Starting phenix.real_space_refine on Tue Feb 11 08:30:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ozg_13123/02_2025/7ozg_13123.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ozg_13123/02_2025/7ozg_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/cci-nas-00/data/ceres_data/7ozg_13123/02_2025/7ozg_13123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ozg_13123/02_2025/7ozg_13123.map" model { file = "/net/cci-nas-00/data/ceres_data/7ozg_13123/02_2025/7ozg_13123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ozg_13123/02_2025/7ozg_13123.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4960 Number of models: 1 Model: "" Number of chains: 1 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 Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.69, per 1000 atoms: 0.34 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 - 3.00 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: 1.07 Conformation dependent library (CDL) restraints added in 672.9 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: 0.58 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: 0.91 Time building geometry restraints manager: 1.26 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: 0.00 - 1.89: 5154 1.89 - 3.78: 1202 3.78 - 5.67: 234 5.67 - 7.55: 70 7.55 - 9.44: 40 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 3.120 nonbonded pdb=" OG1 THR J 44 " pdb=" N LYS J 45 " model vdw 2.254 3.120 nonbonded pdb=" OG1 THR F 44 " pdb=" N LYS F 45 " model vdw 2.255 3.120 nonbonded pdb=" OG1 THR E 44 " pdb=" N LYS E 45 " model vdw 2.255 3.120 nonbonded pdb=" OG1 THR A 44 " pdb=" N LYS A 45 " model vdw 2.255 3.120 ... (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 Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.860 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.390 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.540 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: 0.1850 time to fit residues: 37.6884 Evaluate side-chains 150 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.214197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.184271 restraints weight = 6457.660| |-----------------------------------------------------------------------------| r_work (start): 0.4574 rms_B_bonded: 4.80 r_work (final): 0.4574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4970 Z= 0.406 Angle : 0.748 6.484 6700 Z= 0.436 Chirality : 0.055 0.124 880 Planarity : 0.003 0.012 830 Dihedral : 8.157 24.861 720 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.27 % Allowed : 20.00 % Favored : 76.73 % 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: -4.36 (0.22), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.020 0.004 PHE H 94 TYR 0.022 0.005 TYR H 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 175 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 80 LYS cc_start: 0.8120 (mptt) cc_final: 0.7780 (mptt) REVERT: D 80 LYS cc_start: 0.8109 (mptt) cc_final: 0.7778 (mptt) REVERT: E 80 LYS cc_start: 0.7785 (mttm) cc_final: 0.7300 (mttp) REVERT: F 80 LYS cc_start: 0.7772 (mttm) cc_final: 0.7289 (mttp) REVERT: I 80 LYS cc_start: 0.8522 (mttm) cc_final: 0.8116 (mttp) REVERT: I 96 LYS cc_start: 0.6736 (mttt) cc_final: 0.6293 (tmtt) REVERT: J 80 LYS cc_start: 0.8517 (mttm) cc_final: 0.8101 (mttp) REVERT: J 96 LYS cc_start: 0.6775 (mttt) cc_final: 0.6296 (tmtt) outliers start: 16 outliers final: 15 residues processed: 159 average time/residue: 0.1600 time to fit residues: 32.7232 Evaluate side-chains 164 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 77 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain J residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 0.0770 chunk 55 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 overall best weight: 5.0146 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.217664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.186819 restraints weight = 6177.547| |-----------------------------------------------------------------------------| r_work (start): 0.4577 rms_B_bonded: 4.83 r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.3886 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= 0.343 Angle : 0.664 5.709 6700 Z= 0.383 Chirality : 0.052 0.123 880 Planarity : 0.003 0.013 830 Dihedral : 7.157 21.863 720 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 7.55 % Allowed : 20.20 % Favored : 72.24 % 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: -4.50 (0.22), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.16), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.020 0.004 PHE H 94 TYR 0.016 0.004 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 189 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: D 80 LYS cc_start: 0.8130 (mptt) cc_final: 0.7698 (mptt) REVERT: I 80 LYS cc_start: 0.8397 (mttm) cc_final: 0.8040 (mttp) REVERT: I 96 LYS cc_start: 0.6988 (mttt) cc_final: 0.6263 (tmtt) REVERT: J 80 LYS cc_start: 0.8408 (mttm) cc_final: 0.8076 (mttp) REVERT: J 96 LYS cc_start: 0.6938 (mttt) cc_final: 0.6261 (tmtt) outliers start: 37 outliers final: 27 residues processed: 164 average time/residue: 0.1393 time to fit residues: 29.9219 Evaluate side-chains 169 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 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 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 F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 22 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 77 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 40.0000 chunk 8 optimal weight: 10.0000 chunk 42 optimal weight: 40.0000 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 30.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.216966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.185555 restraints weight = 6197.467| |-----------------------------------------------------------------------------| r_work (start): 0.4550 rms_B_bonded: 4.85 r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4970 Z= 0.329 Angle : 0.644 5.639 6700 Z= 0.369 Chirality : 0.051 0.137 880 Planarity : 0.003 0.014 830 Dihedral : 6.739 21.002 720 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 6.53 % Allowed : 21.63 % Favored : 71.84 % 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: -4.53 (0.21), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.16), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 50 PHE 0.013 0.003 PHE G 94 TYR 0.017 0.004 TYR D 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 178 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 80 LYS cc_start: 0.7798 (mttt) cc_final: 0.7272 (mttp) REVERT: I 80 LYS cc_start: 0.8381 (mttm) cc_final: 0.8058 (mttp) REVERT: I 96 LYS cc_start: 0.7154 (mttt) cc_final: 0.6268 (tmtt) REVERT: J 80 LYS cc_start: 0.8355 (mttm) cc_final: 0.7971 (mttp) REVERT: J 96 LYS cc_start: 0.7004 (mttt) cc_final: 0.6273 (tmtt) outliers start: 32 outliers final: 31 residues processed: 152 average time/residue: 0.1373 time to fit residues: 27.3708 Evaluate side-chains 171 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 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 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 55 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 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 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 22 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 22 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 36 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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** ** 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 = 0.4818 r_free = 0.4818 target = 0.219240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.188485 restraints weight = 6173.915| |-----------------------------------------------------------------------------| r_work (start): 0.4548 rms_B_bonded: 4.82 r_work (final): 0.4548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4970 Z= 0.250 Angle : 0.595 5.337 6700 Z= 0.335 Chirality : 0.051 0.124 880 Planarity : 0.002 0.013 830 Dihedral : 6.108 18.831 720 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 6.33 % Allowed : 22.86 % 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: -4.45 (0.21), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.16), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.010 0.002 PHE G 94 TYR 0.012 0.003 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 176 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6348 (tttt) cc_final: 0.6100 (ttpt) REVERT: E 62 GLN cc_start: 0.8806 (mt0) cc_final: 0.8532 (mt0) REVERT: E 80 LYS cc_start: 0.7702 (mttm) cc_final: 0.7298 (mttp) REVERT: F 62 GLN cc_start: 0.8815 (mt0) cc_final: 0.8553 (mt0) REVERT: F 80 LYS cc_start: 0.7730 (mttm) cc_final: 0.7313 (mttp) REVERT: I 80 LYS cc_start: 0.8320 (mttm) cc_final: 0.8045 (mttp) REVERT: I 96 LYS cc_start: 0.7122 (mttt) cc_final: 0.6254 (tmtt) REVERT: J 80 LYS cc_start: 0.8334 (mttm) cc_final: 0.8059 (mttp) REVERT: J 96 LYS cc_start: 0.7007 (mttt) cc_final: 0.6281 (tmtt) outliers start: 31 outliers final: 29 residues processed: 151 average time/residue: 0.1396 time to fit residues: 27.7125 Evaluate side-chains 164 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 22 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 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 55 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 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 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 77 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 overall best weight: 4.5586 ------------------------------------------------------------------------------- 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** ** 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 = 0.4785 r_free = 0.4785 target = 0.215927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.185208 restraints weight = 6260.836| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 4.91 r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4970 Z= 0.300 Angle : 0.607 6.938 6700 Z= 0.343 Chirality : 0.050 0.122 880 Planarity : 0.003 0.011 830 Dihedral : 6.216 20.797 720 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.90 % Favored : 87.10 % Rotamer: Outliers : 6.94 % Allowed : 20.61 % Favored : 72.45 % 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: -4.39 (0.21), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.16), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 50 PHE 0.011 0.003 PHE G 94 TYR 0.015 0.004 TYR B 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 170 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6550 (tttt) cc_final: 0.6309 (ttpt) REVERT: E 80 LYS cc_start: 0.7745 (mttm) cc_final: 0.7337 (mttp) REVERT: F 80 LYS cc_start: 0.7835 (mttm) cc_final: 0.7413 (mttp) REVERT: G 80 LYS cc_start: 0.7845 (mttt) cc_final: 0.7336 (mttp) REVERT: I 96 LYS cc_start: 0.7147 (mttt) cc_final: 0.6289 (tmtt) REVERT: J 80 LYS cc_start: 0.8389 (mttm) cc_final: 0.8086 (mttp) REVERT: J 96 LYS cc_start: 0.7035 (mttt) cc_final: 0.6307 (tmtt) outliers start: 34 outliers final: 32 residues processed: 144 average time/residue: 0.1479 time to fit residues: 27.9073 Evaluate side-chains 165 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 22 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 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 55 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 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 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 45 LYS 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 22 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 54 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4729 r_free = 0.4729 target = 0.210577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.180462 restraints weight = 6322.069| |-----------------------------------------------------------------------------| r_work (start): 0.4461 rms_B_bonded: 4.89 r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4970 Z= 0.409 Angle : 0.673 6.978 6700 Z= 0.381 Chirality : 0.052 0.136 880 Planarity : 0.003 0.012 830 Dihedral : 6.653 21.923 720 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.19 % Favored : 86.81 % Rotamer: Outliers : 8.16 % Allowed : 20.41 % 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: -4.43 (0.21), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.16), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 50 PHE 0.012 0.003 PHE G 94 TYR 0.020 0.005 TYR B 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 177 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6673 (tttt) cc_final: 0.6441 (ttpt) REVERT: E 80 LYS cc_start: 0.7718 (mttm) cc_final: 0.7319 (mttp) REVERT: F 80 LYS cc_start: 0.7792 (mttm) cc_final: 0.7441 (mttp) REVERT: G 80 LYS cc_start: 0.7840 (mttt) cc_final: 0.7353 (mttp) REVERT: I 96 LYS cc_start: 0.7085 (mttt) cc_final: 0.6392 (tmtt) REVERT: J 80 LYS cc_start: 0.8532 (mttm) cc_final: 0.8230 (mttp) REVERT: J 96 LYS cc_start: 0.7006 (mttt) cc_final: 0.6399 (tmtt) outliers start: 40 outliers final: 36 residues processed: 150 average time/residue: 0.1437 time to fit residues: 28.3276 Evaluate side-chains 170 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 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 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 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 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 75 THR 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 45 LYS 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 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 72 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 44 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** G 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 = 0.4727 r_free = 0.4727 target = 0.210121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.180205 restraints weight = 6391.922| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 4.89 r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4970 Z= 0.391 Angle : 0.685 7.326 6700 Z= 0.383 Chirality : 0.052 0.124 880 Planarity : 0.003 0.012 830 Dihedral : 6.550 21.855 720 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.78 % Favored : 85.22 % Rotamer: Outliers : 9.18 % Allowed : 19.18 % 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: -4.47 (0.22), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS H 50 PHE 0.012 0.003 PHE J 94 TYR 0.019 0.005 TYR B 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 173 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 128 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6830 (tttt) cc_final: 0.6625 (ttmt) REVERT: E 80 LYS cc_start: 0.7681 (mttm) cc_final: 0.7172 (mttp) REVERT: F 80 LYS cc_start: 0.7703 (mttm) cc_final: 0.7378 (mttp) REVERT: G 80 LYS cc_start: 0.7907 (mttt) cc_final: 0.7396 (mttp) REVERT: I 96 LYS cc_start: 0.7104 (mttt) cc_final: 0.6413 (tmtt) REVERT: J 80 LYS cc_start: 0.8564 (mttm) cc_final: 0.8262 (mttp) REVERT: J 96 LYS cc_start: 0.7036 (mttt) cc_final: 0.6415 (tmtt) outliers start: 45 outliers final: 42 residues processed: 148 average time/residue: 0.1339 time to fit residues: 26.2158 Evaluate side-chains 168 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 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 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 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 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 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 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 45 LYS 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 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 54 THR Chi-restraints excluded: chain J residue 72 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 42 optimal weight: 30.0000 chunk 51 optimal weight: 7.9990 chunk 7 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.214396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.184163 restraints weight = 6163.846| |-----------------------------------------------------------------------------| r_work (start): 0.4491 rms_B_bonded: 4.74 r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4970 Z= 0.331 Angle : 0.660 9.360 6700 Z= 0.364 Chirality : 0.051 0.146 880 Planarity : 0.003 0.011 830 Dihedral : 6.224 20.448 720 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 8.37 % Allowed : 21.02 % Favored : 70.61 % 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: -4.41 (0.22), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 50 PHE 0.010 0.002 PHE C 94 TYR 0.015 0.004 TYR C 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 166 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6894 (tttt) cc_final: 0.6668 (ttpt) REVERT: E 80 LYS cc_start: 0.7665 (mttm) cc_final: 0.7297 (mttp) REVERT: F 80 LYS cc_start: 0.7736 (mttm) cc_final: 0.7416 (mttp) REVERT: G 80 LYS cc_start: 0.7868 (mttt) cc_final: 0.7331 (mttp) REVERT: I 96 LYS cc_start: 0.7027 (mttt) cc_final: 0.6395 (tmtt) REVERT: J 80 LYS cc_start: 0.8488 (mttm) cc_final: 0.8209 (mttp) REVERT: J 96 LYS cc_start: 0.7113 (mttt) cc_final: 0.6348 (tmtt) outliers start: 41 outliers final: 40 residues processed: 146 average time/residue: 0.1417 time to fit residues: 27.4476 Evaluate side-chains 164 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 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 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 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 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 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 45 LYS 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 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 54 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 24 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 4 optimal weight: 0.0870 chunk 67 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 overall best weight: 5.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.208842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.178830 restraints weight = 6368.442| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 5.02 r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.5222 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= 0.356 Angle : 0.671 8.680 6700 Z= 0.370 Chirality : 0.051 0.187 880 Planarity : 0.003 0.011 830 Dihedral : 6.371 21.765 720 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer: Outliers : 8.78 % Allowed : 21.22 % 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: -4.43 (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 0.001 0.000 HIS C 50 PHE 0.012 0.003 PHE J 94 TYR 0.018 0.004 TYR C 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 171 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.6962 (tttt) cc_final: 0.6728 (ttpt) REVERT: E 80 LYS cc_start: 0.7789 (mttm) cc_final: 0.7428 (mttp) REVERT: F 80 LYS cc_start: 0.7776 (mttm) cc_final: 0.7458 (mttp) REVERT: G 80 LYS cc_start: 0.7946 (mttt) cc_final: 0.7447 (mttp) REVERT: I 96 LYS cc_start: 0.7086 (mttt) cc_final: 0.6441 (tmtt) REVERT: J 80 LYS cc_start: 0.8557 (mttm) cc_final: 0.8252 (mttp) REVERT: J 96 LYS cc_start: 0.7074 (mttt) cc_final: 0.6356 (tmtt) outliers start: 43 outliers final: 42 residues processed: 151 average time/residue: 0.1306 time to fit residues: 26.1729 Evaluate side-chains 170 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 22 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 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 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 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 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 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 45 LYS 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 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 54 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: 9.9990 chunk 49 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 0.0980 chunk 43 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 overall best weight: 7.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.206019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.176551 restraints weight = 6321.496| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 4.87 r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4970 Z= 0.437 Angle : 0.727 8.786 6700 Z= 0.405 Chirality : 0.052 0.212 880 Planarity : 0.003 0.012 830 Dihedral : 6.696 22.878 720 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.20 % Favored : 85.80 % Rotamer: Outliers : 8.57 % Allowed : 21.84 % 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: -4.49 (0.23), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.013 0.003 PHE J 94 TYR 0.021 0.005 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.62 seconds wall clock time: 34 minutes 2.48 seconds (2042.48 seconds total)