Starting phenix.real_space_refine on Thu Mar 6 04:19:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ozg_13123/03_2025/7ozg_13123.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ozg_13123/03_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_13123/03_2025/7ozg_13123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ozg_13123/03_2025/7ozg_13123.map" model { file = "/net/cci-nas-00/data/ceres_data/7ozg_13123/03_2025/7ozg_13123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ozg_13123/03_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-5624/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: 1.77, per 1000 atoms: 0.36 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: 1.26 Conformation dependent library (CDL) restraints added in 664.7 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: 0.75 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 43 removed outlier: 6.360A pdb=" N TYR A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER C 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY A 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR C 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER E 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY C 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR E 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER G 42 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY E 41 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR G 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER I 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY G 41 " --> pdb=" O SER I 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 49 removed outlier: 6.294A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL C 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL E 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL G 48 " --> pdb=" O VAL I 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.864A pdb=" N ASN A 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN C 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN E 65 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN G 65 " --> pdb=" O VAL I 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 70 through 72 Processing sheet with id=AA7, first strand: chain 'A' and resid 78 through 79 removed outlier: 6.078A pdb=" N ALA A 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA C 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA E 78 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ALA G 78 " --> pdb=" O GLN I 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 15 through 18 Processing sheet with id=AA9, first strand: chain 'B' and resid 39 through 43 removed outlier: 6.360A pdb=" N TYR B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER D 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY B 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR D 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER F 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY D 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR F 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER H 42 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY F 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR H 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N SER J 42 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLY H 41 " --> pdb=" O SER J 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.294A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL D 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL F 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL H 48 " --> pdb=" O VAL J 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 52 through 55 Processing sheet with id=AB3, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.864A pdb=" N ASN B 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN D 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN F 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN H 65 " --> pdb=" O VAL J 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 70 through 72 Processing sheet with id=AB5, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.078A pdb=" N ALA B 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA D 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA F 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ALA H 78 " --> pdb=" O GLN J 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 64 hydrogen bonds defined for protein. 192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 1.50 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: 0.05 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: 0.600 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.360 Find NCS groups from input model: 0.120 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.170 ------------------------------------------------------------------------------- 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 : 0.509 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: 0.1866 time to fit residues: 37.7957 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 : 0.485 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.184270 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 : 0.478 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: 0.7784 (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: 0.1559 time to fit residues: 31.8507 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 : 0.534 ------------------------------------------------------------------------------- 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: 10.0000 chunk 13 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 overall best weight: 6.6146 ------------------------------------------------------------------------------- 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 = 0.4776 r_free = 0.4776 target = 0.213338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.182410 restraints weight = 6319.779| |-----------------------------------------------------------------------------| r_work (start): 0.4493 rms_B_bonded: 4.94 r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.3945 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= 0.429 Angle : 0.710 6.038 6700 Z= 0.415 Chirality : 0.053 0.140 880 Planarity : 0.003 0.013 830 Dihedral : 7.474 23.463 720 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 8.37 % Allowed : 20.20 % 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: -4.60 (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 HIS 0.002 0.001 HIS J 50 PHE 0.019 0.003 PHE H 94 TYR 0.022 0.006 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 191 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 80 LYS cc_start: 0.7762 (mttm) cc_final: 0.7384 (mttp) REVERT: I 80 LYS cc_start: 0.8426 (mttm) cc_final: 0.8083 (mttp) REVERT: I 96 LYS cc_start: 0.7060 (mttt) cc_final: 0.6320 (tmtt) REVERT: J 80 LYS cc_start: 0.8456 (mttm) cc_final: 0.8244 (mttp) REVERT: J 96 LYS cc_start: 0.7061 (mttt) cc_final: 0.6342 (tmtt) outliers start: 41 outliers final: 29 residues processed: 162 average time/residue: 0.1382 time to fit residues: 29.2862 Evaluate side-chains 169 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 15 VAL Chi-restraints excluded: chain E residue 22 THR 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 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 J residue 15 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 42 optimal weight: 40.0000 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.4747 r_free = 0.4747 target = 0.211983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.181220 restraints weight = 6367.714| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 4.97 r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4970 Z= 0.371 Angle : 0.673 5.921 6700 Z= 0.389 Chirality : 0.051 0.130 880 Planarity : 0.003 0.013 830 Dihedral : 6.944 20.978 720 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 7.76 % Allowed : 20.82 % 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: -4.62 (0.21), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.16), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 50 PHE 0.018 0.003 PHE D 94 TYR 0.018 0.005 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 176 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.6508 (tttt) cc_final: 0.6306 (ttmt) REVERT: E 80 LYS cc_start: 0.7663 (mttm) cc_final: 0.7300 (mttp) REVERT: F 80 LYS cc_start: 0.7728 (mttm) cc_final: 0.7332 (mttp) REVERT: I 80 LYS cc_start: 0.8395 (mttm) cc_final: 0.8057 (mttp) REVERT: I 96 LYS cc_start: 0.7038 (mttt) cc_final: 0.6254 (tmtt) REVERT: J 80 LYS cc_start: 0.8416 (mttm) cc_final: 0.8078 (mttp) REVERT: J 96 LYS cc_start: 0.7023 (mttt) cc_final: 0.6292 (tmtt) outliers start: 38 outliers final: 37 residues processed: 148 average time/residue: 0.1555 time to fit residues: 30.4094 Evaluate side-chains 171 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 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 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 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 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** ** H 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 = 0.4761 r_free = 0.4761 target = 0.215072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.184806 restraints weight = 6305.279| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 4.74 r_work: 0.4370 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4970 Z= 0.349 Angle : 0.652 5.800 6700 Z= 0.373 Chirality : 0.052 0.128 880 Planarity : 0.003 0.012 830 Dihedral : 6.617 20.983 720 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 9.39 % Allowed : 20.20 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.21), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.16), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.012 0.003 PHE D 94 TYR 0.017 0.004 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 187 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 62 GLN cc_start: 0.8772 (mt0) cc_final: 0.8533 (mt0) REVERT: E 80 LYS cc_start: 0.7631 (mttm) cc_final: 0.7252 (mttp) REVERT: F 80 LYS cc_start: 0.7591 (mttm) cc_final: 0.7225 (mttp) REVERT: G 80 LYS cc_start: 0.7800 (mttt) cc_final: 0.7266 (mttp) REVERT: I 80 LYS cc_start: 0.8343 (mttm) cc_final: 0.8048 (mttp) REVERT: I 96 LYS cc_start: 0.7071 (mttt) cc_final: 0.6262 (tmtt) REVERT: J 80 LYS cc_start: 0.8373 (mttm) cc_final: 0.8027 (mttp) REVERT: J 96 LYS cc_start: 0.7079 (mttt) cc_final: 0.6285 (tmtt) outliers start: 46 outliers final: 40 residues processed: 155 average time/residue: 0.1352 time to fit residues: 27.6517 Evaluate side-chains 175 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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 44 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 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 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 44 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: 10.0000 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 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 = 0.4730 r_free = 0.4730 target = 0.211684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.181208 restraints weight = 6351.991| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 4.89 r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4970 Z= 0.408 Angle : 0.688 6.606 6700 Z= 0.392 Chirality : 0.052 0.124 880 Planarity : 0.003 0.012 830 Dihedral : 6.813 21.612 720 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 9.59 % Allowed : 19.80 % 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: -4.56 (0.21), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.16), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.012 0.003 PHE D 94 TYR 0.019 0.005 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 185 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 138 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 80 LYS cc_start: 0.7729 (mttm) cc_final: 0.7411 (mttp) REVERT: F 80 LYS cc_start: 0.7696 (mttm) cc_final: 0.7362 (mttp) REVERT: I 80 LYS cc_start: 0.8413 (mttm) cc_final: 0.8158 (mttp) REVERT: I 96 LYS cc_start: 0.7148 (mttt) cc_final: 0.6434 (tmtt) REVERT: J 80 LYS cc_start: 0.8598 (mttm) cc_final: 0.8332 (mttp) REVERT: J 96 LYS cc_start: 0.7107 (mttt) cc_final: 0.6453 (tmtt) outliers start: 47 outliers final: 42 residues processed: 157 average time/residue: 0.1338 time to fit residues: 27.8141 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 : 0.538 ------------------------------------------------------------------------------- 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 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 44 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain 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 55 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 30.0000 chunk 52 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.4733 r_free = 0.4733 target = 0.210806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.180724 restraints weight = 6278.104| |-----------------------------------------------------------------------------| r_work (start): 0.4456 rms_B_bonded: 4.91 r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.4896 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= 0.358 Angle : 0.681 7.641 6700 Z= 0.380 Chirality : 0.052 0.135 880 Planarity : 0.003 0.012 830 Dihedral : 6.492 21.056 720 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 8.78 % Allowed : 20.61 % 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: -4.52 (0.22), 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 HIS 0.001 0.000 HIS G 50 PHE 0.011 0.003 PHE D 94 TYR 0.017 0.004 TYR F 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 173 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 43 LYS cc_start: 0.6245 (tttt) cc_final: 0.5994 (ttpt) REVERT: E 62 GLN cc_start: 0.8784 (mt0) cc_final: 0.8574 (mt0) REVERT: E 80 LYS cc_start: 0.7668 (mttm) cc_final: 0.7308 (mttp) REVERT: F 80 LYS cc_start: 0.7668 (mttm) cc_final: 0.7349 (mttp) REVERT: G 80 LYS cc_start: 0.7845 (mttt) cc_final: 0.7321 (mttp) REVERT: I 80 LYS cc_start: 0.8270 (mttm) cc_final: 0.8016 (mttp) REVERT: I 96 LYS cc_start: 0.7111 (mttt) cc_final: 0.6414 (tmtt) REVERT: J 80 LYS cc_start: 0.8564 (mttm) cc_final: 0.8327 (mttp) REVERT: J 96 LYS cc_start: 0.7038 (mttt) cc_final: 0.6413 (tmtt) outliers start: 43 outliers final: 41 residues processed: 148 average time/residue: 0.1703 time to fit residues: 32.8467 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 : 0.701 ------------------------------------------------------------------------------- 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 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 44 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain 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 55 VAL 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 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 21 optimal weight: 20.0000 chunk 13 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4758 r_free = 0.4758 target = 0.213219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.183019 restraints weight = 6202.494| |-----------------------------------------------------------------------------| r_work (start): 0.4487 rms_B_bonded: 4.82 r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4970 Z= 0.320 Angle : 0.656 6.993 6700 Z= 0.363 Chirality : 0.051 0.131 880 Planarity : 0.003 0.011 830 Dihedral : 6.239 20.345 720 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % 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: -4.46 (0.22), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 50 PHE 0.012 0.003 PHE J 94 TYR 0.015 0.004 TYR F 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 176 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 43 LYS cc_start: 0.6376 (tttt) cc_final: 0.6136 (ttpt) REVERT: E 80 LYS cc_start: 0.7769 (mttm) cc_final: 0.7405 (mttp) REVERT: F 80 LYS cc_start: 0.7783 (mttm) cc_final: 0.7471 (mttp) REVERT: G 80 LYS cc_start: 0.7849 (mttt) cc_final: 0.7321 (mttp) REVERT: I 80 LYS cc_start: 0.8261 (mttm) cc_final: 0.8022 (mttp) REVERT: I 96 LYS cc_start: 0.7166 (mttt) cc_final: 0.6446 (tmtt) REVERT: J 80 LYS cc_start: 0.8526 (mttm) cc_final: 0.8233 (mttp) REVERT: J 96 LYS cc_start: 0.7091 (mttt) cc_final: 0.6437 (tmtt) outliers start: 45 outliers final: 43 residues processed: 152 average time/residue: 0.1869 time to fit residues: 36.9123 Evaluate side-chains 172 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 80 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 45 LYS 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 44 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 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 22 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 42 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 7 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 40.0000 chunk 58 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 12 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: ** 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 = 0.4720 r_free = 0.4720 target = 0.210971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.181678 restraints weight = 6292.947| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 4.73 r_work: 0.4375 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4970 Z= 0.390 Angle : 0.691 6.737 6700 Z= 0.385 Chirality : 0.052 0.137 880 Planarity : 0.003 0.012 830 Dihedral : 6.568 21.894 720 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.49 % Favored : 85.51 % Rotamer: Outliers : 10.00 % Allowed : 18.98 % Favored : 71.02 % 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 : -3.43 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 50 PHE 0.013 0.003 PHE D 94 TYR 0.018 0.005 TYR F 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 181 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 80 LYS cc_start: 0.7740 (mttm) cc_final: 0.7305 (mttp) REVERT: G 80 LYS cc_start: 0.7828 (mttt) cc_final: 0.7363 (mttp) REVERT: I 80 LYS cc_start: 0.8334 (mttm) cc_final: 0.8069 (mttp) REVERT: I 96 LYS cc_start: 0.7231 (mttt) cc_final: 0.6458 (tmtt) REVERT: J 80 LYS cc_start: 0.8620 (mttm) cc_final: 0.8340 (mttp) REVERT: J 96 LYS cc_start: 0.7196 (mttt) cc_final: 0.6392 (tmtt) outliers start: 49 outliers final: 46 residues processed: 162 average time/residue: 0.1749 time to fit residues: 37.0313 Evaluate side-chains 175 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 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 45 LYS 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 44 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain 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 22 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 54 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: 9.9990 chunk 11 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4723 r_free = 0.4723 target = 0.211804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.181648 restraints weight = 6305.250| |-----------------------------------------------------------------------------| r_work (start): 0.4490 rms_B_bonded: 5.08 r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.5329 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= 0.272 Angle : 0.654 7.803 6700 Z= 0.355 Chirality : 0.051 0.141 880 Planarity : 0.002 0.015 830 Dihedral : 6.002 19.180 720 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 8.16 % Allowed : 21.43 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (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 HIS 0.001 0.000 HIS J 50 PHE 0.010 0.002 PHE J 94 TYR 0.012 0.003 TYR D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8113 (mttt) REVERT: F 80 LYS cc_start: 0.7656 (mttm) cc_final: 0.7360 (mttp) REVERT: G 80 LYS cc_start: 0.7918 (mttt) cc_final: 0.7371 (mttp) REVERT: I 80 LYS cc_start: 0.8214 (mttm) cc_final: 0.7984 (mttp) REVERT: I 96 LYS cc_start: 0.7046 (mttt) cc_final: 0.6416 (tmtt) REVERT: J 80 LYS cc_start: 0.8476 (mttm) cc_final: 0.8215 (mttp) REVERT: J 96 LYS cc_start: 0.7073 (mttt) cc_final: 0.6376 (tmtt) outliers start: 40 outliers final: 39 residues processed: 153 average time/residue: 0.1653 time to fit residues: 33.3509 Evaluate side-chains 171 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 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 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 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 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 10.0000 chunk 49 optimal weight: 40.0000 chunk 50 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 40.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 = 0.4679 r_free = 0.4679 target = 0.207616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.177419 restraints weight = 6248.749| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 5.01 r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.5291 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= 0.377 Angle : 0.689 7.313 6700 Z= 0.383 Chirality : 0.051 0.124 880 Planarity : 0.003 0.013 830 Dihedral : 6.434 22.295 720 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.93 % Favored : 85.07 % Rotamer: Outliers : 8.57 % Allowed : 20.41 % Favored : 71.02 % 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: -4.44 (0.23), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 50 PHE 0.013 0.003 PHE G 94 TYR 0.018 0.005 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2153.92 seconds wall clock time: 39 minutes 46.34 seconds (2386.34 seconds total)