Starting phenix.real_space_refine on Wed Mar 5 16:07:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xjx_33236/03_2025/7xjx_33236.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjx_33236/03_2025/7xjx_33236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xjx_33236/03_2025/7xjx_33236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjx_33236/03_2025/7xjx_33236.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjx_33236/03_2025/7xjx_33236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjx_33236/03_2025/7xjx_33236.cif" } resolution = 2.7 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= 0.001 sd= 0.005 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 1644 2.51 5 N 456 2.21 5 O 528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2628 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.54, per 1000 atoms: 0.59 Number of scatterers: 2628 At special positions: 0 Unit cell: (108.272, 95.408, 31.088, 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 528 8.00 N 456 7.00 C 1644 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 349.3 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 46 through 56 removed outlier: 7.570A pdb=" N GLY B 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N HIS E 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N VAL B 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N VAL E 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY B 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N THR E 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA B 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ALA E 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL B 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL F 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N HIS B 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY F 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 60 through 65 removed outlier: 6.476A pdb=" N GLU B 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR F 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 71 through 78 removed outlier: 6.417A pdb=" N THR B 72 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N THR E 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL B 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL E 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA B 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR F 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY B 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA F 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 56 removed outlier: 7.551A pdb=" N GLY A 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N HIS C 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ALA C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL D 49 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N HIS A 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY D 51 " --> pdb=" O HIS A 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 65 removed outlier: 6.490A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR D 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 71 through 78 removed outlier: 6.408A pdb=" N THR A 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N THR C 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL C 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA A 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR D 72 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY A 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA D 78 " --> pdb=" O VAL A 77 " (cutoff:3.500A) 28 hydrogen bonds defined for protein. 84 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.51 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 462 1.28 - 1.35: 408 1.35 - 1.41: 99 1.41 - 1.48: 441 1.48 - 1.54: 1230 Bond restraints: 2640 Sorted by residual: bond pdb=" CA GLY A 68 " pdb=" C GLY A 68 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.25e+00 bond pdb=" CA GLY C 68 " pdb=" C GLY C 68 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.24e+00 bond pdb=" CA GLY B 68 " pdb=" C GLY B 68 " ideal model delta sigma weight residual 1.530 1.515 0.016 1.04e-02 9.25e+03 2.23e+00 bond pdb=" CA GLY D 68 " pdb=" C GLY D 68 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.04e-02 9.25e+03 2.19e+00 bond pdb=" CA GLY E 68 " pdb=" C GLY E 68 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.04e-02 9.25e+03 2.14e+00 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 3134 1.08 - 2.15: 354 2.15 - 3.23: 55 3.23 - 4.30: 15 4.30 - 5.38: 12 Bond angle restraints: 3570 Sorted by residual: angle pdb=" N HIS E 50 " pdb=" CA HIS E 50 " pdb=" C HIS E 50 " ideal model delta sigma weight residual 108.99 113.74 -4.75 1.57e+00 4.06e-01 9.16e+00 angle pdb=" N HIS B 50 " pdb=" CA HIS B 50 " pdb=" C HIS B 50 " ideal model delta sigma weight residual 108.99 113.74 -4.75 1.57e+00 4.06e-01 9.16e+00 angle pdb=" N HIS C 50 " pdb=" CA HIS C 50 " pdb=" C HIS C 50 " ideal model delta sigma weight residual 108.99 113.74 -4.75 1.57e+00 4.06e-01 9.15e+00 angle pdb=" N HIS F 50 " pdb=" CA HIS F 50 " pdb=" C HIS F 50 " ideal model delta sigma weight residual 108.99 113.69 -4.70 1.57e+00 4.06e-01 8.98e+00 angle pdb=" N HIS A 50 " pdb=" CA HIS A 50 " pdb=" C HIS A 50 " ideal model delta sigma weight residual 108.99 113.69 -4.70 1.57e+00 4.06e-01 8.95e+00 ... (remaining 3565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.68: 1206 9.68 - 19.36: 240 19.36 - 29.03: 60 29.03 - 38.71: 24 38.71 - 48.39: 18 Dihedral angle restraints: 1548 sinusoidal: 522 harmonic: 1026 Sorted by residual: dihedral pdb=" CA ALA C 89 " pdb=" C ALA C 89 " pdb=" N ALA C 90 " pdb=" CA ALA C 90 " ideal model delta harmonic sigma weight residual -180.00 -157.80 -22.20 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ALA E 89 " pdb=" C ALA E 89 " pdb=" N ALA E 90 " pdb=" CA ALA E 90 " ideal model delta harmonic sigma weight residual -180.00 -157.84 -22.16 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ALA A 89 " pdb=" C ALA A 89 " pdb=" N ALA A 90 " pdb=" CA ALA A 90 " ideal model delta harmonic sigma weight residual 180.00 -157.85 -22.15 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 243 0.036 - 0.071: 116 0.071 - 0.106: 61 0.106 - 0.141: 30 0.141 - 0.177: 18 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.65e-01 ... (remaining 465 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 48 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C VAL E 48 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL E 48 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL E 49 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 48 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C VAL D 48 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL D 48 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL D 49 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 48 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C VAL F 48 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL F 48 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL F 49 " 0.010 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 1203 2.93 - 3.42: 2369 3.42 - 3.92: 3923 3.92 - 4.41: 4245 4.41 - 4.90: 9221 Nonbonded interactions: 20961 Sorted by model distance: nonbonded pdb=" O THR C 64 " pdb=" OG1 THR C 64 " model vdw 2.438 3.040 nonbonded pdb=" O THR B 64 " pdb=" OG1 THR B 64 " model vdw 2.438 3.040 nonbonded pdb=" O THR D 64 " pdb=" OG1 THR D 64 " model vdw 2.439 3.040 nonbonded pdb=" O THR A 64 " pdb=" OG1 THR A 64 " model vdw 2.439 3.040 nonbonded pdb=" O THR E 64 " pdb=" OG1 THR E 64 " model vdw 2.439 3.040 ... (remaining 20956 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 1.160 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.370 Find NCS groups from input model: 0.060 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:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.008 0.033 2640 Z= 0.548 Angle : 0.806 5.379 3570 Z= 0.484 Chirality : 0.063 0.177 468 Planarity : 0.003 0.017 444 Dihedral : 12.769 48.390 900 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.39 % Favored : 83.61 % Rotamer: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % 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: -5.02 (0.31), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS E 50 PHE 0.002 0.001 PHE C 94 TYR 0.009 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.282 Fit side-chains REVERT: B 54 THR cc_start: 0.8956 (p) cc_final: 0.8731 (p) REVERT: D 60 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7814 (tttt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 1.2371 time to fit residues: 54.5497 Evaluate side-chains 39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.191090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.157967 restraints weight = 3186.353| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.42 r_work: 0.4105 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3998 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2640 Z= 0.198 Angle : 0.536 3.903 3570 Z= 0.306 Chirality : 0.051 0.129 468 Planarity : 0.002 0.011 444 Dihedral : 6.005 18.357 378 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer: Outliers : 4.07 % Allowed : 22.96 % Favored : 72.96 % 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: -4.48 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 50 PHE 0.001 0.000 PHE B 94 TYR 0.006 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.323 Fit side-chains REVERT: B 43 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7525 (mptt) REVERT: B 60 LYS cc_start: 0.8020 (ttpt) cc_final: 0.7762 (tppp) REVERT: E 83 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7131 (tm-30) REVERT: C 60 LYS cc_start: 0.8288 (tttt) cc_final: 0.8038 (tttt) REVERT: F 43 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7755 (ptpp) REVERT: D 60 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7956 (tttt) outliers start: 11 outliers final: 5 residues processed: 40 average time/residue: 1.2008 time to fit residues: 49.3803 Evaluate side-chains 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.4538 r_free = 0.4538 target = 0.191330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.158171 restraints weight = 3145.566| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 2.42 r_work: 0.4111 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4001 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2640 Z= 0.206 Angle : 0.505 3.358 3570 Z= 0.289 Chirality : 0.050 0.126 468 Planarity : 0.002 0.007 444 Dihedral : 5.768 17.864 378 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 6.30 % Allowed : 20.00 % Favored : 73.70 % 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: -4.03 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 50 PHE 0.002 0.000 PHE C 94 TYR 0.007 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 37 time to evaluate : 0.281 Fit side-chains REVERT: B 43 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7599 (mptt) REVERT: B 60 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7737 (tppp) REVERT: E 83 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7187 (tm-30) REVERT: C 60 LYS cc_start: 0.8318 (tttt) cc_final: 0.8069 (tttt) REVERT: F 43 LYS cc_start: 0.8080 (mptt) cc_final: 0.7839 (ptpt) REVERT: D 60 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7899 (tttt) outliers start: 17 outliers final: 12 residues processed: 47 average time/residue: 1.1122 time to fit residues: 53.7738 Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.4495 r_free = 0.4495 target = 0.187870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.153901 restraints weight = 3216.515| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 2.45 r_work: 0.4056 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3945 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2640 Z= 0.373 Angle : 0.601 3.787 3570 Z= 0.339 Chirality : 0.053 0.125 468 Planarity : 0.002 0.010 444 Dihedral : 6.503 20.301 378 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 8.52 % Allowed : 16.67 % Favored : 74.81 % 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: -3.93 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS B 50 PHE 0.005 0.001 PHE C 94 TYR 0.011 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 37 time to evaluate : 0.298 Fit side-chains REVERT: B 43 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7677 (mptt) REVERT: B 60 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7789 (tppp) REVERT: E 83 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7154 (tm-30) REVERT: C 60 LYS cc_start: 0.8369 (ttmt) cc_final: 0.8001 (ttpt) REVERT: D 60 LYS cc_start: 0.8379 (ttmt) cc_final: 0.8047 (tttt) outliers start: 23 outliers final: 15 residues processed: 51 average time/residue: 1.0438 time to fit residues: 54.8313 Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.191126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.158476 restraints weight = 3185.385| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 2.39 r_work: 0.4112 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2640 Z= 0.212 Angle : 0.511 3.481 3570 Z= 0.292 Chirality : 0.050 0.125 468 Planarity : 0.002 0.013 444 Dihedral : 5.915 19.114 378 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 6.67 % Allowed : 17.41 % Favored : 75.93 % 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: -3.71 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 50 PHE 0.002 0.001 PHE C 94 TYR 0.007 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 0.273 Fit side-chains REVERT: B 43 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7977 (ptpp) REVERT: B 60 LYS cc_start: 0.7965 (ttpt) cc_final: 0.7757 (tppp) REVERT: E 83 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7277 (tm-30) REVERT: C 60 LYS cc_start: 0.8355 (ttmt) cc_final: 0.7975 (ttpt) REVERT: D 60 LYS cc_start: 0.8325 (ttmt) cc_final: 0.8007 (tttt) outliers start: 18 outliers final: 14 residues processed: 46 average time/residue: 1.1114 time to fit residues: 52.5355 Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 0.0020 chunk 14 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- 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 = 0.4489 r_free = 0.4489 target = 0.187050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.153332 restraints weight = 3226.068| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.44 r_work: 0.4049 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 2640 Z= 0.399 Angle : 0.614 3.741 3570 Z= 0.348 Chirality : 0.053 0.124 468 Planarity : 0.003 0.014 444 Dihedral : 6.603 20.842 378 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.39 % Favored : 86.61 % Rotamer: Outliers : 7.04 % Allowed : 16.67 % Favored : 76.30 % 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: -3.75 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS B 50 PHE 0.006 0.001 PHE C 94 TYR 0.010 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.267 Fit side-chains REVERT: B 43 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7668 (mptt) REVERT: B 60 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7724 (tppp) REVERT: E 83 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7163 (tm-30) REVERT: C 60 LYS cc_start: 0.8424 (ttmt) cc_final: 0.8033 (ttpt) REVERT: D 60 LYS cc_start: 0.8392 (ttmt) cc_final: 0.8087 (tttt) outliers start: 19 outliers final: 14 residues processed: 47 average time/residue: 1.0236 time to fit residues: 49.5523 Evaluate side-chains 53 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4540 r_free = 0.4540 target = 0.192195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.160176 restraints weight = 3330.313| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.41 r_work: 0.4128 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4020 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2640 Z= 0.163 Angle : 0.486 3.508 3570 Z= 0.279 Chirality : 0.050 0.124 468 Planarity : 0.002 0.012 444 Dihedral : 5.714 18.985 378 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 5.93 % Allowed : 18.15 % Favored : 75.93 % 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: -3.56 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 50 PHE 0.001 0.000 PHE C 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.300 Fit side-chains REVERT: B 43 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7886 (mptt) REVERT: E 83 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7232 (tm-30) REVERT: C 60 LYS cc_start: 0.8397 (ttmt) cc_final: 0.8047 (ttpt) REVERT: D 60 LYS cc_start: 0.8356 (ttmt) cc_final: 0.8022 (tttt) outliers start: 16 outliers final: 12 residues processed: 45 average time/residue: 1.0325 time to fit residues: 47.8958 Evaluate side-chains 46 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 = 0.4498 r_free = 0.4498 target = 0.188401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.155300 restraints weight = 3165.912| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 2.40 r_work: 0.4074 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3965 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2640 Z= 0.336 Angle : 0.568 3.961 3570 Z= 0.322 Chirality : 0.051 0.123 468 Planarity : 0.002 0.010 444 Dihedral : 6.255 20.241 378 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 5.56 % Allowed : 18.52 % Favored : 75.93 % 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: -3.61 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS B 50 PHE 0.005 0.001 PHE C 94 TYR 0.009 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.269 Fit side-chains REVERT: B 43 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7700 (mptt) REVERT: E 83 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7281 (tm-30) REVERT: C 83 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7415 (tm-30) REVERT: D 60 LYS cc_start: 0.8356 (ttmt) cc_final: 0.8051 (tttt) outliers start: 15 outliers final: 13 residues processed: 46 average time/residue: 1.0226 time to fit residues: 48.4779 Evaluate side-chains 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN A 62 GLN C 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.190532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.158359 restraints weight = 3206.531| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 2.37 r_work: 0.4107 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4001 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2640 Z= 0.228 Angle : 0.537 5.564 3570 Z= 0.303 Chirality : 0.050 0.125 468 Planarity : 0.002 0.009 444 Dihedral : 5.966 19.065 378 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer: Outliers : 5.93 % Allowed : 18.52 % Favored : 75.56 % 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: -3.53 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 50 PHE 0.003 0.001 PHE C 94 TYR 0.007 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.279 Fit side-chains REVERT: B 43 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7788 (mptt) REVERT: E 83 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7261 (tm-30) REVERT: C 43 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7892 (mptt) REVERT: C 83 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7504 (tm-30) REVERT: D 60 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7860 (tttt) outliers start: 16 outliers final: 13 residues processed: 45 average time/residue: 0.9968 time to fit residues: 46.2573 Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 33 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.189611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.157083 restraints weight = 3193.488| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.38 r_work: 0.4091 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3984 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2640 Z= 0.283 Angle : 0.598 8.483 3570 Z= 0.332 Chirality : 0.051 0.124 468 Planarity : 0.002 0.009 444 Dihedral : 6.160 19.634 378 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 5.93 % Allowed : 18.52 % Favored : 75.56 % 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: -3.56 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS B 50 PHE 0.004 0.001 PHE C 94 TYR 0.009 0.002 TYR C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.292 Fit side-chains REVERT: B 43 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7701 (mptt) REVERT: E 83 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7292 (tm-30) REVERT: C 43 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7930 (mptt) REVERT: C 83 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7526 (tm-30) REVERT: F 83 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7392 (tm-30) REVERT: D 60 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7946 (tttt) outliers start: 16 outliers final: 13 residues processed: 48 average time/residue: 1.0008 time to fit residues: 49.4907 Evaluate side-chains 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.188476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.155680 restraints weight = 3219.761| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.39 r_work: 0.4072 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3964 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2640 Z= 0.331 Angle : 0.621 7.831 3570 Z= 0.344 Chirality : 0.052 0.126 468 Planarity : 0.002 0.009 444 Dihedral : 6.435 20.430 378 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer: Outliers : 5.56 % Allowed : 18.89 % Favored : 75.56 % 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: -3.60 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS B 50 PHE 0.006 0.001 PHE C 94 TYR 0.009 0.002 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2573.91 seconds wall clock time: 44 minutes 39.78 seconds (2679.78 seconds total)