Starting phenix.real_space_refine on Sun Mar 10 20:55:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozg_13123/03_2024/7ozg_13123.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozg_13123/03_2024/7ozg_13123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozg_13123/03_2024/7ozg_13123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozg_13123/03_2024/7ozg_13123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozg_13123/03_2024/7ozg_13123.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozg_13123/03_2024/7ozg_13123.pdb" } resolution = 3.3 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= 0.106 sd= 0.874 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: 3 Type Number sf(0) Gaussians C 3100 2.51 5 N 870 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4960 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "B" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "C" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "E" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "F" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "G" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "H" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "I" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Chain: "J" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 496 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain breaks: 1 Time building chain proxies: 2.92, per 1000 atoms: 0.59 Number of scatterers: 4960 At special positions: 0 Unit cell: (103.95, 87.15, 42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 990 8.00 N 870 7.00 C 3100 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: 2.02 Conformation dependent library (CDL) restraints added in 975.8 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 43 removed outlier: 6.360A pdb=" N TYR A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER C 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY A 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR C 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER E 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY C 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR E 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER G 42 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY E 41 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR G 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER I 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY G 41 " --> pdb=" O SER I 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 49 removed outlier: 6.294A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL C 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL E 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL G 48 " --> pdb=" O VAL I 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.864A pdb=" N ASN A 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN C 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN E 65 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN G 65 " --> pdb=" O VAL I 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 70 through 72 Processing sheet with id=AA7, first strand: chain 'A' and resid 78 through 79 removed outlier: 6.078A pdb=" N ALA A 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA C 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA E 78 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ALA G 78 " --> pdb=" O GLN I 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 15 through 18 Processing sheet with id=AA9, first strand: chain 'B' and resid 39 through 43 removed outlier: 6.360A pdb=" N TYR B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER D 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY B 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR D 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER F 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY D 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR F 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER H 42 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY F 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR H 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER J 42 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY H 41 " --> pdb=" O SER J 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.294A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL D 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL F 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL H 48 " --> pdb=" O VAL J 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 52 through 55 Processing sheet with id=AB3, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.864A pdb=" N ASN B 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN D 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN F 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN H 65 " --> pdb=" O VAL J 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 70 through 72 Processing sheet with id=AB5, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.078A pdb=" N ALA B 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA D 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA F 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ALA H 78 " --> pdb=" O GLN J 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 64 hydrogen bonds defined for protein. 192 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: 1.34 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 870 1.28 - 1.34: 780 1.34 - 1.41: 170 1.41 - 1.48: 1168 1.48 - 1.55: 1982 Bond restraints: 4970 Sorted by residual: bond pdb=" CB LYS I 45 " pdb=" CG LYS I 45 " ideal model delta sigma weight residual 1.520 1.411 0.109 3.00e-02 1.11e+03 1.31e+01 bond pdb=" CB LYS J 45 " pdb=" CG LYS J 45 " ideal model delta sigma weight residual 1.520 1.411 0.109 3.00e-02 1.11e+03 1.31e+01 bond pdb=" CB LYS A 45 " pdb=" CG LYS A 45 " ideal model delta sigma weight residual 1.520 1.412 0.108 3.00e-02 1.11e+03 1.30e+01 bond pdb=" CB LYS B 45 " pdb=" CG LYS B 45 " ideal model delta sigma weight residual 1.520 1.412 0.108 3.00e-02 1.11e+03 1.30e+01 bond pdb=" CB LYS H 45 " pdb=" CG LYS H 45 " ideal model delta sigma weight residual 1.520 1.412 0.108 3.00e-02 1.11e+03 1.30e+01 ... (remaining 4965 not shown) Histogram of bond angle deviations from ideal: 102.68 - 108.31: 636 108.31 - 113.94: 2440 113.94 - 119.57: 1362 119.57 - 125.20: 2202 125.20 - 130.83: 60 Bond angle restraints: 6700 Sorted by residual: angle pdb=" N GLY I 93 " pdb=" CA GLY I 93 " pdb=" C GLY I 93 " ideal model delta sigma weight residual 111.21 120.65 -9.44 1.04e+00 9.25e-01 8.24e+01 angle pdb=" N GLY J 93 " pdb=" CA GLY J 93 " pdb=" C GLY J 93 " ideal model delta sigma weight residual 111.21 120.65 -9.44 1.04e+00 9.25e-01 8.24e+01 angle pdb=" N GLY D 93 " pdb=" CA GLY D 93 " pdb=" C GLY D 93 " ideal model delta sigma weight residual 111.21 120.65 -9.44 1.04e+00 9.25e-01 8.24e+01 angle pdb=" N GLY C 93 " pdb=" CA GLY C 93 " pdb=" C GLY C 93 " ideal model delta sigma weight residual 111.21 120.65 -9.44 1.04e+00 9.25e-01 8.24e+01 angle pdb=" N GLY B 93 " pdb=" CA GLY B 93 " pdb=" C GLY B 93 " ideal model delta sigma weight residual 111.21 120.64 -9.43 1.04e+00 9.25e-01 8.23e+01 ... (remaining 6695 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 8.88: 2090 8.88 - 17.76: 530 17.76 - 26.63: 200 26.63 - 35.51: 50 35.51 - 44.38: 20 Dihedral angle restraints: 2890 sinusoidal: 950 harmonic: 1940 Sorted by residual: dihedral pdb=" CA GLY D 84 " pdb=" C GLY D 84 " pdb=" N ALA D 85 " pdb=" CA ALA D 85 " ideal model delta harmonic sigma weight residual 180.00 143.03 36.97 0 5.00e+00 4.00e-02 5.47e+01 dihedral pdb=" CA GLY C 84 " pdb=" C GLY C 84 " pdb=" N ALA C 85 " pdb=" CA ALA C 85 " ideal model delta harmonic sigma weight residual 180.00 143.03 36.97 0 5.00e+00 4.00e-02 5.47e+01 dihedral pdb=" CA GLY I 84 " pdb=" C GLY I 84 " pdb=" N ALA I 85 " pdb=" CA ALA I 85 " ideal model delta harmonic sigma weight residual 180.00 143.06 36.94 0 5.00e+00 4.00e-02 5.46e+01 ... (remaining 2887 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.050: 320 0.050 - 0.100: 294 0.100 - 0.150: 146 0.150 - 0.199: 90 0.199 - 0.249: 30 Chirality restraints: 880 Sorted by residual: chirality pdb=" CB VAL B 49 " pdb=" CA VAL B 49 " pdb=" CG1 VAL B 49 " pdb=" CG2 VAL B 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB VAL A 49 " pdb=" CA VAL A 49 " pdb=" CG1 VAL A 49 " pdb=" CG2 VAL A 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB VAL D 49 " pdb=" CA VAL D 49 " pdb=" CG1 VAL D 49 " pdb=" CG2 VAL D 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 877 not shown) Planarity restraints: 830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 63 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C VAL B 63 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL B 63 " -0.025 2.00e-02 2.50e+03 pdb=" N THR B 64 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 63 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C VAL A 63 " -0.067 2.00e-02 2.50e+03 pdb=" O VAL A 63 " 0.025 2.00e-02 2.50e+03 pdb=" N THR A 64 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 63 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C VAL H 63 " 0.066 2.00e-02 2.50e+03 pdb=" O VAL H 63 " -0.025 2.00e-02 2.50e+03 pdb=" N THR H 64 " -0.023 2.00e-02 2.50e+03 ... (remaining 827 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1272 2.78 - 3.31: 4432 3.31 - 3.84: 7936 3.84 - 4.37: 9516 4.37 - 4.90: 19004 Nonbonded interactions: 42160 Sorted by model distance: nonbonded pdb=" OG1 THR I 44 " pdb=" N LYS I 45 " model vdw 2.254 2.520 nonbonded pdb=" OG1 THR J 44 " pdb=" N LYS J 45 " model vdw 2.254 2.520 nonbonded pdb=" OG1 THR F 44 " pdb=" N LYS F 45 " model vdw 2.255 2.520 nonbonded pdb=" OG1 THR E 44 " pdb=" N LYS E 45 " model vdw 2.255 2.520 nonbonded pdb=" OG1 THR A 44 " pdb=" N LYS A 45 " model vdw 2.255 2.520 ... (remaining 42155 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' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.690 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: 1.980 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.710 Find NCS groups from input model: 0.380 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 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 : 0.023 0.110 4970 Z= 1.598 Angle : 1.828 9.442 6700 Z= 1.128 Chirality : 0.097 0.249 880 Planarity : 0.012 0.038 830 Dihedral : 12.753 44.381 1670 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.82 % 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: -4.01 (0.23), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.18), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.014 HIS F 50 PHE 0.012 0.005 PHE B 94 TYR 0.028 0.012 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.518 Fit side-chains REVERT: A 77 VAL cc_start: 0.8245 (t) cc_final: 0.8014 (p) REVERT: A 96 LYS cc_start: 0.6471 (mttt) cc_final: 0.6150 (tmtt) REVERT: B 96 LYS cc_start: 0.6478 (mttt) cc_final: 0.6148 (tmtt) REVERT: C 96 LYS cc_start: 0.6773 (mttt) cc_final: 0.6185 (tmtt) REVERT: D 96 LYS cc_start: 0.6788 (mttt) cc_final: 0.6195 (tmtt) REVERT: E 96 LYS cc_start: 0.6512 (mttt) cc_final: 0.6202 (tmtt) REVERT: F 96 LYS cc_start: 0.6511 (mttt) cc_final: 0.6208 (tmtt) REVERT: G 96 LYS cc_start: 0.6631 (mttt) cc_final: 0.6186 (tptm) REVERT: H 96 LYS cc_start: 0.6595 (mttt) cc_final: 0.6156 (tptm) REVERT: I 96 LYS cc_start: 0.6983 (mttt) cc_final: 0.6608 (tmtt) REVERT: J 96 LYS cc_start: 0.6981 (mttt) cc_final: 0.6584 (tmtt) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1900 time to fit residues: 38.3676 Evaluate side-chains 150 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4970 Z= 0.369 Angle : 0.730 6.605 6700 Z= 0.424 Chirality : 0.053 0.123 880 Planarity : 0.003 0.012 830 Dihedral : 8.115 24.123 720 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.92 % Allowed : 17.55 % Favored : 76.53 % 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: -4.43 (0.23), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.018 0.004 PHE H 94 TYR 0.020 0.005 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.6552 (mttt) cc_final: 0.6312 (tptm) REVERT: B 96 LYS cc_start: 0.6594 (mttt) cc_final: 0.6241 (tptp) REVERT: C 96 LYS cc_start: 0.6251 (mttt) cc_final: 0.5862 (tmtt) REVERT: D 96 LYS cc_start: 0.6278 (mttt) cc_final: 0.5877 (tmtt) REVERT: E 96 LYS cc_start: 0.6652 (mttt) cc_final: 0.6204 (tmtt) REVERT: F 96 LYS cc_start: 0.6722 (mttt) cc_final: 0.6232 (tmtt) REVERT: G 96 LYS cc_start: 0.6620 (mttt) cc_final: 0.6053 (tptm) REVERT: H 96 LYS cc_start: 0.6511 (mttt) cc_final: 0.6042 (tptm) REVERT: I 80 LYS cc_start: 0.8655 (mttm) cc_final: 0.8401 (mttp) REVERT: I 96 LYS cc_start: 0.6960 (mttt) cc_final: 0.6539 (tmtt) REVERT: J 80 LYS cc_start: 0.8609 (mttm) cc_final: 0.8337 (mttp) REVERT: J 96 LYS cc_start: 0.6916 (mttt) cc_final: 0.6513 (tmtt) outliers start: 29 outliers final: 26 residues processed: 167 average time/residue: 0.1490 time to fit residues: 32.0576 Evaluate side-chains 184 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 30.0000 chunk 68 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 4970 Z= 0.520 Angle : 0.769 6.328 6700 Z= 0.452 Chirality : 0.052 0.147 880 Planarity : 0.004 0.015 830 Dihedral : 7.758 23.095 720 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.49 % Favored : 85.51 % Rotamer: Outliers : 10.20 % Allowed : 18.16 % Favored : 71.63 % 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: -4.75 (0.22), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.16), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 50 PHE 0.019 0.004 PHE H 94 TYR 0.026 0.007 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 169 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7078 (mttt) cc_final: 0.6302 (tmtt) REVERT: B 96 LYS cc_start: 0.7010 (mttt) cc_final: 0.6312 (tmtt) REVERT: C 96 LYS cc_start: 0.6645 (mttt) cc_final: 0.6048 (tptt) REVERT: D 96 LYS cc_start: 0.6840 (mttt) cc_final: 0.6165 (tmtt) REVERT: E 96 LYS cc_start: 0.7047 (mttt) cc_final: 0.6141 (tmtt) REVERT: F 96 LYS cc_start: 0.7041 (mttt) cc_final: 0.6159 (tmtt) REVERT: G 96 LYS cc_start: 0.7145 (mttt) cc_final: 0.6400 (tptm) REVERT: H 96 LYS cc_start: 0.6987 (mttt) cc_final: 0.6396 (tptm) REVERT: I 96 LYS cc_start: 0.7445 (mttt) cc_final: 0.6749 (tmtt) REVERT: J 96 LYS cc_start: 0.7419 (mttt) cc_final: 0.6708 (tmtt) outliers start: 50 outliers final: 43 residues processed: 186 average time/residue: 0.1595 time to fit residues: 37.7738 Evaluate side-chains 206 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 163 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4970 Z= 0.209 Angle : 0.613 5.320 6700 Z= 0.342 Chirality : 0.051 0.121 880 Planarity : 0.002 0.013 830 Dihedral : 6.255 18.143 720 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 5.10 % Allowed : 23.47 % Favored : 71.43 % 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: -4.63 (0.23), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 50 PHE 0.012 0.003 PHE G 94 TYR 0.009 0.002 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8315 (mttm) cc_final: 0.8069 (mttp) REVERT: A 96 LYS cc_start: 0.6865 (mttt) cc_final: 0.6255 (tmtt) REVERT: B 96 LYS cc_start: 0.6801 (mttt) cc_final: 0.6176 (tmtt) REVERT: C 96 LYS cc_start: 0.6740 (mttt) cc_final: 0.6132 (tmtt) REVERT: D 96 LYS cc_start: 0.6768 (mttt) cc_final: 0.6130 (tmtt) REVERT: E 80 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7924 (mttp) REVERT: E 96 LYS cc_start: 0.6943 (mttt) cc_final: 0.6129 (tmtt) REVERT: F 80 LYS cc_start: 0.8155 (mttm) cc_final: 0.7938 (mttp) REVERT: F 96 LYS cc_start: 0.6941 (mttt) cc_final: 0.6120 (tmtt) REVERT: G 96 LYS cc_start: 0.7019 (mttt) cc_final: 0.6260 (tptm) REVERT: H 96 LYS cc_start: 0.6854 (mttt) cc_final: 0.6257 (tptm) REVERT: I 96 LYS cc_start: 0.7439 (mttt) cc_final: 0.6623 (tmtt) REVERT: J 96 LYS cc_start: 0.7297 (mttt) cc_final: 0.6608 (tmtt) outliers start: 25 outliers final: 21 residues processed: 168 average time/residue: 0.1547 time to fit residues: 33.4892 Evaluate side-chains 176 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 15 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 30.0000 chunk 50 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 60 optimal weight: 0.2980 chunk 17 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 overall best weight: 9.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 4970 Z= 0.549 Angle : 0.781 6.052 6700 Z= 0.455 Chirality : 0.053 0.197 880 Planarity : 0.004 0.015 830 Dihedral : 7.369 23.211 720 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.41 % Favored : 81.59 % Rotamer: Outliers : 11.22 % Allowed : 19.18 % Favored : 69.59 % 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: -4.91 (0.22), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.16), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 50 PHE 0.015 0.004 PHE C 94 TYR 0.026 0.007 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 146 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7025 (mttt) cc_final: 0.6257 (tmtt) REVERT: B 96 LYS cc_start: 0.6999 (mttt) cc_final: 0.6211 (tmtt) REVERT: C 96 LYS cc_start: 0.6948 (mttt) cc_final: 0.6130 (tptt) REVERT: D 96 LYS cc_start: 0.6993 (mttt) cc_final: 0.6149 (tptt) REVERT: E 96 LYS cc_start: 0.7275 (mttt) cc_final: 0.6250 (tmtt) REVERT: F 96 LYS cc_start: 0.7173 (mttt) cc_final: 0.6251 (tmtt) REVERT: G 96 LYS cc_start: 0.7229 (mttt) cc_final: 0.6443 (tptm) REVERT: H 96 LYS cc_start: 0.7023 (mttt) cc_final: 0.6450 (tptm) REVERT: I 96 LYS cc_start: 0.7584 (mttt) cc_final: 0.6802 (tmtt) REVERT: J 96 LYS cc_start: 0.7466 (mttt) cc_final: 0.6727 (tmtt) outliers start: 55 outliers final: 47 residues processed: 168 average time/residue: 0.1595 time to fit residues: 34.2623 Evaluate side-chains 189 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 142 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 30.0000 chunk 65 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4970 Z= 0.310 Angle : 0.661 6.206 6700 Z= 0.371 Chirality : 0.051 0.128 880 Planarity : 0.003 0.012 830 Dihedral : 6.306 17.731 720 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 9.59 % Allowed : 19.59 % Favored : 70.82 % 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 (0.22), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.019 0.003 PHE D 94 TYR 0.015 0.004 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 147 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7028 (mttt) cc_final: 0.6337 (tmtt) REVERT: B 96 LYS cc_start: 0.7050 (mttt) cc_final: 0.6342 (tmtt) REVERT: C 96 LYS cc_start: 0.6906 (mttt) cc_final: 0.6112 (tmtt) REVERT: D 96 LYS cc_start: 0.6905 (mttt) cc_final: 0.6114 (tmtt) REVERT: E 96 LYS cc_start: 0.7115 (mttt) cc_final: 0.6173 (tmtt) REVERT: F 80 LYS cc_start: 0.8187 (mttm) cc_final: 0.7908 (mttp) REVERT: F 96 LYS cc_start: 0.7128 (mttt) cc_final: 0.6148 (tmtt) REVERT: G 96 LYS cc_start: 0.7157 (mttt) cc_final: 0.6423 (tptm) REVERT: H 96 LYS cc_start: 0.6924 (mttt) cc_final: 0.6381 (tptm) REVERT: I 96 LYS cc_start: 0.7523 (mttt) cc_final: 0.6741 (tmtt) REVERT: J 96 LYS cc_start: 0.7442 (mttt) cc_final: 0.6695 (tmtt) outliers start: 47 outliers final: 42 residues processed: 169 average time/residue: 0.1566 time to fit residues: 33.9147 Evaluate side-chains 188 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 146 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 42 optimal weight: 30.0000 chunk 41 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 62 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4970 Z= 0.379 Angle : 0.694 6.093 6700 Z= 0.391 Chirality : 0.051 0.162 880 Planarity : 0.003 0.011 830 Dihedral : 6.493 20.138 720 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.83 % Favored : 82.17 % Rotamer: Outliers : 10.41 % Allowed : 20.20 % Favored : 69.39 % 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: -4.79 (0.23), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 50 PHE 0.015 0.003 PHE D 94 TYR 0.018 0.004 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 139 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.6945 (mttt) cc_final: 0.6219 (tmtt) REVERT: B 96 LYS cc_start: 0.6945 (mttt) cc_final: 0.6192 (tmtt) REVERT: C 96 LYS cc_start: 0.7049 (mttt) cc_final: 0.6066 (tptt) REVERT: D 96 LYS cc_start: 0.7139 (mttt) cc_final: 0.6162 (tptt) REVERT: E 96 LYS cc_start: 0.7171 (mttt) cc_final: 0.6155 (tmtt) REVERT: F 96 LYS cc_start: 0.7201 (mttt) cc_final: 0.6224 (tmtt) REVERT: G 96 LYS cc_start: 0.7044 (mttt) cc_final: 0.6452 (tptm) REVERT: H 96 LYS cc_start: 0.7060 (mttt) cc_final: 0.6531 (tptm) REVERT: I 96 LYS cc_start: 0.7612 (mttt) cc_final: 0.6846 (tmtt) REVERT: J 96 LYS cc_start: 0.7407 (mttt) cc_final: 0.6746 (tmtt) outliers start: 51 outliers final: 48 residues processed: 165 average time/residue: 0.1538 time to fit residues: 32.4545 Evaluate side-chains 184 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 136 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 61 optimal weight: 0.2980 chunk 64 optimal weight: 0.0010 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 overall best weight: 4.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4970 Z= 0.286 Angle : 0.652 7.222 6700 Z= 0.360 Chirality : 0.051 0.141 880 Planarity : 0.003 0.012 830 Dihedral : 5.941 18.305 720 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 11.02 % Allowed : 18.98 % Favored : 70.00 % 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: -4.71 (0.23), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.015 0.003 PHE D 94 TYR 0.014 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 138 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.6884 (mttt) cc_final: 0.6198 (tmtt) REVERT: B 96 LYS cc_start: 0.6938 (mttt) cc_final: 0.6191 (tmtt) REVERT: C 96 LYS cc_start: 0.7080 (mttt) cc_final: 0.6103 (tptt) REVERT: D 96 LYS cc_start: 0.7176 (mttt) cc_final: 0.6148 (tptt) REVERT: E 96 LYS cc_start: 0.7150 (mttt) cc_final: 0.6231 (tmtt) REVERT: F 80 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7920 (mttp) REVERT: F 96 LYS cc_start: 0.7173 (mttt) cc_final: 0.6269 (tmtt) REVERT: G 96 LYS cc_start: 0.7092 (mttt) cc_final: 0.6565 (tptm) REVERT: H 96 LYS cc_start: 0.7023 (mttt) cc_final: 0.6476 (tptm) REVERT: I 96 LYS cc_start: 0.7515 (mttt) cc_final: 0.6810 (tmtt) REVERT: J 96 LYS cc_start: 0.7427 (mttt) cc_final: 0.6759 (tmtt) outliers start: 54 outliers final: 49 residues processed: 167 average time/residue: 0.1486 time to fit residues: 32.0238 Evaluate side-chains 187 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 137 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 8.9990 chunk 49 optimal weight: 40.0000 chunk 19 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4970 Z= 0.362 Angle : 0.685 7.997 6700 Z= 0.379 Chirality : 0.051 0.165 880 Planarity : 0.003 0.012 830 Dihedral : 6.186 19.382 720 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 10.82 % Allowed : 18.98 % Favored : 70.20 % 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: -4.73 (0.23), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.18), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.016 0.003 PHE D 94 TYR 0.018 0.004 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 135 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.6852 (mttt) cc_final: 0.6175 (tmtt) REVERT: B 96 LYS cc_start: 0.6974 (mttt) cc_final: 0.6217 (tmtt) REVERT: C 96 LYS cc_start: 0.7142 (mttt) cc_final: 0.6188 (tptt) REVERT: D 96 LYS cc_start: 0.7292 (mttt) cc_final: 0.6324 (tptt) REVERT: E 96 LYS cc_start: 0.7209 (mttt) cc_final: 0.6340 (tmtt) REVERT: F 96 LYS cc_start: 0.7281 (mttt) cc_final: 0.6394 (tmtt) REVERT: G 96 LYS cc_start: 0.7130 (mttt) cc_final: 0.6566 (tptm) REVERT: H 96 LYS cc_start: 0.7059 (mttt) cc_final: 0.6480 (tptm) REVERT: I 96 LYS cc_start: 0.7472 (mttt) cc_final: 0.6806 (tmtt) REVERT: J 96 LYS cc_start: 0.7430 (mttt) cc_final: 0.6742 (tmtt) outliers start: 53 outliers final: 52 residues processed: 164 average time/residue: 0.1475 time to fit residues: 31.1158 Evaluate side-chains 187 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 135 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 55 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4970 Z= 0.360 Angle : 0.692 8.385 6700 Z= 0.383 Chirality : 0.051 0.160 880 Planarity : 0.003 0.013 830 Dihedral : 6.134 19.720 720 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 10.82 % Allowed : 18.78 % Favored : 70.41 % 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: -4.70 (0.23), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.18), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 50 PHE 0.016 0.003 PHE D 94 TYR 0.018 0.004 TYR D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 137 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.6936 (mttt) cc_final: 0.6268 (tmtt) REVERT: B 96 LYS cc_start: 0.7031 (mttt) cc_final: 0.6196 (tmtt) REVERT: C 96 LYS cc_start: 0.7263 (mttt) cc_final: 0.6310 (tptt) REVERT: D 96 LYS cc_start: 0.7302 (mttt) cc_final: 0.6325 (tptt) REVERT: E 96 LYS cc_start: 0.7383 (mttt) cc_final: 0.6450 (tmtt) REVERT: F 96 LYS cc_start: 0.7307 (mttt) cc_final: 0.6397 (tmtt) REVERT: G 96 LYS cc_start: 0.7173 (mttt) cc_final: 0.6566 (tptm) REVERT: H 96 LYS cc_start: 0.7172 (mttt) cc_final: 0.6451 (tptm) REVERT: I 96 LYS cc_start: 0.7464 (mttt) cc_final: 0.6804 (tmtt) REVERT: J 96 LYS cc_start: 0.7486 (mttt) cc_final: 0.6723 (tmtt) outliers start: 53 outliers final: 53 residues processed: 170 average time/residue: 0.1591 time to fit residues: 34.9842 Evaluate side-chains 190 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 137 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 7 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.215187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.188146 restraints weight = 6720.157| |-----------------------------------------------------------------------------| r_work (start): 0.4514 rms_B_bonded: 4.43 r_work: 0.4404 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 4970 Z= 0.399 Angle : 0.712 8.585 6700 Z= 0.395 Chirality : 0.052 0.162 880 Planarity : 0.003 0.012 830 Dihedral : 6.339 20.489 720 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.54 % Favored : 82.46 % Rotamer: Outliers : 10.82 % Allowed : 18.98 % Favored : 70.20 % 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: -4.72 (0.24), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.18), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.016 0.003 PHE D 94 TYR 0.020 0.005 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1356.19 seconds wall clock time: 25 minutes 25.75 seconds (1525.75 seconds total)