Starting phenix.real_space_refine on Thu Jun 5 06:45:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mnx_48442/06_2025/9mnx_48442.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mnx_48442/06_2025/9mnx_48442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mnx_48442/06_2025/9mnx_48442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mnx_48442/06_2025/9mnx_48442.map" model { file = "/net/cci-nas-00/data/ceres_data/9mnx_48442/06_2025/9mnx_48442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mnx_48442/06_2025/9mnx_48442.cif" } resolution = 3.11 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= 0.019 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 379 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 29 5.16 5 C 3332 2.51 5 N 909 2.21 5 O 970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5240 Number of models: 1 Model: "" Number of chains: 7 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: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 823 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "D" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 962 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "E" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} 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: "F" Number of atoms: 672 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 669 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 85, 669 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain breaks: 1 bond proxies already assigned to first conformer: 672 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: 4.25, per 1000 atoms: 0.81 Number of scatterers: 5240 At special positions: 0 Unit cell: (94.6, 72.24, 148.78, 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 29 16.00 O 970 8.00 N 909 7.00 C 3332 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=2.06 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 94 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.05 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: 1.66 Conformation dependent library (CDL) restraints added in 848.0 milliseconds 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1222 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 10 sheets defined 37.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'B' and resid 9 through 24 removed outlier: 3.597A pdb=" N ARG B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 43 through 60 removed outlier: 4.007A pdb=" N ILE B 47 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU B 52 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N CYS B 54 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA B 55 " --> pdb=" O GLY B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 89 removed outlier: 3.659A pdb=" N SER B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ARG B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 86 " --> pdb=" O TRP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 121 removed outlier: 3.671A pdb=" N ARG B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B 117 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 119 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 22 Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.585A pdb=" N TRP A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 43 removed outlier: 4.121A pdb=" N ASN A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) Proline residue: A 37 - end of helix Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 52 through 72 removed outlier: 3.666A pdb=" N CYS A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU A 64 " --> pdb=" O CYS A 60 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 70 " --> pdb=" O PHE A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 107 removed outlier: 3.854A pdb=" N VAL A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 77 Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.873A pdb=" N THR C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 382 removed outlier: 4.050A pdb=" N GLY F 380 " --> pdb=" O GLU F 376 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE F 382 " --> pdb=" O ARG F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 400 Processing helix chain 'F' and resid 400 through 406 removed outlier: 3.665A pdb=" N GLU F 404 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS F 405 " --> pdb=" O LYS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 429 removed outlier: 3.512A pdb=" N TYR F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU F 426 " --> pdb=" O SER F 422 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN F 429 " --> pdb=" O TYR F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 448 removed outlier: 3.590A pdb=" N ARG F 438 " --> pdb=" O ASN F 434 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN F 439 " --> pdb=" O GLU F 435 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY F 440 " --> pdb=" O ALA F 436 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN F 443 " --> pdb=" O ASN F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 467 removed outlier: 3.682A pdb=" N LYS F 461 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER F 465 " --> pdb=" O LYS F 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.506A pdb=" N LEU D 81 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER D 71 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.586A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY D 33 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG D 99 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR D 117 " --> pdb=" O TYR D 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AA4, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.518A pdb=" N ASP E 76 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.633A pdb=" N TYR E 92 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR E 93 " --> pdb=" O TYR E 42 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU E 39 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N TYR E 55 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP E 41 " --> pdb=" O LEU E 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.633A pdb=" N TYR E 92 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR E 102 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 30 through 31 removed outlier: 3.697A pdb=" N LYS E 36 " --> pdb=" O TYR E 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2 through 7 removed outlier: 3.603A pdb=" N SER C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.546A pdb=" N ALA C 96 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 50 " --> pdb=" O ASN C 58 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 13 231 hydrogen bonds defined for protein. 615 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: 1.29 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1000 1.32 - 1.45: 1661 1.45 - 1.58: 2658 1.58 - 1.71: 0 1.71 - 1.84: 48 Bond restraints: 5367 Sorted by residual: bond pdb=" C22 I2R A 201 " pdb=" N4 I2R A 201 " ideal model delta sigma weight residual 1.156 1.371 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C SER B 95 " pdb=" O SER B 95 " ideal model delta sigma weight residual 1.236 1.315 -0.079 1.18e-02 7.18e+03 4.46e+01 bond pdb=" C9 I2R A 201 " pdb=" N3 I2R A 201 " ideal model delta sigma weight residual 1.413 1.299 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C ALA B 98 " pdb=" O ALA B 98 " ideal model delta sigma weight residual 1.236 1.293 -0.057 1.16e-02 7.43e+03 2.38e+01 bond pdb=" C PHE B 97 " pdb=" O PHE B 97 " ideal model delta sigma weight residual 1.236 1.290 -0.054 1.15e-02 7.56e+03 2.21e+01 ... (remaining 5362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 6917 3.18 - 6.36: 318 6.36 - 9.54: 25 9.54 - 12.72: 4 12.72 - 15.90: 1 Bond angle restraints: 7265 Sorted by residual: angle pdb=" N ASP B 18 " pdb=" CA ASP B 18 " pdb=" C ASP B 18 " ideal model delta sigma weight residual 111.36 103.26 8.10 1.09e+00 8.42e-01 5.52e+01 angle pdb=" N PRO B 91 " pdb=" CA PRO B 91 " pdb=" C PRO B 91 " ideal model delta sigma weight residual 110.55 101.15 9.40 1.63e+00 3.76e-01 3.33e+01 angle pdb=" C LEU B 96 " pdb=" N PHE B 97 " pdb=" CA PHE B 97 " ideal model delta sigma weight residual 120.54 112.92 7.62 1.35e+00 5.49e-01 3.18e+01 angle pdb=" C12 I2R A 201 " pdb=" C19 I2R A 201 " pdb=" C22 I2R A 201 " ideal model delta sigma weight residual 122.00 137.90 -15.90 3.00e+00 1.11e-01 2.81e+01 angle pdb=" N TYR E 92 " pdb=" CA TYR E 92 " pdb=" CB TYR E 92 " ideal model delta sigma weight residual 110.57 103.35 7.22 1.57e+00 4.06e-01 2.12e+01 ... (remaining 7260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2876 17.88 - 35.75: 247 35.75 - 53.63: 43 53.63 - 71.50: 7 71.50 - 89.38: 6 Dihedral angle restraints: 3179 sinusoidal: 1265 harmonic: 1914 Sorted by residual: dihedral pdb=" CA SER A 47 " pdb=" C SER A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta harmonic sigma weight residual -180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA PHE B 80 " pdb=" C PHE B 80 " pdb=" N ILE B 81 " pdb=" CA ILE B 81 " ideal model delta harmonic sigma weight residual 180.00 155.49 24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA THR B 12 " pdb=" C THR B 12 " pdb=" N TYR B 13 " pdb=" CA TYR B 13 " ideal model delta harmonic sigma weight residual 180.00 157.10 22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 3176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 364 0.054 - 0.108: 247 0.108 - 0.162: 111 0.162 - 0.216: 37 0.216 - 0.269: 14 Chirality restraints: 773 Sorted by residual: chirality pdb=" CG LEU C 18 " pdb=" CB LEU C 18 " pdb=" CD1 LEU C 18 " pdb=" CD2 LEU C 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.82e+00 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 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CG LEU B 52 " pdb=" CB LEU B 52 " pdb=" CD1 LEU B 52 " pdb=" CD2 LEU B 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 770 not shown) Planarity restraints: 929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 37 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO B 38 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 29 " -0.060 5.00e-02 4.00e+02 8.96e-02 1.28e+01 pdb=" N PRO B 30 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 34 " 0.028 2.00e-02 2.50e+03 2.76e-02 1.14e+01 pdb=" CG HIS B 34 " -0.059 2.00e-02 2.50e+03 pdb=" ND1 HIS B 34 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 34 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS B 34 " 0.004 2.00e-02 2.50e+03 pdb=" NE2 HIS B 34 " 0.009 2.00e-02 2.50e+03 ... (remaining 926 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 822 2.74 - 3.28: 4581 3.28 - 3.82: 7666 3.82 - 4.36: 9513 4.36 - 4.90: 16024 Nonbonded interactions: 38606 Sorted by model distance: nonbonded pdb=" N GLU B 26 " pdb=" OE1 GLU B 26 " model vdw 2.195 3.120 nonbonded pdb=" OG1 THR D 69 " pdb=" OG SER F 444 " model vdw 2.196 3.040 nonbonded pdb=" O GLU B 120 " pdb=" N LYS B 124 " model vdw 2.197 3.120 nonbonded pdb=" NZ LYS E 24 " pdb=" OD1 ASP E 76 " model vdw 2.202 3.120 nonbonded pdb=" O LYS F 461 " pdb=" OG SER F 465 " model vdw 2.227 3.040 ... (remaining 38601 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: 1.760 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.350 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 : 0.021 0.215 5370 Z= 0.937 Angle : 1.466 15.901 7271 Z= 0.856 Chirality : 0.087 0.269 773 Planarity : 0.011 0.102 929 Dihedral : 14.420 89.376 1948 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.56 % Favored : 86.44 % Rotamer: Outliers : 0.54 % Allowed : 1.26 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.28), residues: 650 helix: -2.64 (0.28), residues: 219 sheet: -1.89 (0.38), residues: 176 loop : -3.59 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP A 28 HIS 0.027 0.005 HIS B 34 PHE 0.041 0.005 PHE E 103 TYR 0.045 0.005 TYR A 71 ARG 0.012 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.29320 ( 217) hydrogen bonds : angle 9.49301 ( 615) SS BOND : bond 0.01975 ( 3) SS BOND : angle 1.80772 ( 6) covalent geometry : bond 0.02093 ( 5367) covalent geometry : angle 1.46596 ( 7265) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.498 Fit side-chains REVERT: D 73 ASP cc_start: 0.7458 (t0) cc_final: 0.7198 (t0) REVERT: E 3 MET cc_start: 0.6953 (mmm) cc_final: 0.6436 (mmm) outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.2045 time to fit residues: 20.1106 Evaluate side-chains 78 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TYR Chi-restraints excluded: chain A residue 115 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN F 383 GLN F 406 GLN ** F 432 ASN ** 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 = 0.3786 r_free = 0.3786 target = 0.140350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115470 restraints weight = 7675.609| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.17 r_work: 0.3325 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5370 Z= 0.182 Angle : 0.734 8.513 7271 Z= 0.380 Chirality : 0.044 0.140 773 Planarity : 0.007 0.082 929 Dihedral : 6.246 48.487 743 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.72 % Allowed : 7.58 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.31), residues: 650 helix: -1.23 (0.33), residues: 219 sheet: -1.31 (0.36), residues: 193 loop : -2.95 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 94 HIS 0.010 0.002 HIS E 95 PHE 0.015 0.002 PHE D 29 TYR 0.018 0.002 TYR A 62 ARG 0.003 0.001 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.07169 ( 217) hydrogen bonds : angle 5.84430 ( 615) SS BOND : bond 0.01208 ( 3) SS BOND : angle 1.67824 ( 6) covalent geometry : bond 0.00398 ( 5367) covalent geometry : angle 0.73265 ( 7265) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.503 Fit side-chains REVERT: D 87 ARG cc_start: 0.7556 (mtt180) cc_final: 0.7334 (mtt180) REVERT: E 3 MET cc_start: 0.8104 (mmm) cc_final: 0.7618 (mmm) REVERT: C 120 GLU cc_start: 0.7882 (pt0) cc_final: 0.7661 (pt0) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.2045 time to fit residues: 19.7117 Evaluate side-chains 75 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain C residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.139484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114772 restraints weight = 7738.925| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.17 r_work: 0.3308 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5370 Z= 0.180 Angle : 0.688 7.679 7271 Z= 0.354 Chirality : 0.043 0.136 773 Planarity : 0.006 0.066 929 Dihedral : 5.383 18.884 738 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.08 % Allowed : 9.57 % Favored : 89.35 % 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: -2.30 (0.32), residues: 650 helix: -0.63 (0.35), residues: 219 sheet: -0.92 (0.37), residues: 190 loop : -2.82 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 36 HIS 0.010 0.002 HIS E 95 PHE 0.011 0.001 PHE D 29 TYR 0.019 0.002 TYR A 62 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.06880 ( 217) hydrogen bonds : angle 5.42331 ( 615) SS BOND : bond 0.01031 ( 3) SS BOND : angle 1.65227 ( 6) covalent geometry : bond 0.00407 ( 5367) covalent geometry : angle 0.68661 ( 7265) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.572 Fit side-chains REVERT: B 66 LYS cc_start: 0.7921 (mtpp) cc_final: 0.7702 (mtpt) REVERT: E 3 MET cc_start: 0.8099 (mmm) cc_final: 0.7623 (mmm) outliers start: 6 outliers final: 5 residues processed: 73 average time/residue: 0.2097 time to fit residues: 19.3934 Evaluate side-chains 74 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 37 optimal weight: 0.4980 chunk 11 optimal weight: 0.0470 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.0370 chunk 16 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 overall best weight: 0.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.139805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114500 restraints weight = 7924.233| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.25 r_work: 0.3304 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.233 5370 Z= 0.290 Angle : 0.695 7.679 7271 Z= 0.358 Chirality : 0.043 0.136 773 Planarity : 0.006 0.066 929 Dihedral : 5.383 18.884 738 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.90 % Allowed : 10.83 % Favored : 88.27 % 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: -2.30 (0.32), residues: 650 helix: -0.63 (0.35), residues: 219 sheet: -0.92 (0.37), residues: 190 loop : -2.82 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 36 HIS 0.010 0.002 HIS E 95 PHE 0.011 0.001 PHE D 29 TYR 0.019 0.002 TYR A 62 ARG 0.003 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.06880 ( 217) hydrogen bonds : angle 5.42331 ( 615) SS BOND : bond 0.01031 ( 3) SS BOND : angle 1.65227 ( 6) covalent geometry : bond 0.00516 ( 5367) covalent geometry : angle 0.69387 ( 7265) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.577 Fit side-chains REVERT: B 66 LYS cc_start: 0.7939 (mtpp) cc_final: 0.7720 (mtpt) REVERT: E 3 MET cc_start: 0.8133 (mmm) cc_final: 0.7665 (mmm) outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.2100 time to fit residues: 18.8979 Evaluate side-chains 74 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 8 optimal weight: 0.0270 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 0.0070 chunk 58 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.116866 restraints weight = 7846.980| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.25 r_work: 0.3330 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5370 Z= 0.130 Angle : 0.632 7.144 7271 Z= 0.321 Chirality : 0.041 0.128 773 Planarity : 0.006 0.065 929 Dihedral : 5.091 18.304 738 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.90 % Allowed : 12.09 % Favored : 87.00 % 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: -2.00 (0.32), residues: 650 helix: -0.24 (0.36), residues: 221 sheet: -0.72 (0.36), residues: 190 loop : -2.83 (0.34), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 47 HIS 0.003 0.001 HIS A 84 PHE 0.012 0.001 PHE D 68 TYR 0.014 0.001 TYR A 62 ARG 0.007 0.001 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.05837 ( 217) hydrogen bonds : angle 5.03990 ( 615) SS BOND : bond 0.00744 ( 3) SS BOND : angle 1.21122 ( 6) covalent geometry : bond 0.00266 ( 5367) covalent geometry : angle 0.63151 ( 7265) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: E 3 MET cc_start: 0.8123 (mmm) cc_final: 0.7691 (mmm) outliers start: 5 outliers final: 5 residues processed: 69 average time/residue: 0.2051 time to fit residues: 17.7985 Evaluate side-chains 71 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain F residue 464 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.0070 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.0370 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.142267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117312 restraints weight = 7791.721| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.21 r_work: 0.3329 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5370 Z= 0.132 Angle : 0.632 7.144 7271 Z= 0.321 Chirality : 0.041 0.128 773 Planarity : 0.006 0.065 929 Dihedral : 5.091 18.304 738 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.90 % Allowed : 12.27 % Favored : 86.82 % 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: -2.00 (0.32), residues: 650 helix: -0.24 (0.36), residues: 221 sheet: -0.72 (0.36), residues: 190 loop : -2.83 (0.34), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 47 HIS 0.003 0.001 HIS A 84 PHE 0.012 0.001 PHE D 68 TYR 0.014 0.001 TYR A 62 ARG 0.007 0.001 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.05837 ( 217) hydrogen bonds : angle 5.03990 ( 615) SS BOND : bond 0.00744 ( 3) SS BOND : angle 1.21122 ( 6) covalent geometry : bond 0.00268 ( 5367) covalent geometry : angle 0.63173 ( 7265) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: E 3 MET cc_start: 0.8115 (mmm) cc_final: 0.7683 (mmm) outliers start: 5 outliers final: 5 residues processed: 69 average time/residue: 0.2072 time to fit residues: 17.9743 Evaluate side-chains 71 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain F residue 464 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.0020 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 57 optimal weight: 0.0050 chunk 17 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116826 restraints weight = 7771.440| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.24 r_work: 0.3331 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5370 Z= 0.130 Angle : 0.608 6.903 7271 Z= 0.310 Chirality : 0.041 0.128 773 Planarity : 0.006 0.059 929 Dihedral : 4.810 18.562 738 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.08 % Allowed : 13.54 % Favored : 85.38 % 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: -1.69 (0.32), residues: 650 helix: 0.04 (0.36), residues: 222 sheet: -0.57 (0.36), residues: 190 loop : -2.69 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.007 0.001 HIS E 95 PHE 0.025 0.001 PHE D 68 TYR 0.015 0.001 TYR A 62 ARG 0.006 0.001 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.05530 ( 217) hydrogen bonds : angle 4.78280 ( 615) SS BOND : bond 0.00755 ( 3) SS BOND : angle 1.23056 ( 6) covalent geometry : bond 0.00282 ( 5367) covalent geometry : angle 0.60734 ( 7265) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: B 52 LEU cc_start: 0.6980 (mt) cc_final: 0.6554 (mp) REVERT: E 3 MET cc_start: 0.8130 (mmm) cc_final: 0.7686 (mmm) REVERT: C 76 ASN cc_start: 0.8569 (m-40) cc_final: 0.8348 (m110) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.2129 time to fit residues: 18.5438 Evaluate side-chains 70 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain F residue 464 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 9 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.0070 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 0.0570 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.116965 restraints weight = 7829.276| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.22 r_work: 0.3330 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5370 Z= 0.130 Angle : 0.608 6.903 7271 Z= 0.310 Chirality : 0.041 0.128 773 Planarity : 0.006 0.059 929 Dihedral : 4.816 18.563 738 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.90 % Allowed : 13.72 % Favored : 85.38 % 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: -1.69 (0.32), residues: 650 helix: 0.04 (0.36), residues: 222 sheet: -0.57 (0.36), residues: 190 loop : -2.69 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.007 0.001 HIS E 95 PHE 0.024 0.001 PHE D 68 TYR 0.015 0.001 TYR A 62 ARG 0.006 0.001 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.05530 ( 217) hydrogen bonds : angle 4.78281 ( 615) SS BOND : bond 0.00755 ( 3) SS BOND : angle 1.23066 ( 6) covalent geometry : bond 0.00282 ( 5367) covalent geometry : angle 0.60725 ( 7265) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: B 52 LEU cc_start: 0.6998 (mt) cc_final: 0.6578 (mp) REVERT: E 3 MET cc_start: 0.8131 (mmm) cc_final: 0.7690 (mmm) REVERT: C 76 ASN cc_start: 0.8562 (m-40) cc_final: 0.8344 (m110) outliers start: 5 outliers final: 5 residues processed: 67 average time/residue: 0.2203 time to fit residues: 18.6192 Evaluate side-chains 70 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain F residue 464 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.1980 chunk 58 optimal weight: 0.0050 chunk 53 optimal weight: 0.0570 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 52 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.0770 chunk 1 optimal weight: 0.9990 overall best weight: 0.1470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 432 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.143518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118262 restraints weight = 7791.854| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.23 r_work: 0.3357 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5370 Z= 0.111 Angle : 0.581 7.075 7271 Z= 0.293 Chirality : 0.040 0.131 773 Planarity : 0.006 0.086 929 Dihedral : 4.662 17.984 738 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.26 % Allowed : 13.54 % Favored : 85.20 % 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: -1.45 (0.32), residues: 650 helix: 0.23 (0.36), residues: 222 sheet: -0.46 (0.36), residues: 192 loop : -2.53 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.003 0.001 HIS C 105 PHE 0.047 0.001 PHE D 68 TYR 0.013 0.001 TYR A 62 ARG 0.010 0.001 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.04917 ( 217) hydrogen bonds : angle 4.56774 ( 615) SS BOND : bond 0.00611 ( 3) SS BOND : angle 1.08207 ( 6) covalent geometry : bond 0.00223 ( 5367) covalent geometry : angle 0.58057 ( 7265) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: B 52 LEU cc_start: 0.6905 (mt) cc_final: 0.6574 (mp) REVERT: E 3 MET cc_start: 0.8120 (mmm) cc_final: 0.7684 (mmm) REVERT: C 76 ASN cc_start: 0.8548 (m-40) cc_final: 0.8323 (m110) outliers start: 7 outliers final: 5 residues processed: 70 average time/residue: 0.2692 time to fit residues: 24.1875 Evaluate side-chains 70 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain F residue 464 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 0.2980 chunk 60 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.0270 chunk 8 optimal weight: 0.0980 chunk 29 optimal weight: 0.1980 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 overall best weight: 0.2438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.143780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118792 restraints weight = 7804.134| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.21 r_work: 0.3356 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 5370 Z= 0.111 Angle : 0.581 7.075 7271 Z= 0.293 Chirality : 0.040 0.131 773 Planarity : 0.006 0.086 929 Dihedral : 4.661 17.984 738 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.90 % Allowed : 14.08 % Favored : 85.02 % 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: -1.45 (0.32), residues: 650 helix: 0.23 (0.36), residues: 222 sheet: -0.46 (0.36), residues: 192 loop : -2.53 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 36 HIS 0.003 0.001 HIS C 105 PHE 0.047 0.001 PHE D 68 TYR 0.013 0.001 TYR A 62 ARG 0.010 0.001 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.04917 ( 217) hydrogen bonds : angle 4.56774 ( 615) SS BOND : bond 0.00611 ( 3) SS BOND : angle 1.08207 ( 6) covalent geometry : bond 0.00223 ( 5367) covalent geometry : angle 0.58057 ( 7265) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: B 52 LEU cc_start: 0.6927 (mt) cc_final: 0.6582 (mp) REVERT: E 3 MET cc_start: 0.8118 (mmm) cc_final: 0.7686 (mmm) REVERT: C 76 ASN cc_start: 0.8553 (m-40) cc_final: 0.8329 (m110) outliers start: 5 outliers final: 5 residues processed: 68 average time/residue: 0.2087 time to fit residues: 17.7731 Evaluate side-chains 70 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain F residue 464 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 61 optimal weight: 0.0470 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117975 restraints weight = 7827.426| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.23 r_work: 0.3342 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5370 Z= 0.157 Angle : 0.595 7.081 7271 Z= 0.301 Chirality : 0.042 0.124 773 Planarity : 0.007 0.114 929 Dihedral : 4.648 18.294 738 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.26 % Allowed : 13.90 % Favored : 84.84 % 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: -1.46 (0.32), residues: 650 helix: 0.21 (0.36), residues: 222 sheet: -0.45 (0.36), residues: 192 loop : -2.53 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 HIS 0.006 0.001 HIS E 95 PHE 0.028 0.001 PHE D 68 TYR 0.015 0.001 TYR A 62 ARG 0.020 0.001 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.05117 ( 217) hydrogen bonds : angle 4.57469 ( 615) SS BOND : bond 0.00692 ( 3) SS BOND : angle 1.35148 ( 6) covalent geometry : bond 0.00376 ( 5367) covalent geometry : angle 0.59436 ( 7265) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4133.43 seconds wall clock time: 71 minutes 46.73 seconds (4306.73 seconds total)