Starting phenix.real_space_refine on Fri Dec 27 08:49:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r47_18881/12_2024/8r47_18881.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r47_18881/12_2024/8r47_18881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r47_18881/12_2024/8r47_18881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r47_18881/12_2024/8r47_18881.map" model { file = "/net/cci-nas-00/data/ceres_data/8r47_18881/12_2024/8r47_18881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r47_18881/12_2024/8r47_18881.cif" } resolution = 2.25 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= 0.000 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2376 2.51 5 N 636 2.21 5 O 756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3780 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 630 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.05, per 1000 atoms: 0.54 Number of scatterers: 3780 At special positions: 0 Unit cell: (77.522, 81.258, 45.766, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 756 8.00 N 636 7.00 C 2376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=2.04 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: 0.92 Conformation dependent library (CDL) restraints added in 466.1 milliseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 864 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 22 removed outlier: 6.776A pdb=" N CYS B 22 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS C 22 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS D 22 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS E 22 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS F 22 " --> pdb=" O THR E 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 31 removed outlier: 6.803A pdb=" N LEU A 27 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG B 28 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 27 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG C 28 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C 27 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG D 28 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU D 27 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG E 28 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU E 27 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG F 28 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37 removed outlier: 6.409A pdb=" N TYR A 35 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR B 35 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR C 35 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR D 35 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR E 35 " --> pdb=" O GLN F 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 48 removed outlier: 6.591A pdb=" N LEU A 44 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE B 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N VAL A 46 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 44 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE C 47 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N VAL B 46 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU C 44 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE D 47 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL C 46 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 44 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE E 47 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL D 46 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU E 44 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE F 47 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL E 46 " --> pdb=" O ILE F 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 74 removed outlier: 6.542A pdb=" N ALA A 70 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR B 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 72 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 70 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR C 73 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU B 72 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA C 70 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR D 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU C 72 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA D 70 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR E 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU D 72 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA E 70 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR F 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU E 72 " --> pdb=" O THR F 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 86 Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA8, first strand: chain 'A' and resid 104 through 105 60 hydrogen bonds defined for protein. 180 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: 0.84 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 648 1.31 - 1.44: 1116 1.44 - 1.57: 2082 1.57 - 1.69: 0 1.69 - 1.82: 12 Bond restraints: 3858 Sorted by residual: bond pdb=" C GLN F 16 " pdb=" O GLN F 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN A 16 " pdb=" O GLN A 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN C 16 " pdb=" O GLN C 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN D 16 " pdb=" O GLN D 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN B 16 " pdb=" O GLN B 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.24e+01 ... (remaining 3853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 3849 1.97 - 3.94: 989 3.94 - 5.91: 328 5.91 - 7.88: 54 7.88 - 9.85: 18 Bond angle restraints: 5238 Sorted by residual: angle pdb=" CA GLY E 94 " pdb=" C GLY E 94 " pdb=" O GLY E 94 " ideal model delta sigma weight residual 121.04 115.87 5.17 7.90e-01 1.60e+00 4.28e+01 angle pdb=" CA GLY C 94 " pdb=" C GLY C 94 " pdb=" O GLY C 94 " ideal model delta sigma weight residual 121.04 115.87 5.17 7.90e-01 1.60e+00 4.28e+01 angle pdb=" CA GLY F 94 " pdb=" C GLY F 94 " pdb=" O GLY F 94 " ideal model delta sigma weight residual 121.04 115.87 5.17 7.90e-01 1.60e+00 4.28e+01 angle pdb=" CA GLY A 94 " pdb=" C GLY A 94 " pdb=" O GLY A 94 " ideal model delta sigma weight residual 121.04 115.89 5.15 7.90e-01 1.60e+00 4.24e+01 angle pdb=" CA GLY D 94 " pdb=" C GLY D 94 " pdb=" O GLY D 94 " ideal model delta sigma weight residual 121.04 115.90 5.14 7.90e-01 1.60e+00 4.23e+01 ... (remaining 5233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 1921 16.00 - 32.00: 200 32.00 - 48.00: 42 48.00 - 64.00: 24 64.00 - 80.00: 6 Dihedral angle restraints: 2193 sinusoidal: 813 harmonic: 1380 Sorted by residual: dihedral pdb=" CA PRO D 39 " pdb=" C PRO D 39 " pdb=" N GLY D 40 " pdb=" CA GLY D 40 " ideal model delta harmonic sigma weight residual -180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PRO F 39 " pdb=" C PRO F 39 " pdb=" N GLY F 40 " pdb=" CA GLY F 40 " ideal model delta harmonic sigma weight residual -180.00 -162.42 -17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PRO A 39 " pdb=" C PRO A 39 " pdb=" N GLY A 40 " pdb=" CA GLY A 40 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 2190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 399 0.083 - 0.165: 135 0.165 - 0.248: 30 0.248 - 0.330: 6 0.330 - 0.413: 6 Chirality restraints: 576 Sorted by residual: chirality pdb=" CA ILE F 65 " pdb=" N ILE F 65 " pdb=" C ILE F 65 " pdb=" CB ILE F 65 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA ILE D 65 " pdb=" N ILE D 65 " pdb=" C ILE D 65 " pdb=" CB ILE D 65 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CA ILE C 65 " pdb=" N ILE C 65 " pdb=" C ILE C 65 " pdb=" CB ILE C 65 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 573 not shown) Planarity restraints: 672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 63 " 0.024 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C GLY B 63 " -0.085 2.00e-02 2.50e+03 pdb=" O GLY B 63 " 0.032 2.00e-02 2.50e+03 pdb=" N SER B 64 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 63 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C GLY A 63 " -0.085 2.00e-02 2.50e+03 pdb=" O GLY A 63 " 0.032 2.00e-02 2.50e+03 pdb=" N SER A 64 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 63 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C GLY D 63 " -0.085 2.00e-02 2.50e+03 pdb=" O GLY D 63 " 0.032 2.00e-02 2.50e+03 pdb=" N SER D 64 " 0.029 2.00e-02 2.50e+03 ... (remaining 669 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 45 2.61 - 3.18: 3074 3.18 - 3.76: 6106 3.76 - 4.33: 9435 4.33 - 4.90: 17013 Nonbonded interactions: 35673 Sorted by model distance: nonbonded pdb=" SG CYS B 22 " pdb=" SG CYS B 87 " model vdw 2.041 3.760 nonbonded pdb=" SG CYS F 22 " pdb=" SG CYS F 87 " model vdw 2.042 3.760 nonbonded pdb=" SG CYS D 22 " pdb=" SG CYS D 87 " model vdw 2.042 3.760 nonbonded pdb=" SG CYS E 22 " pdb=" SG CYS E 87 " model vdw 2.042 3.760 nonbonded pdb=" SG CYS C 22 " pdb=" SG CYS C 87 " model vdw 2.042 3.760 ... (remaining 35668 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' } 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: 0.510 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.300 Find NCS groups from input model: 0.140 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:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.013 0.054 3858 Z= 0.842 Angle : 2.036 9.847 5238 Z= 1.468 Chirality : 0.097 0.413 576 Planarity : 0.016 0.070 672 Dihedral : 15.668 79.999 1326 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 18.43 % Favored : 81.57 % 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: -4.59 (0.21), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.16), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 97 PHE 0.008 0.001 PHE C 61 TYR 0.004 0.001 TYR C 30 ARG 0.002 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.416 Fit side-chains REVERT: B 66 SER cc_start: 0.8301 (p) cc_final: 0.8059 (t) REVERT: D 90 ARG cc_start: 0.6960 (ttm170) cc_final: 0.6716 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.5662 time to fit residues: 45.4142 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN B 23 GLN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN D 23 GLN E 23 GLN ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3858 Z= 0.177 Angle : 0.606 8.378 5238 Z= 0.313 Chirality : 0.043 0.148 576 Planarity : 0.005 0.052 672 Dihedral : 5.883 14.817 534 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.76 % Allowed : 17.17 % Favored : 82.07 % 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: -4.20 (0.25), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.19), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 97 PHE 0.006 0.001 PHE D 61 TYR 0.010 0.001 TYR B 48 ARG 0.004 0.001 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.476 Fit side-chains REVERT: C 82 GLU cc_start: 0.8089 (tp30) cc_final: 0.7870 (mm-30) REVERT: E 90 ARG cc_start: 0.7461 (ttm170) cc_final: 0.7096 (mtt90) REVERT: F 66 SER cc_start: 0.8377 (p) cc_final: 0.8160 (p) REVERT: F 69 THR cc_start: 0.8195 (m) cc_final: 0.7839 (t) outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.6318 time to fit residues: 52.8931 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 47 optimal weight: 0.0970 chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3858 Z= 0.157 Angle : 0.565 7.282 5238 Z= 0.291 Chirality : 0.043 0.148 576 Planarity : 0.005 0.046 672 Dihedral : 5.612 14.936 534 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.27 % Allowed : 18.18 % Favored : 79.55 % 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 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.21), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 97 PHE 0.007 0.001 PHE B 99 TYR 0.008 0.001 TYR B 48 ARG 0.003 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.419 Fit side-chains REVERT: D 69 THR cc_start: 0.8333 (m) cc_final: 0.7986 (t) REVERT: F 69 THR cc_start: 0.8194 (m) cc_final: 0.7866 (t) outliers start: 9 outliers final: 2 residues processed: 73 average time/residue: 0.6768 time to fit residues: 52.5095 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN C 16 GLN F 16 GLN F 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 3858 Z= 0.483 Angle : 0.814 7.451 5238 Z= 0.428 Chirality : 0.053 0.180 576 Planarity : 0.006 0.050 672 Dihedral : 6.980 22.402 534 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.27 % Allowed : 15.40 % Favored : 82.32 % 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 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.21), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 97 PHE 0.011 0.002 PHE F 86 TYR 0.017 0.003 TYR F 48 ARG 0.010 0.002 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.438 Fit side-chains REVERT: D 69 THR cc_start: 0.8397 (m) cc_final: 0.8094 (t) REVERT: E 80 GLU cc_start: 0.7364 (tt0) cc_final: 0.7071 (tm-30) REVERT: F 66 SER cc_start: 0.8339 (p) cc_final: 0.8099 (p) REVERT: F 69 THR cc_start: 0.8246 (m) cc_final: 0.7972 (t) outliers start: 9 outliers final: 6 residues processed: 74 average time/residue: 0.8526 time to fit residues: 66.0251 Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3858 Z= 0.244 Angle : 0.635 7.111 5238 Z= 0.332 Chirality : 0.046 0.150 576 Planarity : 0.005 0.049 672 Dihedral : 6.436 19.594 534 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.77 % Allowed : 15.91 % Favored : 82.32 % 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: -4.06 (0.26), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 97 PHE 0.008 0.001 PHE B 99 TYR 0.009 0.001 TYR C 48 ARG 0.004 0.001 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.434 Fit side-chains REVERT: C 80 GLU cc_start: 0.7459 (tt0) cc_final: 0.7178 (tm-30) REVERT: C 90 ARG cc_start: 0.7541 (ttm170) cc_final: 0.7276 (mtp85) REVERT: D 69 THR cc_start: 0.8379 (m) cc_final: 0.8053 (t) REVERT: F 66 SER cc_start: 0.8262 (p) cc_final: 0.7988 (p) REVERT: F 69 THR cc_start: 0.8258 (m) cc_final: 0.7972 (t) REVERT: F 103 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8087 (m) outliers start: 7 outliers final: 3 residues processed: 71 average time/residue: 0.8387 time to fit residues: 62.4248 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 3 optimal weight: 0.0010 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 5 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.0150 ------------------------------------------------------------------------------- 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: 0.8027 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3858 Z= 0.290 Angle : 0.670 6.127 5238 Z= 0.352 Chirality : 0.047 0.191 576 Planarity : 0.005 0.052 672 Dihedral : 6.577 19.342 534 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.53 % Allowed : 16.16 % Favored : 81.31 % 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: -3.99 (0.26), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 97 PHE 0.007 0.002 PHE F 99 TYR 0.014 0.002 TYR A 48 ARG 0.005 0.001 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.573 Fit side-chains REVERT: C 80 GLU cc_start: 0.7460 (tt0) cc_final: 0.7138 (tm-30) REVERT: C 90 ARG cc_start: 0.7562 (ttm170) cc_final: 0.7278 (mtp85) REVERT: D 44 LEU cc_start: 0.8511 (tp) cc_final: 0.8077 (tp) REVERT: D 69 THR cc_start: 0.8384 (m) cc_final: 0.8041 (t) REVERT: E 80 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6637 (tt0) REVERT: F 66 SER cc_start: 0.8238 (p) cc_final: 0.7995 (p) REVERT: F 69 THR cc_start: 0.8243 (m) cc_final: 0.7966 (t) REVERT: F 103 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8119 (m) outliers start: 10 outliers final: 3 residues processed: 73 average time/residue: 0.8873 time to fit residues: 67.8481 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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: 0.7971 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3858 Z= 0.178 Angle : 0.589 7.259 5238 Z= 0.306 Chirality : 0.043 0.147 576 Planarity : 0.005 0.051 672 Dihedral : 6.074 17.521 534 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.76 % Allowed : 18.43 % Favored : 80.81 % 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: -3.95 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 97 PHE 0.006 0.001 PHE B 99 TYR 0.012 0.001 TYR A 48 ARG 0.002 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.406 Fit side-chains REVERT: C 80 GLU cc_start: 0.7365 (tt0) cc_final: 0.7046 (tm-30) REVERT: C 90 ARG cc_start: 0.7538 (ttm170) cc_final: 0.7256 (mtp85) REVERT: D 69 THR cc_start: 0.8327 (m) cc_final: 0.7990 (t) REVERT: F 69 THR cc_start: 0.8241 (m) cc_final: 0.7949 (t) REVERT: F 103 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8116 (m) outliers start: 3 outliers final: 1 residues processed: 66 average time/residue: 0.8671 time to fit residues: 59.9308 Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 3858 Z= 0.434 Angle : 0.785 7.034 5238 Z= 0.410 Chirality : 0.052 0.199 576 Planarity : 0.005 0.054 672 Dihedral : 6.893 19.816 534 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.77 % Allowed : 18.69 % Favored : 79.55 % 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: -3.98 (0.26), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 97 PHE 0.008 0.002 PHE F 99 TYR 0.007 0.002 TYR F 35 ARG 0.008 0.002 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.433 Fit side-chains REVERT: C 80 GLU cc_start: 0.7575 (tt0) cc_final: 0.7299 (tm-30) REVERT: D 69 THR cc_start: 0.8397 (m) cc_final: 0.8067 (t) REVERT: F 69 THR cc_start: 0.8315 (m) cc_final: 0.8043 (t) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 0.9126 time to fit residues: 61.9966 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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: 0.8059 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3858 Z= 0.417 Angle : 0.786 7.694 5238 Z= 0.409 Chirality : 0.051 0.176 576 Planarity : 0.005 0.056 672 Dihedral : 6.954 20.293 534 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.52 % Allowed : 19.19 % Favored : 79.29 % 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: -4.02 (0.26), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 97 PHE 0.007 0.002 PHE B 99 TYR 0.015 0.002 TYR A 48 ARG 0.007 0.001 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.423 Fit side-chains REVERT: C 80 GLU cc_start: 0.7576 (tt0) cc_final: 0.7253 (tm-30) REVERT: D 69 THR cc_start: 0.8394 (m) cc_final: 0.8066 (t) REVERT: D 80 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: F 69 THR cc_start: 0.8322 (m) cc_final: 0.8065 (t) outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 0.9267 time to fit residues: 62.8570 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 3 optimal weight: 0.0570 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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: 0.7973 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3858 Z= 0.178 Angle : 0.628 8.509 5238 Z= 0.319 Chirality : 0.044 0.147 576 Planarity : 0.005 0.052 672 Dihedral : 6.185 16.675 534 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.26 % Allowed : 19.95 % Favored : 78.79 % 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: -4.01 (0.26), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 97 PHE 0.005 0.001 PHE B 99 TYR 0.013 0.001 TYR D 48 ARG 0.002 0.000 ARG A 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.432 Fit side-chains REVERT: C 80 GLU cc_start: 0.7458 (tt0) cc_final: 0.7173 (tm-30) REVERT: C 90 ARG cc_start: 0.7465 (ttm170) cc_final: 0.7223 (mtp85) REVERT: D 69 THR cc_start: 0.8377 (m) cc_final: 0.8028 (t) REVERT: F 69 THR cc_start: 0.8279 (m) cc_final: 0.8002 (t) REVERT: F 103 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8110 (m) outliers start: 5 outliers final: 4 residues processed: 65 average time/residue: 0.8715 time to fit residues: 59.3385 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.143146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.125572 restraints weight = 3933.171| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.39 r_work: 0.3779 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3858 Z= 0.189 Angle : 0.629 8.179 5238 Z= 0.320 Chirality : 0.044 0.147 576 Planarity : 0.005 0.053 672 Dihedral : 6.107 16.653 534 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.77 % Allowed : 19.44 % Favored : 78.79 % 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: -3.98 (0.26), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 97 PHE 0.005 0.001 PHE B 99 TYR 0.013 0.001 TYR D 48 ARG 0.002 0.000 ARG C 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1766.40 seconds wall clock time: 32 minutes 56.07 seconds (1976.07 seconds total)