral : 5.160 14.592 540 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.47 % Allowed : 15.00 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.007 0.002 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.427 Fit side-chains REVERT: A 83 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7728 (mp0) REVERT: B 46 LYS cc_start: 0.7867 (tttt) cc_final: 0.7297 (tppt) REVERT: B 83 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8348 (mp0) REVERT: B 97 LYS cc_start: 0.8162 (mttt) cc_final: 0.7201 (mmtt) REVERT: C 83 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7530 (mp0) REVERT: D 46 LYS cc_start: 0.7845 (tttt) cc_final: 0.7332 (tppt) REVERT: D 83 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8217 (mp0) REVERT: J 46 LYS cc_start: 0.8051 (tttm) cc_final: 0.7789 (tptt) REVERT: J 79 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8846 (mt0) REVERT: J 83 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8030 (mt-10) outliers start: 17 outliers final: 12 residues processed: 89 average time/residue: 0.2171 time to fit residues: 22.8722 Evaluate side-chains 88 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain J residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 GLN H 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.8065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 4030 Z= 0.500 Angle : 0.671 5.169 5446 Z= 0.358 Chirality : 0.056 0.161 670 Planarity : 0.002 0.016 664 Dihedral : 5.864 17.600 540 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 7.11 % Allowed : 12.89 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.010 0.002 PHE B 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 0.433 Fit side-chains REVERT: A 83 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7830 (mp0) REVERT: B 46 LYS cc_start: 0.7828 (tttt) cc_final: 0.7227 (tppt) REVERT: B 97 LYS cc_start: 0.8179 (mttt) cc_final: 0.7198 (mmtt) REVERT: D 46 LYS cc_start: 0.7947 (tttt) cc_final: 0.7431 (tppt) REVERT: D 83 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8270 (mp0) REVERT: D 97 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7043 (mmtt) outliers start: 27 outliers final: 25 residues processed: 101 average time/residue: 0.2099 time to fit residues: 25.3537 Evaluate side-chains 108 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.8233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4030 Z= 0.271 Angle : 0.551 4.733 5446 Z= 0.294 Chirality : 0.053 0.153 670 Planarity : 0.002 0.013 664 Dihedral : 5.220 16.250 540 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 5.53 % Allowed : 14.47 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.007 0.002 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.429 Fit side-chains REVERT: A 83 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7745 (mp0) REVERT: B 46 LYS cc_start: 0.7825 (tttt) cc_final: 0.7244 (tppt) REVERT: B 97 LYS cc_start: 0.8130 (mttt) cc_final: 0.7187 (mmtt) REVERT: D 46 LYS cc_start: 0.7931 (tttt) cc_final: 0.7352 (tppt) REVERT: D 83 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8229 (mp0) REVERT: J 83 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7964 (mt-10) outliers start: 21 outliers final: 19 residues processed: 95 average time/residue: 0.2105 time to fit residues: 23.5961 Evaluate side-chains 99 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.8511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 4030 Z= 0.481 Angle : 0.663 5.068 5446 Z= 0.352 Chirality : 0.056 0.163 670 Planarity : 0.002 0.010 664 Dihedral : 5.690 17.455 540 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 7.11 % Allowed : 13.95 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.06 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 50 PHE 0.010 0.002 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 82 time to evaluate : 0.474 Fit side-chains REVERT: A 83 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7854 (mp0) REVERT: B 46 LYS cc_start: 0.7858 (tttt) cc_final: 0.7241 (tppt) REVERT: B 97 LYS cc_start: 0.8181 (mttt) cc_final: 0.7216 (mmtt) REVERT: D 46 LYS cc_start: 0.7930 (tttt) cc_final: 0.7330 (tppt) REVERT: D 83 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8252 (mp0) REVERT: J 83 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8059 (mt-10) outliers start: 27 outliers final: 25 residues processed: 101 average time/residue: 0.2348 time to fit residues: 27.9763 Evaluate side-chains 107 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.8605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4030 Z= 0.304 Angle : 0.584 5.238 5446 Z= 0.309 Chirality : 0.053 0.154 670 Planarity : 0.001 0.010 664 Dihedral : 5.166 16.722 540 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 6.58 % Allowed : 14.47 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.007 0.002 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 0.383 Fit side-chains REVERT: A 83 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7746 (mp0) REVERT: B 46 LYS cc_start: 0.7874 (tttt) cc_final: 0.7223 (tppt) REVERT: B 97 LYS cc_start: 0.8196 (mttt) cc_final: 0.7271 (mmmt) REVERT: D 46 LYS cc_start: 0.7961 (tttt) cc_final: 0.7380 (tppt) REVERT: D 83 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8242 (mp0) REVERT: D 98 ASP cc_start: 0.7917 (m-30) cc_final: 0.7406 (m-30) REVERT: J 83 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8001 (mt-10) outliers start: 25 outliers final: 25 residues processed: 97 average time/residue: 0.2210 time to fit residues: 25.1329 Evaluate side-chains 107 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 20.0000 chunk 42 optimal weight: 0.0370 chunk 44 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.8732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4030 Z= 0.367 Angle : 0.616 5.435 5446 Z= 0.327 Chirality : 0.054 0.156 670 Planarity : 0.002 0.007 664 Dihedral : 5.302 17.028 540 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 6.84 % Allowed : 15.00 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.06 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.008 0.002 PHE G 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 0.450 Fit side-chains REVERT: A 83 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7779 (mp0) REVERT: B 46 LYS cc_start: 0.7860 (tttt) cc_final: 0.7220 (tppt) REVERT: B 97 LYS cc_start: 0.8195 (mttt) cc_final: 0.7246 (mmtt) REVERT: D 46 LYS cc_start: 0.7979 (tttt) cc_final: 0.7387 (tppt) REVERT: J 83 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7817 (mp0) outliers start: 26 outliers final: 26 residues processed: 101 average time/residue: 0.2210 time to fit residues: 26.3102 Evaluate side-chains 111 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.0570 chunk 5 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.8798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4030 Z= 0.271 Angle : 0.590 5.561 5446 Z= 0.311 Chirality : 0.053 0.152 670 Planarity : 0.001 0.008 664 Dihedral : 4.999 16.473 540 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 7.37 % Allowed : 15.53 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.006 0.001 PHE E 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 85 time to evaluate : 0.430 Fit side-chains REVERT: A 83 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7728 (mp0) REVERT: B 46 LYS cc_start: 0.7947 (tttt) cc_final: 0.7265 (tppt) REVERT: B 97 LYS cc_start: 0.8195 (mttt) cc_final: 0.7258 (mmtt) REVERT: D 46 LYS cc_start: 0.8004 (tttt) cc_final: 0.7459 (tppt) REVERT: G 57 GLU cc_start: 0.7507 (mp0) cc_final: 0.7182 (mp0) REVERT: J 83 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7979 (mt-10) outliers start: 28 outliers final: 27 residues processed: 102 average time/residue: 0.2345 time to fit residues: 27.9171 Evaluate side-chains 112 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 85 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 96 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.0970 chunk 45 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.148541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.102210 restraints weight = 4260.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.105975 restraints weight = 2186.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.108435 restraints weight = 1556.949| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.8864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4030 Z= 0.192 Angle : 0.541 5.759 5446 Z= 0.285 Chirality : 0.052 0.147 670 Planarity : 0.001 0.009 664 Dihedral : 4.631 15.020 540 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.26 % Allowed : 17.63 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E 50 PHE 0.004 0.001 PHE E 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1125.92 seconds wall clock time: 27 minutes 21.97 seconds (1641.97 seconds total)