Starting phenix.real_space_refine on Fri Dec 27 12:49:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ozg_13123/12_2024/7ozg_13123.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ozg_13123/12_2024/7ozg_13123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ozg_13123/12_2024/7ozg_13123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ozg_13123/12_2024/7ozg_13123.map" model { file = "/net/cci-nas-00/data/ceres_data/7ozg_13123/12_2024/7ozg_13123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ozg_13123/12_2024/7ozg_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-5532/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: 1.92, per 1000 atoms: 0.39 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: 1.16 Conformation dependent library (CDL) restraints added in 651.2 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: 0.80 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: 1.21 Time building geometry restraints manager: 1.35 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: 0.00 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.260 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- 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 : 0.525 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: 0.1855 time to fit residues: 37.4851 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 : 0.481 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 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 : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.6675 (mttt) cc_final: 0.6366 (tptm) REVERT: B 96 LYS cc_start: 0.6608 (mttt) cc_final: 0.6299 (tptm) REVERT: C 96 LYS cc_start: 0.6322 (mttt) cc_final: 0.5908 (tmtt) REVERT: D 96 LYS cc_start: 0.6336 (mttt) cc_final: 0.5913 (tmtt) REVERT: E 80 LYS cc_start: 0.8386 (mttm) cc_final: 0.8027 (mttp) REVERT: E 96 LYS cc_start: 0.6766 (mttt) cc_final: 0.6240 (tmtt) REVERT: F 80 LYS cc_start: 0.8379 (mttm) cc_final: 0.8015 (mttp) REVERT: F 96 LYS cc_start: 0.6766 (mttt) cc_final: 0.6260 (tmtt) REVERT: G 96 LYS cc_start: 0.6613 (mttt) cc_final: 0.6074 (tptm) REVERT: H 96 LYS cc_start: 0.6568 (mttt) cc_final: 0.6074 (tmtt) REVERT: I 80 LYS cc_start: 0.8650 (mttm) cc_final: 0.8390 (mttp) REVERT: I 96 LYS cc_start: 0.6952 (mttt) cc_final: 0.6528 (tmtt) REVERT: J 80 LYS cc_start: 0.8646 (mttm) cc_final: 0.8376 (mttp) REVERT: J 96 LYS cc_start: 0.6988 (mttt) cc_final: 0.6559 (tmtt) outliers start: 16 outliers final: 15 residues processed: 159 average time/residue: 0.1563 time to fit residues: 31.9977 Evaluate side-chains 170 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 35 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 30.0000 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3664 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= 0.441 Angle : 0.719 6.150 6700 Z= 0.418 Chirality : 0.053 0.149 880 Planarity : 0.003 0.013 830 Dihedral : 7.494 23.653 720 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 8.98 % Allowed : 18.57 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (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 0.019 0.004 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 201 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.525 Fit side-chains REVERT: A 96 LYS cc_start: 0.7057 (mttt) cc_final: 0.6370 (tmtt) REVERT: B 96 LYS cc_start: 0.7035 (mttt) cc_final: 0.6345 (tmtt) REVERT: C 96 LYS cc_start: 0.6645 (mttt) cc_final: 0.6123 (tmtt) REVERT: D 96 LYS cc_start: 0.6808 (mttt) cc_final: 0.6185 (tmtt) REVERT: E 96 LYS cc_start: 0.6949 (mttt) cc_final: 0.6141 (tmtt) REVERT: F 80 LYS cc_start: 0.8407 (mttm) cc_final: 0.8105 (mttp) REVERT: F 96 LYS cc_start: 0.6926 (mttt) cc_final: 0.6204 (tmtt) REVERT: G 96 LYS cc_start: 0.7084 (mttt) cc_final: 0.6308 (tptm) REVERT: H 96 LYS cc_start: 0.6995 (mttt) cc_final: 0.6282 (tptm) REVERT: I 96 LYS cc_start: 0.7381 (mttt) cc_final: 0.6715 (tmtt) REVERT: J 96 LYS cc_start: 0.7373 (mttt) cc_final: 0.6676 (tmtt) outliers start: 44 outliers final: 31 residues processed: 169 average time/residue: 0.1660 time to fit residues: 35.5543 Evaluate side-chains 179 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 E residue 55 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 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 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 47 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4050 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= 0.424 Angle : 0.708 6.110 6700 Z= 0.410 Chirality : 0.052 0.134 880 Planarity : 0.003 0.013 830 Dihedral : 7.164 21.912 720 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer: Outliers : 8.37 % Allowed : 18.78 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.71 (0.20), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (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 D 94 TYR 0.021 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 188 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.546 Fit side-chains REVERT: A 96 LYS cc_start: 0.7060 (mttt) cc_final: 0.6318 (tmtt) REVERT: B 96 LYS cc_start: 0.6983 (mttt) cc_final: 0.6254 (tmtt) REVERT: C 96 LYS cc_start: 0.6830 (mttt) cc_final: 0.6094 (tptt) REVERT: D 96 LYS cc_start: 0.6844 (mttt) cc_final: 0.6114 (tmtt) REVERT: E 96 LYS cc_start: 0.7044 (mttt) cc_final: 0.6136 (tmtt) REVERT: F 80 LYS cc_start: 0.8336 (mttm) cc_final: 0.8043 (mttp) REVERT: F 96 LYS cc_start: 0.7046 (mttt) cc_final: 0.6143 (tmtt) REVERT: G 96 LYS cc_start: 0.7133 (mttt) cc_final: 0.6451 (tptm) REVERT: H 80 LYS cc_start: 0.8390 (mttt) cc_final: 0.7996 (mttp) REVERT: H 96 LYS cc_start: 0.7048 (mttt) cc_final: 0.6406 (tptm) REVERT: I 96 LYS cc_start: 0.7410 (mttt) cc_final: 0.6663 (tmtt) REVERT: J 96 LYS cc_start: 0.7346 (mttt) cc_final: 0.6647 (tmtt) outliers start: 41 outliers final: 36 residues processed: 158 average time/residue: 0.1794 time to fit residues: 35.8702 Evaluate side-chains 177 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 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 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 30.0000 chunk 50 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.4317 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= 0.329 Angle : 0.654 5.711 6700 Z= 0.371 Chirality : 0.052 0.127 880 Planarity : 0.003 0.015 830 Dihedral : 6.528 20.239 720 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 8.16 % Allowed : 20.61 % Favored : 71.22 % 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: -4.57 (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 B 50 PHE 0.013 0.003 PHE D 94 TYR 0.015 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: 40 poor density : 147 time to evaluate : 0.525 Fit side-chains REVERT: A 96 LYS cc_start: 0.7049 (mttt) cc_final: 0.6314 (tmtt) REVERT: B 96 LYS cc_start: 0.7064 (mttt) cc_final: 0.6354 (tmtt) REVERT: C 96 LYS cc_start: 0.6843 (mttt) cc_final: 0.6064 (tptt) REVERT: D 96 LYS cc_start: 0.6859 (mttt) cc_final: 0.6137 (tmtt) REVERT: E 80 LYS cc_start: 0.8161 (mttm) cc_final: 0.7917 (mttp) REVERT: E 96 LYS cc_start: 0.6964 (mttt) cc_final: 0.6124 (tmtt) REVERT: F 80 LYS cc_start: 0.8254 (mttm) cc_final: 0.7991 (mttp) REVERT: F 96 LYS cc_start: 0.7082 (mttt) cc_final: 0.6166 (tmtt) REVERT: G 80 LYS cc_start: 0.8303 (mttt) cc_final: 0.7939 (mttp) REVERT: G 96 LYS cc_start: 0.7106 (mttt) cc_final: 0.6431 (tptm) REVERT: H 96 LYS cc_start: 0.6816 (mttt) cc_final: 0.6297 (tptm) REVERT: I 96 LYS cc_start: 0.7381 (mttt) cc_final: 0.6620 (tmtt) REVERT: J 96 LYS cc_start: 0.7347 (mttt) cc_final: 0.6616 (tmtt) outliers start: 40 outliers final: 34 residues processed: 159 average time/residue: 0.1587 time to fit residues: 32.0552 Evaluate side-chains 177 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain 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 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 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 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 J residue 15 VAL 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 16 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 7 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4519 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= 0.356 Angle : 0.665 6.111 6700 Z= 0.377 Chirality : 0.052 0.127 880 Planarity : 0.003 0.012 830 Dihedral : 6.538 21.038 720 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % 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 (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: -4.51 (0.21), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.16), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 50 PHE 0.013 0.003 PHE D 94 TYR 0.016 0.004 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.534 Fit side-chains REVERT: A 96 LYS cc_start: 0.7014 (mttt) cc_final: 0.6329 (tmtt) REVERT: B 96 LYS cc_start: 0.7016 (mttt) cc_final: 0.6303 (tmtt) REVERT: C 96 LYS cc_start: 0.6981 (mttt) cc_final: 0.6168 (tptt) REVERT: D 43 LYS cc_start: 0.7037 (tttt) cc_final: 0.6785 (ttpt) REVERT: D 96 LYS cc_start: 0.7142 (mttt) cc_final: 0.6172 (tptt) REVERT: E 80 LYS cc_start: 0.8261 (mttm) cc_final: 0.8024 (mttp) REVERT: E 96 LYS cc_start: 0.7132 (mttt) cc_final: 0.6232 (tmtt) REVERT: F 80 LYS cc_start: 0.8245 (mttm) cc_final: 0.7999 (mttp) REVERT: F 96 LYS cc_start: 0.7133 (mttt) cc_final: 0.6400 (tmtt) REVERT: G 80 LYS cc_start: 0.8307 (mttt) cc_final: 0.7942 (mttp) REVERT: G 96 LYS cc_start: 0.6961 (mttt) cc_final: 0.6417 (tptm) REVERT: H 96 LYS cc_start: 0.6838 (mttt) cc_final: 0.6333 (tptm) REVERT: I 96 LYS cc_start: 0.7433 (mttt) cc_final: 0.6666 (tmtt) REVERT: J 96 LYS cc_start: 0.7422 (mttt) cc_final: 0.6695 (tmtt) outliers start: 44 outliers final: 40 residues processed: 163 average time/residue: 0.1732 time to fit residues: 35.6863 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 : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 41 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 30.0000 chunk 13 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4970 Z= 0.259 Angle : 0.624 7.167 6700 Z= 0.344 Chirality : 0.051 0.130 880 Planarity : 0.002 0.011 830 Dihedral : 5.940 19.157 720 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 7.14 % Allowed : 21.02 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (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 0.011 0.002 PHE D 94 TYR 0.012 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.606 Fit side-chains REVERT: A 96 LYS cc_start: 0.6965 (mttt) cc_final: 0.6348 (tmtt) REVERT: B 96 LYS cc_start: 0.6944 (mttt) cc_final: 0.6314 (tmtt) REVERT: C 96 LYS cc_start: 0.7115 (mttt) cc_final: 0.6362 (tmtt) REVERT: D 43 LYS cc_start: 0.7014 (tttt) cc_final: 0.6800 (ttpt) REVERT: D 96 LYS cc_start: 0.7179 (mttt) cc_final: 0.6365 (tmtt) REVERT: E 80 LYS cc_start: 0.8126 (mttm) cc_final: 0.7906 (mttp) REVERT: E 96 LYS cc_start: 0.7051 (mttt) cc_final: 0.6367 (tmtt) REVERT: F 80 LYS cc_start: 0.8156 (mttm) cc_final: 0.7906 (mttp) REVERT: F 96 LYS cc_start: 0.7122 (mttt) cc_final: 0.6387 (tmtt) REVERT: G 80 LYS cc_start: 0.8235 (mttt) cc_final: 0.7862 (mttp) REVERT: G 96 LYS cc_start: 0.6942 (mttt) cc_final: 0.6314 (tptm) REVERT: H 96 LYS cc_start: 0.6843 (mttt) cc_final: 0.6225 (tptm) REVERT: I 96 LYS cc_start: 0.7331 (mttt) cc_final: 0.6710 (tmtt) REVERT: J 96 LYS cc_start: 0.7359 (mttt) cc_final: 0.6666 (tmtt) outliers start: 35 outliers final: 33 residues processed: 151 average time/residue: 0.1693 time to fit residues: 32.3841 Evaluate side-chains 169 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain 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 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 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.4801 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= 0.312 Angle : 0.634 6.433 6700 Z= 0.353 Chirality : 0.051 0.128 880 Planarity : 0.003 0.011 830 Dihedral : 6.131 20.649 720 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 8.57 % Allowed : 18.98 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.22), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.012 0.003 PHE D 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 179 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.536 Fit side-chains REVERT: A 96 LYS cc_start: 0.6918 (mttt) cc_final: 0.6310 (tmtt) REVERT: B 96 LYS cc_start: 0.6968 (mttt) cc_final: 0.6275 (tmtt) REVERT: C 96 LYS cc_start: 0.7175 (mttt) cc_final: 0.6253 (tptt) REVERT: D 43 LYS cc_start: 0.6925 (tttt) cc_final: 0.6704 (ttpt) REVERT: D 96 LYS cc_start: 0.7211 (mttt) cc_final: 0.6269 (tptt) REVERT: E 80 LYS cc_start: 0.8212 (mttm) cc_final: 0.7993 (mttp) REVERT: E 96 LYS cc_start: 0.7140 (mttt) cc_final: 0.6349 (tmtt) REVERT: F 80 LYS cc_start: 0.8225 (mttm) cc_final: 0.7996 (mttp) REVERT: F 96 LYS cc_start: 0.7222 (mttt) cc_final: 0.6374 (tmtt) REVERT: G 80 LYS cc_start: 0.8275 (mttt) cc_final: 0.7910 (mttp) REVERT: G 96 LYS cc_start: 0.6945 (mttt) cc_final: 0.6323 (tptm) REVERT: H 96 LYS cc_start: 0.6888 (mttt) cc_final: 0.6232 (tptm) REVERT: I 96 LYS cc_start: 0.7412 (mttt) cc_final: 0.6749 (tmtt) REVERT: J 96 LYS cc_start: 0.7332 (mttt) cc_final: 0.6695 (tmtt) outliers start: 42 outliers final: 40 residues processed: 159 average time/residue: 0.1627 time to fit residues: 32.8973 Evaluate side-chains 176 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 22 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 10.0000 chunk 49 optimal weight: 30.0000 chunk 19 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4970 Z= 0.277 Angle : 0.635 7.013 6700 Z= 0.347 Chirality : 0.051 0.133 880 Planarity : 0.002 0.011 830 Dihedral : 5.850 19.532 720 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 8.37 % Allowed : 19.80 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (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 0.001 0.000 HIS J 50 PHE 0.010 0.002 PHE D 94 TYR 0.012 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.532 Fit side-chains REVERT: A 96 LYS cc_start: 0.6996 (mttt) cc_final: 0.6356 (tmtt) REVERT: B 96 LYS cc_start: 0.6972 (mttt) cc_final: 0.6282 (tmtt) REVERT: C 96 LYS cc_start: 0.7157 (mttt) cc_final: 0.6248 (tptt) REVERT: D 43 LYS cc_start: 0.6930 (tttt) cc_final: 0.6715 (ttpt) REVERT: D 96 LYS cc_start: 0.7199 (mttt) cc_final: 0.6308 (tptt) REVERT: E 80 LYS cc_start: 0.8277 (mttm) cc_final: 0.7997 (mttp) REVERT: E 96 LYS cc_start: 0.7203 (mttt) cc_final: 0.6433 (tmtt) REVERT: F 80 LYS cc_start: 0.8234 (mttm) cc_final: 0.7996 (mttp) REVERT: F 96 LYS cc_start: 0.7223 (mttt) cc_final: 0.6350 (tmtt) REVERT: G 80 LYS cc_start: 0.8302 (mttt) cc_final: 0.7938 (mttp) REVERT: G 96 LYS cc_start: 0.6940 (mttt) cc_final: 0.6302 (tptm) REVERT: H 96 LYS cc_start: 0.6893 (mttt) cc_final: 0.6243 (tptm) REVERT: I 96 LYS cc_start: 0.7356 (mttt) cc_final: 0.6707 (tmtt) REVERT: J 96 LYS cc_start: 0.7307 (mttt) cc_final: 0.6580 (tmtt) outliers start: 41 outliers final: 41 residues processed: 158 average time/residue: 0.1658 time to fit residues: 33.2652 Evaluate side-chains 174 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 22 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain 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 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 69 optimal weight: 20.0000 chunk 64 optimal weight: 0.0060 chunk 55 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 40.0000 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4970 Z= 0.281 Angle : 0.634 7.001 6700 Z= 0.346 Chirality : 0.051 0.166 880 Planarity : 0.002 0.011 830 Dihedral : 5.838 20.088 720 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer: Outliers : 9.39 % Allowed : 18.98 % 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: -4.34 (0.22), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.17), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 50 PHE 0.011 0.003 PHE D 94 TYR 0.013 0.003 TYR F 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 182 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.789 Fit side-chains REVERT: A 96 LYS cc_start: 0.7077 (mttt) cc_final: 0.6481 (tmtt) REVERT: B 96 LYS cc_start: 0.7137 (mttt) cc_final: 0.6411 (tmtt) REVERT: C 96 LYS cc_start: 0.7163 (mttt) cc_final: 0.6245 (tptt) REVERT: D 43 LYS cc_start: 0.6951 (tttt) cc_final: 0.6727 (ttpt) REVERT: D 96 LYS cc_start: 0.7212 (mttt) cc_final: 0.6305 (tptt) REVERT: E 80 LYS cc_start: 0.8256 (mttm) cc_final: 0.7992 (mttp) REVERT: E 96 LYS cc_start: 0.7185 (mttt) cc_final: 0.6430 (tmtt) REVERT: F 80 LYS cc_start: 0.8240 (mttm) cc_final: 0.8003 (mttp) REVERT: F 96 LYS cc_start: 0.7215 (mttt) cc_final: 0.6344 (tmtt) REVERT: G 80 LYS cc_start: 0.8305 (mttt) cc_final: 0.7933 (mttp) REVERT: G 96 LYS cc_start: 0.6953 (mttt) cc_final: 0.6298 (tptm) REVERT: H 96 LYS cc_start: 0.6964 (mttt) cc_final: 0.6351 (tptm) REVERT: I 96 LYS cc_start: 0.7371 (mttt) cc_final: 0.6712 (tmtt) REVERT: J 96 LYS cc_start: 0.7327 (mttt) cc_final: 0.6588 (tmtt) outliers start: 46 outliers final: 43 residues processed: 164 average time/residue: 0.1672 time to fit residues: 34.8614 Evaluate side-chains 178 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 55 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 30.0000 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.220137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.191961 restraints weight = 6478.875| |-----------------------------------------------------------------------------| r_work (start): 0.4565 rms_B_bonded: 4.62 r_work: 0.4449 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.5073 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= 0.341 Angle : 0.674 7.233 6700 Z= 0.370 Chirality : 0.051 0.183 880 Planarity : 0.003 0.012 830 Dihedral : 6.096 21.038 720 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 8.98 % Allowed : 19.59 % 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: -4.37 (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 0.000 HIS J 50 PHE 0.012 0.003 PHE D 94 TYR 0.016 0.004 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1327.81 seconds wall clock time: 25 minutes 10.25 seconds (1510.25 seconds total)