Starting phenix.real_space_refine on Sun Apr 27 12:10:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mnz_48444/04_2025/9mnz_48444.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mnz_48444/04_2025/9mnz_48444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mnz_48444/04_2025/9mnz_48444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mnz_48444/04_2025/9mnz_48444.map" model { file = "/net/cci-nas-00/data/ceres_data/9mnz_48444/04_2025/9mnz_48444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mnz_48444/04_2025/9mnz_48444.cif" } resolution = 2.73 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 387 atoms to isotropic. 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 30 5.16 5 C 3426 2.51 5 N 930 2.21 5 O 996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5382 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 973 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "C" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "B" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "A" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 860 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "F" Number of atoms: 749 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain breaks: 1 bond proxies already assigned to first conformer: 751 Chain: "E" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'I2R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.04, per 1000 atoms: 1.31 Number of scatterers: 5382 At special positions: 0 Unit cell: (82.56, 86.86, 147.92, 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 30 16.00 O 996 8.00 N 930 7.00 C 3426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 94 " 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: 1.75 Conformation dependent library (CDL) restraints added in 717.3 milliseconds 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1260 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 39.7% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.662A pdb=" N THR C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 43 through 59 removed outlier: 4.266A pdb=" N ILE B 47 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET B 48 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU B 52 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS B 54 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 55 " --> pdb=" O GLY B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 89 removed outlier: 3.734A pdb=" N SER B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER B 86 " --> pdb=" O TRP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 125 removed outlier: 4.441A pdb=" N PHE B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 98 " --> pdb=" O TRP B 94 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN B 119 " --> pdb=" O TRP B 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 16 through 23 Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 29 through 34 removed outlier: 4.045A pdb=" N ASN A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 52 through 71 removed outlier: 3.589A pdb=" N CYS A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 64 " --> pdb=" O CYS A 60 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 70 " --> pdb=" O PHE A 66 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 71 " --> pdb=" O MET A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 107 removed outlier: 3.943A pdb=" N PHE A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 370 Processing helix chain 'F' and resid 374 through 387 removed outlier: 3.685A pdb=" N ARG F 378 " --> pdb=" O THR F 374 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN F 383 " --> pdb=" O ASN F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 403 Processing helix chain 'F' and resid 420 through 430 removed outlier: 3.951A pdb=" N MET F 430 " --> pdb=" O GLU F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 448 Processing helix chain 'F' and resid 451 through 464 Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.735A pdb=" N VAL D 5 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU D 81 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.656A pdb=" N THR D 117 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR D 94 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET D 93 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY D 33 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.831A pdb=" N SER C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.438A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N SER C 117 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C 12 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL C 92 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG C 38 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR C 94 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TRP C 36 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA C 96 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N MET C 34 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS C 98 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.438A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N SER C 117 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C 12 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.577A pdb=" N ILE E 81 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 79 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP E 76 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.567A pdb=" N LEU E 11 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA E 90 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU E 39 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR E 55 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP E 41 " --> pdb=" O LEU E 53 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 666 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 860 1.27 - 1.41: 1507 1.41 - 1.54: 3083 1.54 - 1.68: 12 1.68 - 1.82: 50 Bond restraints: 5512 Sorted by residual: bond pdb=" CA ARG B 113 " pdb=" C ARG B 113 " ideal model delta sigma weight residual 1.523 1.403 0.120 1.34e-02 5.57e+03 8.05e+01 bond pdb=" CA ASN B 93 " pdb=" C ASN B 93 " ideal model delta sigma weight residual 1.524 1.454 0.070 1.22e-02 6.72e+03 3.30e+01 bond pdb=" C9 I2R A 201 " pdb=" N3 I2R A 201 " ideal model delta sigma weight residual 1.413 1.309 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C19 I2R A 201 " pdb=" C22 I2R A 201 " ideal model delta sigma weight residual 1.419 1.508 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" CA PHE B 42 " pdb=" C PHE B 42 " ideal model delta sigma weight residual 1.522 1.447 0.074 1.72e-02 3.38e+03 1.87e+01 ... (remaining 5507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 7123 3.25 - 6.50: 302 6.50 - 9.75: 33 9.75 - 13.00: 4 13.00 - 16.25: 1 Bond angle restraints: 7463 Sorted by residual: angle pdb=" N LEU B 28 " pdb=" CA LEU B 28 " pdb=" C LEU B 28 " ideal model delta sigma weight residual 112.59 101.81 10.78 1.22e+00 6.72e-01 7.80e+01 angle pdb=" N GLU E 87 " pdb=" CA GLU E 87 " pdb=" C GLU E 87 " ideal model delta sigma weight residual 112.54 103.18 9.36 1.22e+00 6.72e-01 5.88e+01 angle pdb=" N LEU B 17 " pdb=" CA LEU B 17 " pdb=" C LEU B 17 " ideal model delta sigma weight residual 111.36 104.66 6.70 1.09e+00 8.42e-01 3.78e+01 angle pdb=" CA ARG B 113 " pdb=" C ARG B 113 " pdb=" O ARG B 113 " ideal model delta sigma weight residual 120.51 111.85 8.66 1.43e+00 4.89e-01 3.67e+01 angle pdb=" N ILE F 427 " pdb=" CA ILE F 427 " pdb=" C ILE F 427 " ideal model delta sigma weight residual 111.81 106.77 5.04 8.60e-01 1.35e+00 3.43e+01 ... (remaining 7458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 2945 17.36 - 34.73: 264 34.73 - 52.09: 43 52.09 - 69.45: 11 69.45 - 86.82: 5 Dihedral angle restraints: 3268 sinusoidal: 1296 harmonic: 1972 Sorted by residual: dihedral pdb=" CA ASP D 73 " pdb=" C ASP D 73 " pdb=" N ASN D 74 " pdb=" CA ASN D 74 " ideal model delta harmonic sigma weight residual -180.00 -151.39 -28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA LYS F 400 " pdb=" C LYS F 400 " pdb=" N LYS F 401 " pdb=" CA LYS F 401 " ideal model delta harmonic sigma weight residual 180.00 151.89 28.11 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASP C 72 " pdb=" C ASP C 72 " pdb=" N ASN C 73 " pdb=" CA ASN C 73 " ideal model delta harmonic sigma weight residual -180.00 -154.45 -25.55 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 3265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 523 0.087 - 0.175: 224 0.175 - 0.262: 43 0.262 - 0.349: 6 0.349 - 0.436: 1 Chirality restraints: 797 Sorted by residual: chirality pdb=" CB VAL C 78 " pdb=" CA VAL C 78 " pdb=" CG1 VAL C 78 " pdb=" CG2 VAL C 78 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CB THR C 115 " pdb=" CA THR C 115 " pdb=" OG1 THR C 115 " pdb=" CG2 THR C 115 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CG LEU A 110 " pdb=" CB LEU A 110 " pdb=" CD1 LEU A 110 " pdb=" CD2 LEU A 110 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 794 not shown) Planarity restraints: 954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 37 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.07e+01 pdb=" N PRO B 38 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 47 " 0.063 5.00e-02 4.00e+02 9.62e-02 1.48e+01 pdb=" N PRO A 48 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 48 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 48 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 45 " -0.063 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO B 46 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO B 46 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 46 " -0.052 5.00e-02 4.00e+02 ... (remaining 951 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 445 2.70 - 3.25: 4980 3.25 - 3.80: 7940 3.80 - 4.35: 10114 4.35 - 4.90: 17127 Nonbonded interactions: 40606 Sorted by model distance: nonbonded pdb=" O SER F 392 " pdb=" OG SER F 392 " model vdw 2.151 3.040 nonbonded pdb=" NZ LYS B 66 " pdb=" O GLU A 49 " model vdw 2.219 3.120 nonbonded pdb=" O MET B 60 " pdb=" NH1 ARG B 113 " model vdw 2.292 3.120 nonbonded pdb=" O SER B 83 " pdb=" N SER B 86 " model vdw 2.314 3.120 nonbonded pdb=" OD1 ASN F 429 " pdb=" N MET F 430 " model vdw 2.318 3.120 ... (remaining 40601 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.41 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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 21.690 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 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 : 0.020 0.148 5515 Z= 0.939 Angle : 1.499 16.253 7469 Z= 0.903 Chirality : 0.094 0.436 797 Planarity : 0.011 0.114 954 Dihedral : 14.216 86.815 1999 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 0.70 % Allowed : 3.52 % Favored : 95.77 % 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: -3.42 (0.30), residues: 669 helix: -2.05 (0.28), residues: 247 sheet: -1.40 (0.40), residues: 188 loop : -3.03 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP D 36 HIS 0.024 0.005 HIS A 84 PHE 0.029 0.004 PHE B 43 TYR 0.043 0.005 TYR C 103 ARG 0.019 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.22924 ( 236) hydrogen bonds : angle 8.22091 ( 666) SS BOND : bond 0.00915 ( 3) SS BOND : angle 0.91926 ( 6) covalent geometry : bond 0.02036 ( 5512) covalent geometry : angle 1.49967 ( 7463) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: C 34 MET cc_start: 0.8050 (mtp) cc_final: 0.7830 (mtm) REVERT: C 88 GLU cc_start: 0.6960 (mp0) cc_final: 0.6686 (mp0) outliers start: 4 outliers final: 0 residues processed: 93 average time/residue: 1.0884 time to fit residues: 106.1514 Evaluate side-chains 85 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 38 optimal weight: 0.0170 chunk 59 optimal weight: 0.7980 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN C 39 GLN F 379 ASN F 406 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.155546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.130863 restraints weight = 8084.158| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.13 r_work: 0.3633 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5515 Z= 0.141 Angle : 0.692 9.176 7469 Z= 0.358 Chirality : 0.043 0.139 797 Planarity : 0.006 0.091 954 Dihedral : 5.719 30.002 758 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.29 % Allowed : 10.04 % Favored : 87.68 % 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: -1.92 (0.31), residues: 669 helix: -0.12 (0.33), residues: 241 sheet: -0.63 (0.40), residues: 183 loop : -2.94 (0.33), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 34 HIS 0.006 0.001 HIS A 84 PHE 0.017 0.001 PHE D 29 TYR 0.012 0.001 TYR A 71 ARG 0.005 0.000 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.05522 ( 236) hydrogen bonds : angle 5.49318 ( 666) SS BOND : bond 0.00751 ( 3) SS BOND : angle 1.50798 ( 6) covalent geometry : bond 0.00302 ( 5512) covalent geometry : angle 0.69097 ( 7463) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7557 (mp0) cc_final: 0.7285 (mp0) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 1.0329 time to fit residues: 100.9030 Evaluate side-chains 89 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN C 39 GLN C 113 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.152032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.127068 restraints weight = 8070.089| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.14 r_work: 0.3586 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5515 Z= 0.210 Angle : 0.718 9.392 7469 Z= 0.370 Chirality : 0.046 0.196 797 Planarity : 0.006 0.076 954 Dihedral : 5.539 26.378 758 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.17 % Allowed : 13.38 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.33), residues: 669 helix: 0.27 (0.34), residues: 241 sheet: -0.37 (0.38), residues: 201 loop : -2.75 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 34 HIS 0.013 0.002 HIS E 95 PHE 0.011 0.001 PHE D 29 TYR 0.020 0.002 TYR E 38 ARG 0.003 0.000 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.06171 ( 236) hydrogen bonds : angle 5.28753 ( 666) SS BOND : bond 0.01138 ( 3) SS BOND : angle 2.10075 ( 6) covalent geometry : bond 0.00496 ( 5512) covalent geometry : angle 0.71606 ( 7463) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7611 (mp0) cc_final: 0.7276 (mp0) REVERT: B 40 THR cc_start: 0.6773 (OUTLIER) cc_final: 0.6464 (p) outliers start: 18 outliers final: 9 residues processed: 91 average time/residue: 1.0544 time to fit residues: 100.6064 Evaluate side-chains 91 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 56 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN C 39 GLN C 83 ASN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.152567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.127354 restraints weight = 8238.454| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.18 r_work: 0.3579 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5515 Z= 0.210 Angle : 0.718 9.392 7469 Z= 0.370 Chirality : 0.046 0.196 797 Planarity : 0.006 0.076 954 Dihedral : 5.539 26.378 758 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.76 % Allowed : 15.32 % Favored : 82.92 % 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: -1.41 (0.33), residues: 669 helix: 0.27 (0.34), residues: 241 sheet: -0.37 (0.38), residues: 201 loop : -2.75 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 34 HIS 0.013 0.002 HIS E 95 PHE 0.011 0.001 PHE D 29 TYR 0.020 0.002 TYR E 38 ARG 0.003 0.000 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.06171 ( 236) hydrogen bonds : angle 5.28753 ( 666) SS BOND : bond 0.01138 ( 3) SS BOND : angle 2.10075 ( 6) covalent geometry : bond 0.00496 ( 5512) covalent geometry : angle 0.71606 ( 7463) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7621 (mp0) cc_final: 0.7286 (mp0) REVERT: B 40 THR cc_start: 0.6780 (OUTLIER) cc_final: 0.6475 (p) outliers start: 10 outliers final: 9 residues processed: 86 average time/residue: 1.1367 time to fit residues: 102.3537 Evaluate side-chains 91 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 0.0670 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN C 39 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.152772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.127691 restraints weight = 8098.241| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.15 r_work: 0.3585 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5515 Z= 0.170 Angle : 0.693 8.997 7469 Z= 0.353 Chirality : 0.044 0.149 797 Planarity : 0.006 0.070 954 Dihedral : 5.412 26.685 758 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.64 % Allowed : 15.85 % Favored : 81.51 % 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: -1.28 (0.33), residues: 669 helix: 0.36 (0.34), residues: 242 sheet: -0.34 (0.38), residues: 201 loop : -2.62 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 34 HIS 0.008 0.002 HIS E 95 PHE 0.012 0.001 PHE D 29 TYR 0.018 0.002 TYR E 38 ARG 0.002 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.05837 ( 236) hydrogen bonds : angle 5.17934 ( 666) SS BOND : bond 0.01024 ( 3) SS BOND : angle 1.86742 ( 6) covalent geometry : bond 0.00392 ( 5512) covalent geometry : angle 0.69132 ( 7463) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7616 (mp0) cc_final: 0.7291 (mp0) REVERT: C 101 LEU cc_start: 0.7476 (tp) cc_final: 0.7097 (tp) REVERT: F 374 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7545 (p) outliers start: 15 outliers final: 10 residues processed: 85 average time/residue: 1.0905 time to fit residues: 97.2268 Evaluate side-chains 90 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 39 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN C 39 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.153044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127906 restraints weight = 8097.929| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.17 r_work: 0.3586 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5515 Z= 0.170 Angle : 0.693 8.997 7469 Z= 0.353 Chirality : 0.044 0.149 797 Planarity : 0.006 0.070 954 Dihedral : 5.416 26.672 758 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.11 % Allowed : 16.02 % Favored : 81.87 % 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: -1.28 (0.33), residues: 669 helix: 0.36 (0.34), residues: 242 sheet: -0.34 (0.38), residues: 201 loop : -2.62 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 34 HIS 0.008 0.002 HIS E 95 PHE 0.012 0.001 PHE D 29 TYR 0.018 0.002 TYR E 38 ARG 0.002 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.05837 ( 236) hydrogen bonds : angle 5.17932 ( 666) SS BOND : bond 0.01024 ( 3) SS BOND : angle 1.86741 ( 6) covalent geometry : bond 0.00392 ( 5512) covalent geometry : angle 0.69122 ( 7463) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7609 (mp0) cc_final: 0.7281 (mp0) REVERT: C 101 LEU cc_start: 0.7478 (tp) cc_final: 0.7097 (tp) REVERT: F 374 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7541 (p) outliers start: 12 outliers final: 11 residues processed: 84 average time/residue: 1.1350 time to fit residues: 100.1641 Evaluate side-chains 91 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN C 39 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.152780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127611 restraints weight = 8123.162| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.17 r_work: 0.3585 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5515 Z= 0.170 Angle : 0.688 8.341 7469 Z= 0.351 Chirality : 0.045 0.156 797 Planarity : 0.005 0.067 954 Dihedral : 5.295 23.581 758 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.99 % Allowed : 15.67 % Favored : 81.34 % 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: -1.16 (0.33), residues: 669 helix: 0.45 (0.34), residues: 242 sheet: -0.30 (0.38), residues: 201 loop : -2.53 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 34 HIS 0.008 0.002 HIS E 95 PHE 0.012 0.001 PHE D 29 TYR 0.016 0.002 TYR A 62 ARG 0.002 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.05728 ( 236) hydrogen bonds : angle 5.05639 ( 666) SS BOND : bond 0.01012 ( 3) SS BOND : angle 1.87379 ( 6) covalent geometry : bond 0.00393 ( 5512) covalent geometry : angle 0.68661 ( 7463) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7597 (mp0) cc_final: 0.7268 (mp0) REVERT: B 40 THR cc_start: 0.6771 (OUTLIER) cc_final: 0.6458 (p) REVERT: F 374 THR cc_start: 0.7751 (OUTLIER) cc_final: 0.7527 (p) REVERT: E 85 GLN cc_start: 0.6416 (mm110) cc_final: 0.6168 (mm-40) outliers start: 17 outliers final: 10 residues processed: 90 average time/residue: 1.0556 time to fit residues: 99.8590 Evaluate side-chains 94 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.0000 chunk 44 optimal weight: 0.5980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN C 39 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.152247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.127248 restraints weight = 8174.467| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.16 r_work: 0.3586 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5515 Z= 0.170 Angle : 0.688 8.341 7469 Z= 0.351 Chirality : 0.045 0.155 797 Planarity : 0.005 0.067 954 Dihedral : 5.297 23.579 758 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.11 % Allowed : 16.55 % Favored : 81.34 % 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: -1.16 (0.33), residues: 669 helix: 0.45 (0.34), residues: 242 sheet: -0.30 (0.38), residues: 201 loop : -2.53 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 34 HIS 0.008 0.002 HIS E 95 PHE 0.012 0.001 PHE D 29 TYR 0.016 0.002 TYR A 62 ARG 0.002 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.05728 ( 236) hydrogen bonds : angle 5.05638 ( 666) SS BOND : bond 0.01012 ( 3) SS BOND : angle 1.87365 ( 6) covalent geometry : bond 0.00393 ( 5512) covalent geometry : angle 0.68656 ( 7463) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7606 (mp0) cc_final: 0.7277 (mp0) REVERT: B 40 THR cc_start: 0.6772 (OUTLIER) cc_final: 0.6458 (p) REVERT: F 374 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7527 (p) REVERT: E 85 GLN cc_start: 0.6413 (mm110) cc_final: 0.6165 (mm-40) outliers start: 12 outliers final: 10 residues processed: 89 average time/residue: 1.0863 time to fit residues: 101.5042 Evaluate side-chains 94 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.0870 chunk 22 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN C 39 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.152247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127307 restraints weight = 8123.744| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.14 r_work: 0.3587 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5515 Z= 0.170 Angle : 0.688 8.341 7469 Z= 0.351 Chirality : 0.045 0.155 797 Planarity : 0.005 0.067 954 Dihedral : 5.295 23.579 758 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.11 % Allowed : 16.55 % Favored : 81.34 % 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: -1.16 (0.33), residues: 669 helix: 0.45 (0.34), residues: 242 sheet: -0.30 (0.38), residues: 201 loop : -2.53 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 34 HIS 0.008 0.002 HIS E 95 PHE 0.012 0.001 PHE D 29 TYR 0.016 0.002 TYR A 62 ARG 0.002 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.05728 ( 236) hydrogen bonds : angle 5.05638 ( 666) SS BOND : bond 0.01012 ( 3) SS BOND : angle 1.87365 ( 6) covalent geometry : bond 0.00393 ( 5512) covalent geometry : angle 0.68656 ( 7463) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7601 (mp0) cc_final: 0.7272 (mp0) REVERT: B 40 THR cc_start: 0.6769 (OUTLIER) cc_final: 0.6456 (p) REVERT: F 374 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7527 (p) REVERT: E 85 GLN cc_start: 0.6416 (mm110) cc_final: 0.6171 (mm-40) outliers start: 12 outliers final: 10 residues processed: 89 average time/residue: 1.1520 time to fit residues: 107.5912 Evaluate side-chains 94 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 0.0040 chunk 61 optimal weight: 0.9990 overall best weight: 0.3510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN C 39 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.152247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127282 restraints weight = 8123.071| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.15 r_work: 0.3586 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5515 Z= 0.170 Angle : 0.688 8.341 7469 Z= 0.351 Chirality : 0.045 0.155 797 Planarity : 0.005 0.067 954 Dihedral : 5.295 23.579 758 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.11 % Allowed : 16.55 % Favored : 81.34 % 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: -1.16 (0.33), residues: 669 helix: 0.45 (0.34), residues: 242 sheet: -0.30 (0.38), residues: 201 loop : -2.53 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 34 HIS 0.008 0.002 HIS E 95 PHE 0.012 0.001 PHE D 29 TYR 0.016 0.002 TYR A 62 ARG 0.002 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.05728 ( 236) hydrogen bonds : angle 5.05638 ( 666) SS BOND : bond 0.01012 ( 3) SS BOND : angle 1.87365 ( 6) covalent geometry : bond 0.00393 ( 5512) covalent geometry : angle 0.68656 ( 7463) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1338 Ramachandran restraints generated. 669 Oldfield, 0 Emsley, 669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7601 (mp0) cc_final: 0.7271 (mp0) REVERT: B 40 THR cc_start: 0.6770 (OUTLIER) cc_final: 0.6459 (p) REVERT: F 374 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.7527 (p) REVERT: E 85 GLN cc_start: 0.6413 (mm110) cc_final: 0.6166 (mm-40) outliers start: 12 outliers final: 10 residues processed: 89 average time/residue: 1.1460 time to fit residues: 107.0913 Evaluate side-chains 94 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 29 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN C 39 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.152506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127415 restraints weight = 8192.965| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.17 r_work: 0.3587 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5515 Z= 0.160 Angle : 0.683 8.239 7469 Z= 0.348 Chirality : 0.044 0.160 797 Planarity : 0.005 0.066 954 Dihedral : 5.258 22.688 758 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.64 % Allowed : 16.02 % Favored : 81.34 % 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: -1.13 (0.33), residues: 669 helix: 0.48 (0.34), residues: 242 sheet: -0.28 (0.38), residues: 201 loop : -2.52 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 34 HIS 0.008 0.002 HIS E 95 PHE 0.011 0.001 PHE D 29 TYR 0.016 0.002 TYR E 38 ARG 0.002 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.05659 ( 236) hydrogen bonds : angle 5.04065 ( 666) SS BOND : bond 0.01008 ( 3) SS BOND : angle 1.86022 ( 6) covalent geometry : bond 0.00363 ( 5512) covalent geometry : angle 0.68137 ( 7463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5950.13 seconds wall clock time: 104 minutes 6.73 seconds (6246.73 seconds total)