Starting phenix.real_space_refine on Fri Aug 22 16:10:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mnz_48444/08_2025/9mnz_48444.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mnz_48444/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9mnz_48444/08_2025/9mnz_48444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mnz_48444/08_2025/9mnz_48444.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mnz_48444/08_2025/9mnz_48444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mnz_48444/08_2025/9mnz_48444.map" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.26, per 1000 atoms: 0.23 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: 0.28 Conformation dependent library (CDL) restraints added in 138.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.15 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: 0.64 Time building geometry restraints manager: 0.36 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.790 Find NCS groups from input model: 0.040 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:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.170 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.019 0.001 ARG D 19 TYR 0.043 0.005 TYR C 103 PHE 0.029 0.004 PHE B 43 TRP 0.023 0.004 TRP D 36 HIS 0.024 0.005 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.02036 ( 5512) covalent geometry : angle 1.49967 ( 7463) SS BOND : bond 0.00915 ( 3) SS BOND : angle 0.91926 ( 6) hydrogen bonds : bond 0.22924 ( 236) hydrogen bonds : angle 8.22091 ( 666) *********************** 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 : 0.121 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: 0.4570 time to fit residues: 44.4212 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 : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.153465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.128579 restraints weight = 8163.242| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.15 r_work: 0.3604 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5515 Z= 0.172 Angle : 0.740 9.897 7469 Z= 0.382 Chirality : 0.045 0.145 797 Planarity : 0.007 0.093 954 Dihedral : 5.917 31.731 758 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.46 % Allowed : 10.74 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.31), residues: 669 helix: -0.24 (0.33), residues: 241 sheet: -0.73 (0.39), residues: 192 loop : -2.96 (0.34), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 113 TYR 0.016 0.002 TYR A 62 PHE 0.016 0.001 PHE D 29 TRP 0.021 0.001 TRP A 34 HIS 0.007 0.002 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 5512) covalent geometry : angle 0.73785 ( 7463) SS BOND : bond 0.00909 ( 3) SS BOND : angle 1.96825 ( 6) hydrogen bonds : bond 0.06114 ( 236) hydrogen bonds : angle 5.56529 ( 666) *********************** 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 103 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7566 (mp0) cc_final: 0.7353 (mp0) outliers start: 14 outliers final: 8 residues processed: 93 average time/residue: 0.4590 time to fit residues: 44.7665 Evaluate side-chains 90 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.0060 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.152276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127494 restraints weight = 8106.197| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.14 r_work: 0.3589 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2198 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= 0.164 Angle : 0.675 8.930 7469 Z= 0.348 Chirality : 0.044 0.185 797 Planarity : 0.006 0.075 954 Dihedral : 5.362 22.003 758 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.70 % Allowed : 12.68 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.33), residues: 669 helix: 0.34 (0.34), residues: 242 sheet: -0.39 (0.38), residues: 201 loop : -2.64 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 116 TYR 0.016 0.002 TYR E 38 PHE 0.013 0.001 PHE D 29 TRP 0.015 0.001 TRP A 34 HIS 0.007 0.002 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5512) covalent geometry : angle 0.67324 ( 7463) SS BOND : bond 0.01007 ( 3) SS BOND : angle 1.91465 ( 6) hydrogen bonds : bond 0.05692 ( 236) hydrogen bonds : angle 5.19874 ( 666) *********************** 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 103 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7626 (mp0) cc_final: 0.7315 (mp0) REVERT: B 40 THR cc_start: 0.6768 (OUTLIER) cc_final: 0.6458 (p) REVERT: E 21 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7840 (mtt) outliers start: 21 outliers final: 9 residues processed: 91 average time/residue: 0.4213 time to fit residues: 40.1489 Evaluate side-chains 92 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.115 ------------------------------------------------------------------------------- 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 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 21 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 48 optimal weight: 0.0370 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 = 0.152376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127483 restraints weight = 8059.991| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.14 r_work: 0.3589 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2209 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= 0.164 Angle : 0.675 8.930 7469 Z= 0.348 Chirality : 0.044 0.185 797 Planarity : 0.006 0.075 954 Dihedral : 5.363 22.003 758 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.94 % Allowed : 15.32 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.33), residues: 669 helix: 0.34 (0.34), residues: 242 sheet: -0.39 (0.38), residues: 201 loop : -2.64 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 116 TYR 0.016 0.002 TYR E 38 PHE 0.013 0.001 PHE D 29 TRP 0.015 0.001 TRP A 34 HIS 0.007 0.002 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5512) covalent geometry : angle 0.67323 ( 7463) SS BOND : bond 0.01007 ( 3) SS BOND : angle 1.91463 ( 6) hydrogen bonds : bond 0.05692 ( 236) hydrogen bonds : angle 5.19873 ( 666) *********************** 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 92 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7614 (mp0) cc_final: 0.7303 (mp0) REVERT: B 40 THR cc_start: 0.6779 (OUTLIER) cc_final: 0.6471 (p) REVERT: E 21 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7837 (mtt) outliers start: 11 outliers final: 9 residues processed: 86 average time/residue: 0.4619 time to fit residues: 41.4858 Evaluate side-chains 92 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 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 21 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 59 optimal weight: 0.0050 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 0.0770 overall best weight: 0.2952 ------------------------------------------------------------------------------- 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 = 0.152504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.127408 restraints weight = 8286.589| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.19 r_work: 0.3585 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2211 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= 0.164 Angle : 0.675 8.930 7469 Z= 0.348 Chirality : 0.044 0.184 797 Planarity : 0.006 0.075 954 Dihedral : 5.375 22.000 758 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.94 % Allowed : 15.32 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.33), residues: 669 helix: 0.34 (0.34), residues: 242 sheet: -0.39 (0.38), residues: 201 loop : -2.64 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 116 TYR 0.016 0.002 TYR E 38 PHE 0.013 0.001 PHE D 29 TRP 0.015 0.001 TRP A 34 HIS 0.007 0.002 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5512) covalent geometry : angle 0.67303 ( 7463) SS BOND : bond 0.01007 ( 3) SS BOND : angle 1.91400 ( 6) hydrogen bonds : bond 0.05691 ( 236) hydrogen bonds : angle 5.19871 ( 666) *********************** 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 92 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7628 (mp0) cc_final: 0.7315 (mp0) REVERT: B 40 THR cc_start: 0.6773 (OUTLIER) cc_final: 0.6464 (p) REVERT: E 21 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7843 (mtt) outliers start: 11 outliers final: 9 residues processed: 86 average time/residue: 0.4707 time to fit residues: 42.2924 Evaluate side-chains 92 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 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 21 MET 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 3 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 0.0170 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.152532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.127429 restraints weight = 8307.324| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.18 r_work: 0.3586 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2212 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= 0.164 Angle : 0.672 8.907 7469 Z= 0.346 Chirality : 0.044 0.142 797 Planarity : 0.006 0.075 954 Dihedral : 5.489 23.212 758 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.46 % Allowed : 14.96 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.33), residues: 669 helix: 0.36 (0.34), residues: 242 sheet: -0.39 (0.38), residues: 201 loop : -2.63 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 116 TYR 0.015 0.002 TYR E 38 PHE 0.012 0.001 PHE D 29 TRP 0.014 0.001 TRP A 34 HIS 0.007 0.002 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5512) covalent geometry : angle 0.66974 ( 7463) SS BOND : bond 0.01012 ( 3) SS BOND : angle 1.90507 ( 6) hydrogen bonds : bond 0.05687 ( 236) hydrogen bonds : angle 5.19852 ( 666) *********************** 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 95 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7614 (mp0) cc_final: 0.7307 (mp0) REVERT: B 40 THR cc_start: 0.6771 (OUTLIER) cc_final: 0.6465 (p) REVERT: E 21 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7841 (mtt) outliers start: 14 outliers final: 10 residues processed: 87 average time/residue: 0.4611 time to fit residues: 41.8968 Evaluate side-chains 93 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 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 434 ASN Chi-restraints excluded: chain E residue 21 MET 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 37 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 chunk 62 optimal weight: 0.6980 chunk 56 optimal weight: 0.0870 chunk 1 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4033 r_free = 0.4033 target = 0.153152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.128014 restraints weight = 8241.406| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.17 r_work: 0.3597 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5515 Z= 0.143 Angle : 0.676 8.275 7469 Z= 0.343 Chirality : 0.044 0.163 797 Planarity : 0.005 0.070 954 Dihedral : 5.212 20.568 758 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.11 % Allowed : 16.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.33), residues: 669 helix: 0.51 (0.35), residues: 242 sheet: -0.36 (0.38), residues: 201 loop : -2.50 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 116 TYR 0.014 0.001 TYR A 62 PHE 0.012 0.001 PHE D 29 TRP 0.013 0.001 TRP A 34 HIS 0.006 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5512) covalent geometry : angle 0.67483 ( 7463) SS BOND : bond 0.00928 ( 3) SS BOND : angle 1.77242 ( 6) hydrogen bonds : bond 0.05393 ( 236) hydrogen bonds : angle 5.07755 ( 666) *********************** 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 97 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7622 (mp0) cc_final: 0.7307 (mp0) REVERT: C 101 LEU cc_start: 0.7429 (tp) cc_final: 0.7050 (tp) REVERT: A 23 MET cc_start: 0.6581 (OUTLIER) cc_final: 0.5899 (ptp) REVERT: E 21 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7832 (mtt) REVERT: E 85 GLN cc_start: 0.6383 (mm110) cc_final: 0.6134 (mm-40) outliers start: 12 outliers final: 8 residues processed: 89 average time/residue: 0.4581 time to fit residues: 42.6761 Evaluate side-chains 92 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 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 21 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 50 optimal weight: 0.0670 chunk 47 optimal weight: 0.5980 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.152670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.127818 restraints weight = 8078.834| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.14 r_work: 0.3596 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5515 Z= 0.143 Angle : 0.675 8.253 7469 Z= 0.342 Chirality : 0.044 0.162 797 Planarity : 0.005 0.070 954 Dihedral : 5.243 20.525 758 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.76 % Allowed : 16.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.33), residues: 669 helix: 0.51 (0.35), residues: 242 sheet: -0.35 (0.38), residues: 201 loop : -2.50 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 116 TYR 0.014 0.001 TYR A 62 PHE 0.012 0.001 PHE D 29 TRP 0.013 0.001 TRP A 34 HIS 0.006 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5512) covalent geometry : angle 0.67380 ( 7463) SS BOND : bond 0.00928 ( 3) SS BOND : angle 1.77135 ( 6) hydrogen bonds : bond 0.05395 ( 236) hydrogen bonds : angle 5.07762 ( 666) *********************** 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 92 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7617 (mp0) cc_final: 0.7304 (mp0) REVERT: C 101 LEU cc_start: 0.7430 (tp) cc_final: 0.7054 (tp) REVERT: A 23 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.5888 (ptp) REVERT: E 21 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7823 (mtt) REVERT: E 85 GLN cc_start: 0.6384 (mm110) cc_final: 0.6133 (mm-40) outliers start: 10 outliers final: 8 residues processed: 86 average time/residue: 0.4620 time to fit residues: 41.5578 Evaluate side-chains 92 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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 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 21 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4006 r_free = 0.4006 target = 0.151145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125890 restraints weight = 8235.630| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.17 r_work: 0.3563 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5515 Z= 0.204 Angle : 0.718 8.397 7469 Z= 0.367 Chirality : 0.046 0.149 797 Planarity : 0.006 0.068 954 Dihedral : 5.307 21.445 758 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.94 % Allowed : 16.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.33), residues: 669 helix: 0.46 (0.34), residues: 243 sheet: -0.26 (0.38), residues: 201 loop : -2.44 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 378 TYR 0.020 0.002 TYR E 38 PHE 0.012 0.001 PHE A 69 TRP 0.032 0.002 TRP A 34 HIS 0.010 0.002 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 5512) covalent geometry : angle 0.71503 ( 7463) SS BOND : bond 0.01283 ( 3) SS BOND : angle 2.48530 ( 6) hydrogen bonds : bond 0.06171 ( 236) hydrogen bonds : angle 5.05270 ( 666) *********************** 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: 11 poor density : 83 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7636 (mp0) cc_final: 0.7323 (mp0) REVERT: A 23 MET cc_start: 0.6695 (OUTLIER) cc_final: 0.5923 (ptp) REVERT: E 85 GLN cc_start: 0.6420 (mm110) cc_final: 0.6165 (mm-40) outliers start: 11 outliers final: 8 residues processed: 87 average time/residue: 0.4665 time to fit residues: 42.5464 Evaluate side-chains 91 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 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 49 SER 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 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.0000 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 overall best weight: 0.3184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4007 r_free = 0.4007 target = 0.151051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.125913 restraints weight = 8155.446| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.16 r_work: 0.3563 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5515 Z= 0.198 Angle : 0.717 8.395 7469 Z= 0.366 Chirality : 0.046 0.148 797 Planarity : 0.006 0.068 954 Dihedral : 5.500 28.626 758 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.58 % Allowed : 16.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.33), residues: 669 helix: 0.46 (0.34), residues: 243 sheet: -0.26 (0.38), residues: 201 loop : -2.44 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 378 TYR 0.020 0.002 TYR E 38 PHE 0.012 0.001 PHE A 69 TRP 0.030 0.002 TRP A 34 HIS 0.010 0.002 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 5512) covalent geometry : angle 0.71257 ( 7463) SS BOND : bond 0.01023 ( 3) SS BOND : angle 2.87455 ( 6) hydrogen bonds : bond 0.06151 ( 236) hydrogen bonds : angle 5.05255 ( 666) ********************** 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 91 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7615 (mp0) cc_final: 0.7304 (mp0) REVERT: A 23 MET cc_start: 0.6695 (OUTLIER) cc_final: 0.5933 (ptp) REVERT: E 85 GLN cc_start: 0.6420 (mm110) cc_final: 0.6172 (mm-40) outliers start: 9 outliers final: 8 residues processed: 86 average time/residue: 0.4680 time to fit residues: 42.1546 Evaluate side-chains 91 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 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 49 SER 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 36 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 59 optimal weight: 0.0970 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.152024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.127121 restraints weight = 8083.090| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.14 r_work: 0.3579 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5515 Z= 0.145 Angle : 0.677 8.408 7469 Z= 0.344 Chirality : 0.044 0.145 797 Planarity : 0.005 0.069 954 Dihedral : 5.211 22.188 758 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.11 % Allowed : 16.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.33), residues: 669 helix: 0.62 (0.34), residues: 242 sheet: -0.25 (0.38), residues: 201 loop : -2.35 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 378 TYR 0.016 0.001 TYR E 38 PHE 0.012 0.001 PHE D 29 TRP 0.024 0.001 TRP A 34 HIS 0.007 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5512) covalent geometry : angle 0.67538 ( 7463) SS BOND : bond 0.01041 ( 3) SS BOND : angle 1.99572 ( 6) hydrogen bonds : bond 0.05576 ( 236) hydrogen bonds : angle 4.99277 ( 666) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2412.13 seconds wall clock time: 41 minutes 37.72 seconds (2497.72 seconds total)