Starting phenix.real_space_refine on Sat May 10 08:06:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mnz_48444/05_2025/9mnz_48444.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mnz_48444/05_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_48444/05_2025/9mnz_48444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mnz_48444/05_2025/9mnz_48444.map" model { file = "/net/cci-nas-00/data/ceres_data/9mnz_48444/05_2025/9mnz_48444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mnz_48444/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 4.51, per 1000 atoms: 0.84 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: 1.28 Conformation dependent library (CDL) restraints added in 638.5 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: 0.63 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: 1.47 Time building geometry restraints manager: 1.48 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: 3.520 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.680 Find NCS groups from input model: 0.090 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:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.370 ------------------------------------------------------------------------------- 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 : 0.439 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: 1.0563 time to fit residues: 102.9318 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 : 0.713 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.155695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.130960 restraints weight = 8079.502| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.13 r_work: 0.3633 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- 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 0.032 5515 Z= 0.141 Angle : 0.692 9.175 7469 Z= 0.358 Chirality : 0.043 0.139 797 Planarity : 0.006 0.091 954 Dihedral : 5.718 30.030 758 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.26 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 0.05521 ( 236) hydrogen bonds : angle 5.49259 ( 666) SS BOND : bond 0.00751 ( 3) SS BOND : angle 1.50848 ( 6) covalent geometry : bond 0.00302 ( 5512) covalent geometry : angle 0.69087 ( 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 : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7554 (mp0) cc_final: 0.7283 (mp0) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 1.0320 time to fit residues: 100.7368 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 : 0.512 ------------------------------------------------------------------------------- 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: 0.0770 chunk 42 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 60 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.5316 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.153708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128895 restraints weight = 8093.289| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.15 r_work: 0.3612 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2107 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= 0.163 Angle : 0.674 8.782 7469 Z= 0.346 Chirality : 0.044 0.176 797 Planarity : 0.006 0.074 954 Dihedral : 5.509 27.446 758 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.82 % Allowed : 12.32 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.32), residues: 669 helix: 0.26 (0.34), residues: 241 sheet: -0.39 (0.39), residues: 195 loop : -2.79 (0.35), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 34 HIS 0.008 0.002 HIS E 95 PHE 0.011 0.001 PHE D 29 TYR 0.014 0.002 TYR A 62 ARG 0.002 0.000 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.05563 ( 236) hydrogen bonds : angle 5.29018 ( 666) SS BOND : bond 0.00863 ( 3) SS BOND : angle 1.74445 ( 6) covalent geometry : bond 0.00371 ( 5512) covalent geometry : angle 0.67207 ( 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 99 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7578 (mp0) cc_final: 0.7270 (mp0) REVERT: C 101 LEU cc_start: 0.7459 (tp) cc_final: 0.7093 (tp) outliers start: 16 outliers final: 10 residues processed: 90 average time/residue: 1.1676 time to fit residues: 109.7227 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 : 0.555 ------------------------------------------------------------------------------- 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 434 ASN Chi-restraints excluded: chain E residue 28 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 62 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 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 ** 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 = 0.4044 r_free = 0.4044 target = 0.153961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.129044 restraints weight = 8269.776| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.17 r_work: 0.3609 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2115 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= 0.163 Angle : 0.674 8.782 7469 Z= 0.346 Chirality : 0.044 0.176 797 Planarity : 0.006 0.074 954 Dihedral : 5.509 27.446 758 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.76 % Allowed : 13.56 % Favored : 84.68 % 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: -1.47 (0.32), residues: 669 helix: 0.26 (0.34), residues: 241 sheet: -0.39 (0.39), residues: 195 loop : -2.79 (0.35), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 34 HIS 0.008 0.002 HIS E 95 PHE 0.011 0.001 PHE D 29 TYR 0.014 0.002 TYR A 62 ARG 0.002 0.000 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.05563 ( 236) hydrogen bonds : angle 5.29018 ( 666) SS BOND : bond 0.00863 ( 3) SS BOND : angle 1.74445 ( 6) covalent geometry : bond 0.00371 ( 5512) covalent geometry : angle 0.67207 ( 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 : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7607 (mp0) cc_final: 0.7289 (mp0) REVERT: C 101 LEU cc_start: 0.7463 (tp) cc_final: 0.7097 (tp) outliers start: 10 outliers final: 10 residues processed: 85 average time/residue: 1.1513 time to fit residues: 102.5735 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 : 0.559 ------------------------------------------------------------------------------- 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 434 ASN Chi-restraints excluded: chain E residue 28 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 14 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 1 optimal weight: 0.0010 chunk 21 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.153808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.128804 restraints weight = 8111.939| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.15 r_work: 0.3602 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- 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 = 0.36 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 = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 0.033 5515 Z= 0.159 Angle : 0.681 10.101 7469 Z= 0.347 Chirality : 0.044 0.158 797 Planarity : 0.005 0.069 954 Dihedral : 5.355 24.983 758 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.82 % Allowed : 14.44 % 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 (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: -1.24 (0.33), residues: 669 helix: 0.39 (0.34), residues: 242 sheet: -0.37 (0.38), residues: 199 loop : -2.55 (0.37), residues: 228 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 0.011 0.001 PHE D 29 TYR 0.015 0.002 TYR E 38 ARG 0.003 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.05528 ( 236) hydrogen bonds : angle 5.12676 ( 666) SS BOND : bond 0.00909 ( 3) SS BOND : angle 1.69140 ( 6) covalent geometry : bond 0.00362 ( 5512) covalent geometry : angle 0.67970 ( 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 98 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7599 (mp0) cc_final: 0.7251 (mp0) REVERT: B 40 THR cc_start: 0.6791 (OUTLIER) cc_final: 0.6476 (p) REVERT: B 113 ARG cc_start: 0.6790 (ttp-170) cc_final: 0.6478 (mtm180) REVERT: E 85 GLN cc_start: 0.6401 (mm110) cc_final: 0.6147 (mm-40) outliers start: 16 outliers final: 10 residues processed: 90 average time/residue: 1.0264 time to fit residues: 97.1071 Evaluate side-chains 93 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 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: 0.0070 chunk 57 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.153637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128600 restraints weight = 8124.178| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.16 r_work: 0.3598 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2196 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= 0.159 Angle : 0.681 10.101 7469 Z= 0.347 Chirality : 0.044 0.158 797 Planarity : 0.005 0.069 954 Dihedral : 5.396 24.982 758 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.94 % Allowed : 15.49 % 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 (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: -1.24 (0.33), residues: 669 helix: 0.40 (0.34), residues: 242 sheet: -0.37 (0.38), residues: 199 loop : -2.55 (0.37), residues: 228 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 0.011 0.001 PHE D 29 TYR 0.015 0.002 TYR E 38 ARG 0.003 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.05527 ( 236) hydrogen bonds : angle 5.12672 ( 666) SS BOND : bond 0.00909 ( 3) SS BOND : angle 1.69112 ( 6) covalent geometry : bond 0.00362 ( 5512) covalent geometry : angle 0.67956 ( 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 93 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7599 (mp0) cc_final: 0.7253 (mp0) REVERT: B 40 THR cc_start: 0.6794 (OUTLIER) cc_final: 0.6483 (p) REVERT: B 113 ARG cc_start: 0.6788 (ttp-170) cc_final: 0.6474 (mtm180) REVERT: E 85 GLN cc_start: 0.6404 (mm110) cc_final: 0.6149 (mm-40) outliers start: 11 outliers final: 10 residues processed: 87 average time/residue: 1.1383 time to fit residues: 103.7667 Evaluate side-chains 93 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 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: 0.5138 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.153583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.128510 restraints weight = 8145.453| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.16 r_work: 0.3597 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.69 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) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2196 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= 0.158 Angle : 0.680 10.095 7469 Z= 0.346 Chirality : 0.044 0.157 797 Planarity : 0.005 0.069 954 Dihedral : 5.535 27.958 758 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.94 % Allowed : 15.49 % 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 (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: -1.24 (0.33), residues: 669 helix: 0.40 (0.34), residues: 242 sheet: -0.37 (0.38), residues: 199 loop : -2.55 (0.37), residues: 228 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 0.011 0.001 PHE D 29 TYR 0.015 0.002 TYR E 38 ARG 0.002 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.05527 ( 236) hydrogen bonds : angle 5.12641 ( 666) SS BOND : bond 0.00909 ( 3) SS BOND : angle 1.68989 ( 6) covalent geometry : bond 0.00362 ( 5512) covalent geometry : angle 0.67873 ( 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 93 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7604 (mp0) cc_final: 0.7257 (mp0) REVERT: B 40 THR cc_start: 0.6793 (OUTLIER) cc_final: 0.6481 (p) REVERT: B 113 ARG cc_start: 0.6791 (ttp-170) cc_final: 0.6478 (mtm180) REVERT: E 85 GLN cc_start: 0.6404 (mm110) cc_final: 0.6149 (mm-40) outliers start: 11 outliers final: 10 residues processed: 87 average time/residue: 1.0689 time to fit residues: 97.5372 Evaluate side-chains 93 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 0.0170 chunk 39 optimal weight: 0.0030 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 chunk 16 optimal weight: 0.0040 chunk 44 optimal weight: 0.1980 overall best weight: 0.1040 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.156902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.132015 restraints weight = 8277.999| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.16 r_work: 0.3651 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5515 Z= 0.103 Angle : 0.584 7.481 7469 Z= 0.296 Chirality : 0.040 0.135 797 Planarity : 0.005 0.063 954 Dihedral : 4.706 19.237 758 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.94 % Allowed : 16.02 % Favored : 82.04 % 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: -0.85 (0.33), residues: 669 helix: 0.75 (0.35), residues: 241 sheet: -0.20 (0.38), residues: 196 loop : -2.27 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 50 HIS 0.005 0.001 HIS C 105 PHE 0.012 0.001 PHE D 29 TYR 0.008 0.001 TYR C 79 ARG 0.002 0.000 ARG F 378 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 236) hydrogen bonds : angle 4.66606 ( 666) SS BOND : bond 0.00559 ( 3) SS BOND : angle 1.03674 ( 6) covalent geometry : bond 0.00209 ( 5512) covalent geometry : angle 0.58351 ( 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: 11 poor density : 83 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7568 (mp0) cc_final: 0.7259 (mp0) REVERT: C 101 LEU cc_start: 0.7463 (tp) cc_final: 0.7068 (tp) REVERT: B 40 THR cc_start: 0.6836 (OUTLIER) cc_final: 0.6506 (p) REVERT: A 23 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.5918 (ptp) REVERT: F 374 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7270 (p) REVERT: E 85 GLN cc_start: 0.6195 (mm110) cc_final: 0.5993 (mm-40) outliers start: 11 outliers final: 5 residues processed: 88 average time/residue: 1.0232 time to fit residues: 94.9414 Evaluate side-chains 88 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 52 optimal weight: 0.2980 chunk 7 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 53 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.0570 chunk 22 optimal weight: 0.9980 overall best weight: 0.3298 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.156998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.132141 restraints weight = 8220.372| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.16 r_work: 0.3648 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5515 Z= 0.103 Angle : 0.584 7.481 7469 Z= 0.296 Chirality : 0.040 0.135 797 Planarity : 0.005 0.063 954 Dihedral : 4.706 19.237 758 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.41 % Allowed : 16.90 % Favored : 81.69 % 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: -0.85 (0.33), residues: 669 helix: 0.75 (0.35), residues: 241 sheet: -0.20 (0.38), residues: 196 loop : -2.27 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 50 HIS 0.005 0.001 HIS C 105 PHE 0.012 0.001 PHE D 29 TYR 0.008 0.001 TYR C 79 ARG 0.002 0.000 ARG F 378 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 236) hydrogen bonds : angle 4.66606 ( 666) SS BOND : bond 0.00559 ( 3) SS BOND : angle 1.03674 ( 6) covalent geometry : bond 0.00209 ( 5512) covalent geometry : angle 0.58351 ( 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 88 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7554 (mp0) cc_final: 0.7240 (mp0) REVERT: C 101 LEU cc_start: 0.7469 (tp) cc_final: 0.7076 (tp) REVERT: B 40 THR cc_start: 0.6822 (OUTLIER) cc_final: 0.6488 (p) REVERT: A 23 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.5925 (ptp) REVERT: F 374 THR cc_start: 0.7498 (OUTLIER) cc_final: 0.7274 (p) outliers start: 8 outliers final: 5 residues processed: 84 average time/residue: 1.0657 time to fit residues: 93.9995 Evaluate side-chains 88 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.156778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131989 restraints weight = 8223.444| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.16 r_work: 0.3649 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5515 Z= 0.103 Angle : 0.584 7.481 7469 Z= 0.296 Chirality : 0.040 0.135 797 Planarity : 0.005 0.063 954 Dihedral : 4.708 19.238 758 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.41 % Allowed : 17.08 % 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: -0.85 (0.33), residues: 669 helix: 0.75 (0.35), residues: 241 sheet: -0.20 (0.38), residues: 196 loop : -2.27 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 50 HIS 0.005 0.001 HIS C 105 PHE 0.012 0.001 PHE D 29 TYR 0.008 0.001 TYR C 79 ARG 0.002 0.000 ARG F 378 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 236) hydrogen bonds : angle 4.66605 ( 666) SS BOND : bond 0.00558 ( 3) SS BOND : angle 1.03692 ( 6) covalent geometry : bond 0.00209 ( 5512) covalent geometry : angle 0.58350 ( 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 88 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 88 GLU cc_start: 0.7558 (mp0) cc_final: 0.7243 (mp0) REVERT: C 101 LEU cc_start: 0.7468 (tp) cc_final: 0.7075 (tp) REVERT: B 40 THR cc_start: 0.6817 (OUTLIER) cc_final: 0.6483 (p) REVERT: A 23 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.5931 (ptp) REVERT: F 374 THR cc_start: 0.7496 (OUTLIER) cc_final: 0.7273 (p) outliers start: 8 outliers final: 5 residues processed: 84 average time/residue: 1.1306 time to fit residues: 99.6722 Evaluate side-chains 88 residues out of total 566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.0470 chunk 50 optimal weight: 0.0470 chunk 10 optimal weight: 0.2980 chunk 3 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.2576 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.156778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.131940 restraints weight = 8304.114| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.17 r_work: 0.3648 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5515 Z= 0.103 Angle : 0.584 7.481 7469 Z= 0.296 Chirality : 0.040 0.135 797 Planarity : 0.005 0.063 954 Dihedral : 4.706 19.238 758 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.41 % Allowed : 17.08 % 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: -0.85 (0.33), residues: 669 helix: 0.75 (0.35), residues: 241 sheet: -0.20 (0.38), residues: 196 loop : -2.27 (0.37), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 50 HIS 0.005 0.001 HIS C 105 PHE 0.012 0.001 PHE D 29 TYR 0.008 0.001 TYR C 79 ARG 0.002 0.000 ARG F 378 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 236) hydrogen bonds : angle 4.66605 ( 666) SS BOND : bond 0.00558 ( 3) SS BOND : angle 1.03692 ( 6) covalent geometry : bond 0.00209 ( 5512) covalent geometry : angle 0.58350 ( 7463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5522.40 seconds wall clock time: 95 minutes 46.29 seconds (5746.29 seconds total)