Starting phenix.real_space_refine on Tue Feb 3 16:12:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ozg_13123/02_2026/7ozg_13123.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ozg_13123/02_2026/7ozg_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_2026/7ozg_13123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ozg_13123/02_2026/7ozg_13123.map" model { file = "/net/cci-nas-00/data/ceres_data/7ozg_13123/02_2026/7ozg_13123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ozg_13123/02_2026/7ozg_13123.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.51, per 1000 atoms: 0.10 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: 0.28 Conformation dependent library (CDL) restraints added in 294.3 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: 0.15 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: 0.46 Time building geometry restraints manager: 0.40 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: 0.01 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.940 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.510 ------------------------------------------------------------------------------- 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= 1.164 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 TYR 0.028 0.012 TYR J 39 PHE 0.012 0.005 PHE B 94 HIS 0.021 0.014 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.02303 ( 4970) covalent geometry : angle 1.82833 ( 6700) hydrogen bonds : bond 0.12819 ( 64) hydrogen bonds : angle 8.95235 ( 192) *********************** 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 : 0.220 Fit side-chains REVERT: A 77 VAL cc_start: 0.8245 (t) cc_final: 0.8013 (p) REVERT: A 96 LYS cc_start: 0.6471 (mttt) cc_final: 0.6150 (tmtt) REVERT: B 96 LYS cc_start: 0.6479 (mttt) cc_final: 0.6148 (tmtt) REVERT: C 96 LYS cc_start: 0.6774 (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: 0.6512 (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: 0.0802 time to fit residues: 16.3482 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 : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.4850 r_free = 0.4850 target = 0.218610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.188517 restraints weight = 6536.260| |-----------------------------------------------------------------------------| r_work (start): 0.4594 rms_B_bonded: 4.87 r_work (final): 0.4594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.3096 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= 0.254 Angle : 0.724 6.263 6700 Z= 0.419 Chirality : 0.055 0.128 880 Planarity : 0.003 0.013 830 Dihedral : 7.931 23.621 720 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.65 % Allowed : 19.18 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.30 (0.22), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.005 TYR H 39 PHE 0.021 0.004 PHE H 94 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 4970) covalent geometry : angle 0.72379 ( 6700) hydrogen bonds : bond 0.03348 ( 64) hydrogen bonds : angle 5.34271 ( 192) *********************** 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 169 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8281 (mttm) cc_final: 0.8041 (mttp) REVERT: C 80 LYS cc_start: 0.8036 (mptt) cc_final: 0.7761 (mptt) REVERT: D 80 LYS cc_start: 0.8050 (mptt) cc_final: 0.7758 (mptt) REVERT: E 80 LYS cc_start: 0.7664 (mttm) cc_final: 0.7289 (mttp) REVERT: F 80 LYS cc_start: 0.7658 (mttm) cc_final: 0.7203 (mttp) REVERT: G 96 LYS cc_start: 0.5357 (mttt) cc_final: 0.5125 (tmtt) REVERT: H 96 LYS cc_start: 0.5402 (mttt) cc_final: 0.5176 (tmtt) REVERT: I 80 LYS cc_start: 0.8505 (mttm) cc_final: 0.8104 (mttp) REVERT: I 96 LYS cc_start: 0.6656 (mttt) cc_final: 0.6255 (tmtt) REVERT: J 80 LYS cc_start: 0.8506 (mttm) cc_final: 0.8104 (mttp) REVERT: J 96 LYS cc_start: 0.6636 (mttt) cc_final: 0.6253 (tmtt) outliers start: 13 outliers final: 13 residues processed: 156 average time/residue: 0.0637 time to fit residues: 12.9555 Evaluate side-chains 164 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 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 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 8 optimal weight: 9.9990 chunk 49 optimal weight: 40.0000 chunk 34 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 38 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: ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.215762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.185279 restraints weight = 6263.265| |-----------------------------------------------------------------------------| r_work (start): 0.4535 rms_B_bonded: 4.90 r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4970 Z= 0.290 Angle : 0.683 5.862 6700 Z= 0.396 Chirality : 0.052 0.148 880 Planarity : 0.003 0.013 830 Dihedral : 7.314 23.335 720 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.50 (0.22), 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 TYR 0.020 0.005 TYR D 39 PHE 0.019 0.004 PHE D 94 HIS 0.002 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 4970) covalent geometry : angle 0.68254 ( 6700) hydrogen bonds : bond 0.02300 ( 64) hydrogen bonds : angle 5.35406 ( 192) *********************** 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: 34 poor density : 155 time to evaluate : 0.180 Fit side-chains REVERT: C 80 LYS cc_start: 0.8140 (mptt) cc_final: 0.7680 (mptt) REVERT: D 80 LYS cc_start: 0.8154 (mptt) cc_final: 0.7724 (mptt) REVERT: G 96 LYS cc_start: 0.5923 (mttt) cc_final: 0.5463 (tptm) REVERT: H 96 LYS cc_start: 0.5829 (mttt) cc_final: 0.5433 (tptm) REVERT: I 80 LYS cc_start: 0.8487 (mttm) cc_final: 0.8172 (mttp) REVERT: I 96 LYS cc_start: 0.6896 (mttt) cc_final: 0.6314 (tmtt) REVERT: J 80 LYS cc_start: 0.8488 (mttm) cc_final: 0.8199 (mttp) REVERT: J 96 LYS cc_start: 0.6895 (mttt) cc_final: 0.6330 (tmtt) outliers start: 34 outliers final: 25 residues processed: 165 average time/residue: 0.0587 time to fit residues: 12.8762 Evaluate side-chains 169 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 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 22 THR 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 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 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 28 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.4761 r_free = 0.4761 target = 0.214545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.184701 restraints weight = 6289.339| |-----------------------------------------------------------------------------| r_work (start): 0.4494 rms_B_bonded: 4.75 r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.4151 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= 0.277 Angle : 0.670 5.846 6700 Z= 0.387 Chirality : 0.051 0.123 880 Planarity : 0.003 0.014 830 Dihedral : 6.959 21.584 720 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 6.12 % Allowed : 21.22 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.60 (0.21), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.16), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.005 TYR D 39 PHE 0.017 0.003 PHE D 94 HIS 0.002 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 4970) covalent geometry : angle 0.67001 ( 6700) hydrogen bonds : bond 0.02466 ( 64) hydrogen bonds : angle 5.40513 ( 192) *********************** 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 176 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 96 LYS cc_start: 0.5957 (mttt) cc_final: 0.5568 (tptm) REVERT: H 96 LYS cc_start: 0.5964 (mttt) cc_final: 0.5562 (tptm) REVERT: I 80 LYS cc_start: 0.8510 (mttm) cc_final: 0.8229 (mttp) REVERT: I 96 LYS cc_start: 0.7078 (mttt) cc_final: 0.6281 (tmtt) REVERT: J 80 LYS cc_start: 0.8466 (mttm) cc_final: 0.8166 (mttp) REVERT: J 96 LYS cc_start: 0.7015 (mttt) cc_final: 0.6301 (tmtt) outliers start: 30 outliers final: 28 residues processed: 152 average time/residue: 0.0684 time to fit residues: 13.6563 Evaluate side-chains 170 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 72 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 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 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 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 65 optimal weight: 5.9990 chunk 49 optimal weight: 30.0000 chunk 20 optimal weight: 0.0020 chunk 30 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 overall best weight: 5.5996 ------------------------------------------------------------------------------- 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 = 0.4771 r_free = 0.4771 target = 0.215163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.185398 restraints weight = 6302.033| |-----------------------------------------------------------------------------| r_work (start): 0.4499 rms_B_bonded: 4.73 r_work: 0.4378 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4970 Z= 0.261 Angle : 0.657 5.836 6700 Z= 0.377 Chirality : 0.051 0.125 880 Planarity : 0.003 0.014 830 Dihedral : 6.655 21.263 720 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 7.96 % Allowed : 18.98 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.21), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.16), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR D 39 PHE 0.013 0.003 PHE D 94 HIS 0.001 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 4970) covalent geometry : angle 0.65740 ( 6700) hydrogen bonds : bond 0.02335 ( 64) hydrogen bonds : angle 5.29791 ( 192) *********************** 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 181 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.6142 (tttt) cc_final: 0.5926 (ttpt) REVERT: E 62 GLN cc_start: 0.8806 (mt0) cc_final: 0.8582 (mt0) REVERT: E 80 LYS cc_start: 0.7624 (mttm) cc_final: 0.7210 (mttp) REVERT: F 80 LYS cc_start: 0.7670 (mttm) cc_final: 0.7291 (mttp) REVERT: G 80 LYS cc_start: 0.7825 (mttt) cc_final: 0.7309 (mttp) REVERT: G 96 LYS cc_start: 0.5927 (mttt) cc_final: 0.5557 (tptm) REVERT: H 96 LYS cc_start: 0.5738 (mttt) cc_final: 0.5522 (tptm) REVERT: I 80 LYS cc_start: 0.8526 (mttm) cc_final: 0.8307 (mttp) REVERT: I 96 LYS cc_start: 0.6992 (mttt) cc_final: 0.6275 (tmtt) REVERT: J 80 LYS cc_start: 0.8564 (mttm) cc_final: 0.8264 (mttp) REVERT: J 96 LYS cc_start: 0.7040 (mttt) cc_final: 0.6309 (tmtt) outliers start: 39 outliers final: 34 residues processed: 153 average time/residue: 0.0672 time to fit residues: 13.5592 Evaluate side-chains 175 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 72 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 77 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 20 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 40.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 = 0.4771 r_free = 0.4771 target = 0.214613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.184423 restraints weight = 6390.892| |-----------------------------------------------------------------------------| 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: 0.6707 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4970 Z= 0.219 Angle : 0.625 6.101 6700 Z= 0.352 Chirality : 0.051 0.146 880 Planarity : 0.003 0.012 830 Dihedral : 6.227 19.288 720 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 8.16 % Allowed : 19.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.40 (0.22), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.004 TYR D 39 PHE 0.012 0.002 PHE D 94 HIS 0.001 0.000 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 4970) covalent geometry : angle 0.62519 ( 6700) hydrogen bonds : bond 0.02122 ( 64) hydrogen bonds : angle 5.07795 ( 192) *********************** 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 182 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 43 LYS cc_start: 0.6119 (tttt) cc_final: 0.5906 (ttpt) REVERT: E 80 LYS cc_start: 0.7642 (mttm) cc_final: 0.7267 (mttp) REVERT: F 62 GLN cc_start: 0.8818 (mt0) cc_final: 0.8556 (mt0) REVERT: F 80 LYS cc_start: 0.7787 (mttm) cc_final: 0.7425 (mttp) REVERT: G 80 LYS cc_start: 0.7802 (mttt) cc_final: 0.7254 (mttp) REVERT: G 96 LYS cc_start: 0.5790 (mttt) cc_final: 0.5557 (tptm) REVERT: H 96 LYS cc_start: 0.5566 (mttt) cc_final: 0.5281 (tptm) REVERT: I 80 LYS cc_start: 0.8492 (mttm) cc_final: 0.8288 (mttp) REVERT: I 96 LYS cc_start: 0.6898 (mttt) cc_final: 0.6267 (tmtt) REVERT: J 80 LYS cc_start: 0.8457 (mttm) cc_final: 0.8224 (mttp) REVERT: J 96 LYS cc_start: 0.6895 (mttt) cc_final: 0.6258 (tmtt) outliers start: 40 outliers final: 36 residues processed: 155 average time/residue: 0.0682 time to fit residues: 13.8145 Evaluate side-chains 172 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 72 THR Chi-restraints excluded: chain B residue 75 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 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 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 I residue 75 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 7 optimal weight: 30.0000 chunk 22 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 67 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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 = 0.4756 r_free = 0.4756 target = 0.212943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.183296 restraints weight = 6382.564| |-----------------------------------------------------------------------------| r_work (start): 0.4501 rms_B_bonded: 4.91 r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4970 Z= 0.242 Angle : 0.638 6.688 6700 Z= 0.359 Chirality : 0.051 0.158 880 Planarity : 0.003 0.011 830 Dihedral : 6.313 20.372 720 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 8.37 % Allowed : 19.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.40 (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 TYR 0.017 0.004 TYR F 39 PHE 0.012 0.003 PHE J 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 4970) covalent geometry : angle 0.63789 ( 6700) hydrogen bonds : bond 0.02143 ( 64) hydrogen bonds : angle 5.12660 ( 192) *********************** 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 176 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 43 LYS cc_start: 0.6171 (tttt) cc_final: 0.5959 (ttpt) REVERT: E 80 LYS cc_start: 0.7676 (mttm) cc_final: 0.7308 (mttp) REVERT: F 80 LYS cc_start: 0.7763 (mttm) cc_final: 0.7416 (mttp) REVERT: G 80 LYS cc_start: 0.7826 (mttt) cc_final: 0.7304 (mttp) REVERT: G 96 LYS cc_start: 0.5825 (mttt) cc_final: 0.5560 (tptm) REVERT: H 96 LYS cc_start: 0.5671 (mttt) cc_final: 0.5349 (tptm) REVERT: I 96 LYS cc_start: 0.6931 (mttt) cc_final: 0.6283 (tmtt) REVERT: J 80 LYS cc_start: 0.8471 (mttm) cc_final: 0.8205 (mttp) REVERT: J 96 LYS cc_start: 0.6875 (mttt) cc_final: 0.6278 (tmtt) outliers start: 41 outliers final: 38 residues processed: 152 average time/residue: 0.0445 time to fit residues: 9.1000 Evaluate side-chains 174 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 72 THR Chi-restraints excluded: chain B residue 75 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 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 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 22 THR 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 51 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.4789 r_free = 0.4789 target = 0.215553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.185911 restraints weight = 6385.350| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 4.88 r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4970 Z= 0.197 Angle : 0.625 8.131 6700 Z= 0.340 Chirality : 0.051 0.133 880 Planarity : 0.002 0.011 830 Dihedral : 5.896 18.950 720 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 7.55 % Allowed : 20.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.33 (0.22), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR F 39 PHE 0.009 0.002 PHE D 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 4970) covalent geometry : angle 0.62458 ( 6700) hydrogen bonds : bond 0.01910 ( 64) hydrogen bonds : angle 4.84911 ( 192) *********************** 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 172 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 80 LYS cc_start: 0.7641 (mttm) cc_final: 0.7286 (mttp) REVERT: F 80 LYS cc_start: 0.7788 (mttm) cc_final: 0.7417 (mttp) REVERT: G 80 LYS cc_start: 0.7784 (mttt) cc_final: 0.7261 (mttp) REVERT: G 96 LYS cc_start: 0.5767 (mttt) cc_final: 0.5398 (tptm) REVERT: H 96 LYS cc_start: 0.5630 (mttt) cc_final: 0.5249 (tptm) REVERT: I 96 LYS cc_start: 0.6917 (mttt) cc_final: 0.6391 (tmtt) REVERT: J 96 LYS cc_start: 0.6837 (mttt) cc_final: 0.6306 (tmtt) outliers start: 37 outliers final: 34 residues processed: 151 average time/residue: 0.0616 time to fit residues: 12.3481 Evaluate side-chains 165 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 72 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 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 22 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 22 THR Chi-restraints excluded: chain I residue 54 THR 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 26 optimal weight: 9.9990 chunk 49 optimal weight: 40.0000 chunk 44 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.209205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.179709 restraints weight = 6461.369| |-----------------------------------------------------------------------------| r_work (start): 0.4459 rms_B_bonded: 4.93 r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4970 Z= 0.306 Angle : 0.697 6.655 6700 Z= 0.391 Chirality : 0.052 0.176 880 Planarity : 0.003 0.011 830 Dihedral : 6.624 22.572 720 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.93 % Favored : 85.07 % Rotamer: Outliers : 8.57 % Allowed : 18.78 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.44 (0.22), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.005 TYR F 39 PHE 0.014 0.003 PHE G 94 HIS 0.001 0.000 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00609 ( 4970) covalent geometry : angle 0.69698 ( 6700) hydrogen bonds : bond 0.02413 ( 64) hydrogen bonds : angle 5.38831 ( 192) *********************** 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 178 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 80 LYS cc_start: 0.7759 (mttm) cc_final: 0.7256 (mttp) REVERT: F 80 LYS cc_start: 0.7839 (mttm) cc_final: 0.7413 (mttp) REVERT: G 80 LYS cc_start: 0.7866 (mttt) cc_final: 0.7410 (mttp) REVERT: G 96 LYS cc_start: 0.6119 (mttt) cc_final: 0.5720 (tptm) REVERT: H 96 LYS cc_start: 0.6023 (mttt) cc_final: 0.5559 (tptm) REVERT: I 96 LYS cc_start: 0.7038 (mttt) cc_final: 0.6448 (tmtt) REVERT: J 96 LYS cc_start: 0.6948 (mttt) cc_final: 0.6379 (tmtt) outliers start: 42 outliers final: 39 residues processed: 158 average time/residue: 0.0669 time to fit residues: 13.9273 Evaluate side-chains 174 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 72 THR Chi-restraints excluded: chain B residue 75 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 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 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 22 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR 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 45 optimal weight: 6.9990 chunk 35 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.213554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.184464 restraints weight = 6355.046| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 4.73 r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 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 0.036 4970 Z= 0.239 Angle : 0.675 7.484 6700 Z= 0.370 Chirality : 0.051 0.164 880 Planarity : 0.003 0.012 830 Dihedral : 6.196 20.351 720 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 8.37 % Allowed : 18.16 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 TYR 0.015 0.004 TYR F 39 PHE 0.010 0.002 PHE J 94 HIS 0.001 0.000 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 4970) covalent geometry : angle 0.67506 ( 6700) hydrogen bonds : bond 0.01983 ( 64) hydrogen bonds : angle 5.11235 ( 192) ********************** 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: 41 poor density : 130 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 80 LYS cc_start: 0.7684 (mttm) cc_final: 0.7337 (mttp) REVERT: F 80 LYS cc_start: 0.7793 (mttm) cc_final: 0.7486 (mttp) REVERT: G 80 LYS cc_start: 0.7869 (mttt) cc_final: 0.7367 (mttp) REVERT: G 96 LYS cc_start: 0.6160 (mttt) cc_final: 0.5659 (tptm) REVERT: H 96 LYS cc_start: 0.6033 (mttt) cc_final: 0.5569 (tptm) REVERT: I 96 LYS cc_start: 0.6960 (mttt) cc_final: 0.6455 (tmtt) REVERT: J 96 LYS cc_start: 0.6961 (mttt) cc_final: 0.6335 (tmtt) outliers start: 41 outliers final: 41 residues processed: 153 average time/residue: 0.0531 time to fit residues: 10.8550 Evaluate side-chains 170 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 22 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 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 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 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 22 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR 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 57 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 30.0000 chunk 58 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** F 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 = 0.4735 r_free = 0.4735 target = 0.210783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.181519 restraints weight = 6398.022| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 4.87 r_work (final): 0.4474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4970 Z= 0.256 Angle : 0.683 7.355 6700 Z= 0.376 Chirality : 0.051 0.168 880 Planarity : 0.003 0.012 830 Dihedral : 6.350 21.346 720 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.91 % Favored : 86.09 % Rotamer: Outliers : 8.98 % Allowed : 18.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.44 (0.23), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR E 39 PHE 0.011 0.003 PHE G 94 HIS 0.001 0.000 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 4970) covalent geometry : angle 0.68296 ( 6700) hydrogen bonds : bond 0.02185 ( 64) hydrogen bonds : angle 5.16669 ( 192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 981.32 seconds wall clock time: 17 minutes 48.51 seconds (1068.51 seconds total)