Starting phenix.real_space_refine on Thu Jul 2 05:25:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x7t_33047/07_2026/7x7t_33047.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x7t_33047/07_2026/7x7t_33047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x7t_33047/07_2026/7x7t_33047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x7t_33047/07_2026/7x7t_33047.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7x7t_33047/07_2026/7x7t_33047.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x7t_33047/07_2026/7x7t_33047.cif" model { file = "/net/cci-nas-00/data/ceres_data/7x7t_33047/07_2026/7x7t_33047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x7t_33047/07_2026/7x7t_33047.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 4323 2.51 5 N 1123 2.21 5 O 1344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6815 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1494 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Chain breaks: 1 Chain: "L" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 946 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 827 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Chain: "A" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 929 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "C" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.58, per 1000 atoms: 0.23 Number of scatterers: 6815 At special positions: 0 Unit cell: (84.802, 94.138, 112.81, 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 25 16.00 O 1344 8.00 N 1123 7.00 C 4323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=1.57 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 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 Links applied NAG-ASN " NAG G 601 " - " ASN G 343 " Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 345.0 milliseconds 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1580 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 24 sheets defined 5.4% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'G' and resid 365 through 370 removed outlier: 3.649A pdb=" N ASN G 370 " --> pdb=" O SER G 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 390 removed outlier: 4.116A pdb=" N LEU G 390 " --> pdb=" O LEU G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 407 No H-bonds generated for 'chain 'G' and resid 405 through 407' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.719A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.715A pdb=" N GLU H 65 " --> pdb=" O LEU H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 74 through 77 removed outlier: 3.617A pdb=" N ASN H 77 " --> pdb=" O LYS H 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 74 through 77' Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.747A pdb=" N ILE B 83 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.663A pdb=" N SER A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.591A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 356 through 358 removed outlier: 3.509A pdb=" N ILE G 402 " --> pdb=" O TYR G 508 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU G 513 " --> pdb=" O CYS G 432 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR G 376 " --> pdb=" O ALA G 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 473 through 474 removed outlier: 3.616A pdb=" N TYR G 473 " --> pdb=" O TYR G 489 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR G 489 " --> pdb=" O TYR G 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.649A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE L 79 " --> pdb=" O ALA L 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.997A pdb=" N THR L 106 " --> pdb=" O TYR L 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 39 through 41 removed outlier: 6.839A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.580A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.679A pdb=" N THR H 115 " --> pdb=" O PHE H 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AA9, first strand: chain 'H' and resid 49 through 52 removed outlier: 3.769A pdb=" N GLY H 57 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 72 through 73 removed outlier: 3.800A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 19 through 24 removed outlier: 3.845A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 67 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.783A pdb=" N LEU B 54 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B 90 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.673A pdb=" N TYR B 86 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.578A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.586A pdb=" N GLN A 39 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS A 38 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TRP A 47 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.833A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER D 67 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AC2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AC4, first strand: chain 'C' and resid 18 through 20 Processing sheet with id=AC5, first strand: chain 'C' and resid 49 through 51 Processing sheet with id=AC6, first strand: chain 'C' and resid 97 through 98 162 hydrogen bonds defined for protein. 363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.65 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1107 1.29 - 1.42: 2023 1.42 - 1.55: 3825 1.55 - 1.68: 3 1.68 - 1.81: 30 Bond restraints: 6988 Sorted by residual: bond pdb=" C ASN G 334 " pdb=" O ASN G 334 " ideal model delta sigma weight residual 1.235 1.160 0.075 1.21e-02 6.83e+03 3.86e+01 bond pdb=" C GLN C 3 " pdb=" O GLN C 3 " ideal model delta sigma weight residual 1.236 1.302 -0.066 1.19e-02 7.06e+03 3.07e+01 bond pdb=" C LYS C 23 " pdb=" O LYS C 23 " ideal model delta sigma weight residual 1.235 1.299 -0.063 1.23e-02 6.61e+03 2.64e+01 bond pdb=" C LEU C 4 " pdb=" O LEU C 4 " ideal model delta sigma weight residual 1.236 1.289 -0.053 1.14e-02 7.69e+03 2.15e+01 bond pdb=" CA TRP C 47 " pdb=" C TRP C 47 " ideal model delta sigma weight residual 1.527 1.470 0.057 1.35e-02 5.49e+03 1.77e+01 ... (remaining 6983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 9240 2.86 - 5.71: 220 5.71 - 8.57: 26 8.57 - 11.42: 6 11.42 - 14.28: 4 Bond angle restraints: 9496 Sorted by residual: angle pdb=" N PHE G 338 " pdb=" CA PHE G 338 " pdb=" C PHE G 338 " ideal model delta sigma weight residual 112.92 98.64 14.28 1.23e+00 6.61e-01 1.35e+02 angle pdb=" N ILE D 29 " pdb=" CA ILE D 29 " pdb=" C ILE D 29 " ideal model delta sigma weight residual 108.11 93.91 14.20 1.40e+00 5.10e-01 1.03e+02 angle pdb=" N ASN L 35 " pdb=" CA ASN L 35 " pdb=" C ASN L 35 " ideal model delta sigma weight residual 110.17 96.65 13.52 1.61e+00 3.86e-01 7.05e+01 angle pdb=" N TRP C 47 " pdb=" CA TRP C 47 " pdb=" C TRP C 47 " ideal model delta sigma weight residual 110.53 120.04 -9.51 1.32e+00 5.74e-01 5.19e+01 angle pdb=" CA TYR L 91 " pdb=" C TYR L 91 " pdb=" O TYR L 91 " ideal model delta sigma weight residual 122.01 115.31 6.70 1.05e+00 9.07e-01 4.07e+01 ... (remaining 9491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 3665 17.03 - 34.06: 318 34.06 - 51.09: 46 51.09 - 68.12: 15 68.12 - 85.15: 7 Dihedral angle restraints: 4051 sinusoidal: 1545 harmonic: 2506 Sorted by residual: dihedral pdb=" C CYS G 336 " pdb=" N CYS G 336 " pdb=" CA CYS G 336 " pdb=" CB CYS G 336 " ideal model delta harmonic sigma weight residual -122.60 -108.63 -13.97 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" C THR A 113 " pdb=" N THR A 113 " pdb=" CA THR A 113 " pdb=" CB THR A 113 " ideal model delta harmonic sigma weight residual -122.00 -109.65 -12.35 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" CA ASN D 31 " pdb=" C ASN D 31 " pdb=" N TRP D 32 " pdb=" CA TRP D 32 " ideal model delta harmonic sigma weight residual 180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 4048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 898 0.090 - 0.181: 100 0.181 - 0.271: 14 0.271 - 0.361: 4 0.361 - 0.451: 2 Chirality restraints: 1018 Sorted by residual: chirality pdb=" CA TYR D 91 " pdb=" N TYR D 91 " pdb=" C TYR D 91 " pdb=" CB TYR D 91 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CA TYR L 36 " pdb=" N TYR L 36 " pdb=" C TYR L 36 " pdb=" CB TYR L 36 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA CYS G 336 " pdb=" N CYS G 336 " pdb=" C CYS G 336 " pdb=" CB CYS G 336 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 1015 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS G 336 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C CYS G 336 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS G 336 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO G 337 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 335 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.40e+00 pdb=" C LEU G 335 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU G 335 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS G 336 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 77 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C ASN B 77 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN B 77 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 78 " -0.015 2.00e-02 2.50e+03 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 418 2.72 - 3.26: 6442 3.26 - 3.81: 10227 3.81 - 4.35: 13116 4.35 - 4.90: 23035 Nonbonded interactions: 53238 Sorted by model distance: nonbonded pdb=" O ALA A 24 " pdb=" OG SER A 77 " model vdw 2.174 3.040 nonbonded pdb=" OD2 ASP C 73 " pdb=" OG SER C 75 " model vdw 2.246 3.040 nonbonded pdb=" NE2 GLN B 38 " pdb=" OE1 GLN A 39 " model vdw 2.304 3.120 nonbonded pdb=" O SER D 60 " pdb=" OG SER D 60 " model vdw 2.323 3.040 nonbonded pdb=" OH TYR C 60 " pdb=" N LEU C 70 " model vdw 2.332 3.120 ... (remaining 53233 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=0.67 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: 0.010 Normalize map: mean=0, sd=1: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.890 Find NCS groups from input model: 0.050 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 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 : 0.009 0.463 6997 Z= 0.516 Angle : 1.052 14.279 9515 Z= 0.648 Chirality : 0.063 0.451 1018 Planarity : 0.006 0.058 1217 Dihedral : 13.397 85.150 2447 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.96 % Favored : 93.92 % Rotamer: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.91 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.53 (0.24), residues: 855 helix: -5.31 (0.19), residues: 27 sheet: -2.86 (0.26), residues: 317 loop : -3.06 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 466 TYR 0.025 0.002 TYR D 91 PHE 0.027 0.002 PHE A 29 TRP 0.020 0.003 TRP C 47 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.44 ( 6988) covalent geometry : angle 1.03790 / 0.64 ( 9496) SS BOND : bond 0.16360 / 8.61 ( 8) SS BOND : angle 3.77047 / 2.18 ( 16) hydrogen bonds : bond 0.29655 / 18.91 ( 155) hydrogen bonds : angle 11.08529 / 8.08 ( 363) link_NAG-ASN : bond 0.00217 / 0.11 ( 1) link_NAG-ASN : angle 4.76387 / 2.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: G 424 LYS cc_start: 0.5455 (tttp) cc_final: 0.5194 (ttmt) REVERT: G 519 HIS cc_start: 0.6628 (m-70) cc_final: 0.4918 (t-170) REVERT: L 49 LYS cc_start: 0.6549 (mttt) cc_final: 0.5833 (ptmm) REVERT: H 19 LYS cc_start: 0.7649 (mtpt) cc_final: 0.7252 (mtpp) REVERT: H 109 ASP cc_start: 0.7730 (m-30) cc_final: 0.7495 (m-30) REVERT: B 17 ASP cc_start: 0.7873 (m-30) cc_final: 0.7462 (m-30) REVERT: A 59 ARG cc_start: 0.5869 (mtt-85) cc_final: 0.5258 (mtm180) REVERT: D 13 VAL cc_start: 0.6820 (m) cc_final: 0.6524 (p) REVERT: D 78 LEU cc_start: 0.6694 (mp) cc_final: 0.6390 (mp) REVERT: D 105 GLU cc_start: 0.3939 (tp30) cc_final: 0.2873 (tp30) REVERT: C 32 TYR cc_start: 0.7295 (m-80) cc_final: 0.7084 (m-80) REVERT: C 60 TYR cc_start: 0.8110 (m-80) cc_final: 0.7439 (m-80) REVERT: C 74 LYS cc_start: 0.7517 (mtpt) cc_final: 0.6523 (mptt) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.0775 time to fit residues: 20.6543 Evaluate side-chains 156 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 422 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN D 38 GLN C 6 GLN C 39 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.183884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157589 restraints weight = 7628.008| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.32 r_work: 0.3644 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6997 Z= 0.136 Angle : 0.630 10.985 9515 Z= 0.323 Chirality : 0.044 0.155 1018 Planarity : 0.005 0.045 1217 Dihedral : 5.532 31.815 959 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.63 % Allowed : 12.67 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.77 (0.25), residues: 855 helix: -5.18 (0.26), residues: 26 sheet: -2.45 (0.26), residues: 330 loop : -2.41 (0.24), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 61 TYR 0.019 0.001 TYR D 91 PHE 0.016 0.002 PHE G 490 TRP 0.013 0.001 TRP C 47 HIS 0.002 0.001 HIS H 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 6988) covalent geometry : angle 0.62683 / 0.32 ( 9496) SS BOND : bond 0.00354 / 0.18 ( 8) SS BOND : angle 0.82098 / 0.46 ( 16) hydrogen bonds : bond 0.03950 / 2.51 ( 155) hydrogen bonds : angle 7.52785 / 5.38 ( 363) link_NAG-ASN : bond 0.00129 / 0.07 ( 1) link_NAG-ASN : angle 3.26620 / 1.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.199 Fit side-chains REVERT: G 384 PRO cc_start: 0.8478 (Cg_endo) cc_final: 0.8275 (Cg_exo) REVERT: G 405 ASP cc_start: 0.8795 (t0) cc_final: 0.8567 (t0) REVERT: G 490 PHE cc_start: 0.8332 (m-80) cc_final: 0.8049 (m-10) REVERT: G 519 HIS cc_start: 0.8460 (m-70) cc_final: 0.7139 (t-170) REVERT: H 19 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7772 (mtpt) REVERT: H 51 PHE cc_start: 0.8240 (t80) cc_final: 0.7684 (t80) REVERT: B 61 ARG cc_start: 0.8274 (mtm110) cc_final: 0.8061 (mtm-85) REVERT: D 78 LEU cc_start: 0.8298 (mp) cc_final: 0.8070 (mp) REVERT: D 105 GLU cc_start: 0.5241 (tp30) cc_final: 0.3309 (tp30) outliers start: 12 outliers final: 8 residues processed: 158 average time/residue: 0.0770 time to fit residues: 16.5298 Evaluate side-chains 150 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 30 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 56 optimal weight: 0.0170 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 370 ASN ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN D 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.180033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.154365 restraints weight = 7627.654| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.94 r_work: 0.3616 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 6997 Z= 0.202 Angle : 0.652 12.825 9515 Z= 0.331 Chirality : 0.044 0.140 1018 Planarity : 0.004 0.039 1217 Dihedral : 5.558 31.201 959 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.32 % Allowed : 15.26 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.26), residues: 855 helix: -5.08 (0.28), residues: 27 sheet: -2.28 (0.26), residues: 349 loop : -2.08 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.018 0.002 TYR D 91 PHE 0.020 0.002 PHE G 377 TRP 0.012 0.002 TRP C 47 HIS 0.007 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 ( 6988) covalent geometry : angle 0.64798 / 0.33 ( 9496) SS BOND : bond 0.00379 / 0.20 ( 8) SS BOND : angle 1.04700 / 0.54 ( 16) hydrogen bonds : bond 0.03568 / 2.28 ( 155) hydrogen bonds : angle 6.90840 / 4.93 ( 363) link_NAG-ASN : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : angle 3.40366 / 1.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.260 Fit side-chains REVERT: G 399 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8389 (p) REVERT: G 405 ASP cc_start: 0.8735 (t0) cc_final: 0.8478 (t0) REVERT: H 19 LYS cc_start: 0.8357 (mtpt) cc_final: 0.8068 (mtpt) REVERT: D 39 LYS cc_start: 0.8535 (pttp) cc_final: 0.8027 (ptpp) REVERT: D 105 GLU cc_start: 0.5234 (tp30) cc_final: 0.3247 (tp30) outliers start: 17 outliers final: 15 residues processed: 153 average time/residue: 0.0751 time to fit residues: 15.7013 Evaluate side-chains 153 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 445 VAL Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 30 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 57 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN D 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.174740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.149497 restraints weight = 7811.089| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.13 r_work: 0.3596 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6997 Z= 0.212 Angle : 0.655 13.123 9515 Z= 0.332 Chirality : 0.044 0.203 1018 Planarity : 0.005 0.039 1217 Dihedral : 5.566 31.196 959 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.54 % Allowed : 16.49 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.26), residues: 855 helix: -5.14 (0.29), residues: 26 sheet: -2.09 (0.26), residues: 349 loop : -1.87 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 61 TYR 0.020 0.002 TYR C 32 PHE 0.020 0.002 PHE G 377 TRP 0.012 0.002 TRP G 436 HIS 0.007 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 ( 6988) covalent geometry : angle 0.65115 / 0.33 ( 9496) SS BOND : bond 0.00436 / 0.26 ( 8) SS BOND : angle 1.00011 / 0.53 ( 16) hydrogen bonds : bond 0.03287 / 2.10 ( 155) hydrogen bonds : angle 6.49358 / 4.63 ( 363) link_NAG-ASN : bond 0.00049 / 0.03 ( 1) link_NAG-ASN : angle 3.50345 / 1.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.239 Fit side-chains REVERT: G 399 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8248 (p) REVERT: G 405 ASP cc_start: 0.8583 (t0) cc_final: 0.8350 (t0) REVERT: L 111 LYS cc_start: 0.6417 (mtpp) cc_final: 0.6163 (mmmt) REVERT: H 19 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8110 (mtpt) REVERT: A 103 ASN cc_start: 0.8810 (m-40) cc_final: 0.8521 (m-40) REVERT: D 105 GLU cc_start: 0.5218 (tp30) cc_final: 0.3271 (tp30) REVERT: C 60 TYR cc_start: 0.9042 (m-80) cc_final: 0.8813 (m-80) outliers start: 26 outliers final: 19 residues processed: 151 average time/residue: 0.0702 time to fit residues: 14.6107 Evaluate side-chains 154 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 445 VAL Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 30 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 67 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.179559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.155276 restraints weight = 7757.929| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.03 r_work: 0.3646 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6997 Z= 0.174 Angle : 0.623 12.447 9515 Z= 0.314 Chirality : 0.043 0.189 1018 Planarity : 0.004 0.040 1217 Dihedral : 5.395 29.997 959 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.81 % Allowed : 17.57 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.27), residues: 855 helix: -5.13 (0.30), residues: 26 sheet: -1.92 (0.26), residues: 349 loop : -1.68 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 408 TYR 0.021 0.002 TYR C 32 PHE 0.018 0.002 PHE A 29 TRP 0.012 0.002 TRP G 436 HIS 0.006 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 ( 6988) covalent geometry : angle 0.61927 / 0.31 ( 9496) SS BOND : bond 0.00318 / 0.17 ( 8) SS BOND : angle 0.83556 / 0.44 ( 16) hydrogen bonds : bond 0.03004 / 1.91 ( 155) hydrogen bonds : angle 6.14086 / 4.38 ( 363) link_NAG-ASN : bond 0.00077 / 0.04 ( 1) link_NAG-ASN : angle 3.38367 / 1.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: G 399 SER cc_start: 0.8646 (OUTLIER) cc_final: 0.8324 (p) REVERT: G 405 ASP cc_start: 0.8727 (t0) cc_final: 0.8466 (t0) REVERT: L 111 LYS cc_start: 0.6534 (mtpp) cc_final: 0.6194 (mmmt) REVERT: H 19 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8136 (mtpt) REVERT: B 90 GLN cc_start: 0.8957 (pp30) cc_final: 0.8746 (pp30) REVERT: D 105 GLU cc_start: 0.5259 (tp30) cc_final: 0.3335 (tp30) outliers start: 28 outliers final: 21 residues processed: 148 average time/residue: 0.0666 time to fit residues: 13.7933 Evaluate side-chains 147 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 445 VAL Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain C residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** 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 = 0.4013 r_free = 0.4013 target = 0.172973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147655 restraints weight = 7857.302| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.13 r_work: 0.3138 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 6997 Z= 0.352 Angle : 0.773 13.785 9515 Z= 0.393 Chirality : 0.048 0.213 1018 Planarity : 0.005 0.041 1217 Dihedral : 5.993 34.112 959 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.36 % Allowed : 17.71 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.27), residues: 855 helix: -5.16 (0.28), residues: 26 sheet: -1.98 (0.26), residues: 354 loop : -1.87 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 466 TYR 0.019 0.002 TYR C 50 PHE 0.027 0.003 PHE G 400 TRP 0.018 0.002 TRP L 96 HIS 0.010 0.003 HIS L 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00843 / 0.35 ( 6988) covalent geometry : angle 0.76795 / 0.39 ( 9496) SS BOND : bond 0.00490 / 0.31 ( 8) SS BOND : angle 1.28098 / 0.68 ( 16) hydrogen bonds : bond 0.03676 / 2.32 ( 155) hydrogen bonds : angle 6.54786 / 4.69 ( 363) link_NAG-ASN : bond 0.00017 / 0.01 ( 1) link_NAG-ASN : angle 4.17827 / 2.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.251 Fit side-chains REVERT: G 399 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8347 (p) REVERT: G 405 ASP cc_start: 0.8711 (t0) cc_final: 0.8468 (t0) REVERT: G 418 ILE cc_start: 0.9165 (mm) cc_final: 0.8946 (mm) REVERT: G 501 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7844 (m110) REVERT: G 516 GLU cc_start: 0.5101 (tp30) cc_final: 0.4857 (tp30) REVERT: L 111 LYS cc_start: 0.6500 (mtpp) cc_final: 0.6038 (mmmt) REVERT: H 19 LYS cc_start: 0.8503 (mtpt) cc_final: 0.8095 (mtpp) REVERT: A 103 ASN cc_start: 0.8848 (m-40) cc_final: 0.8522 (m-40) REVERT: C 60 TYR cc_start: 0.9204 (m-80) cc_final: 0.8786 (m-80) outliers start: 32 outliers final: 29 residues processed: 152 average time/residue: 0.0641 time to fit residues: 13.4743 Evaluate side-chains 162 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 438 SER Chi-restraints excluded: chain G residue 445 VAL Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 73 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** 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 = 0.4082 r_free = 0.4082 target = 0.179681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.154536 restraints weight = 7616.121| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.90 r_work: 0.3221 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.004 0.044 6997 Z= 0.146 Angle : 0.619 10.295 9515 Z= 0.311 Chirality : 0.042 0.191 1018 Planarity : 0.004 0.043 1217 Dihedral : 5.371 30.824 959 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.68 % Allowed : 18.66 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.27), residues: 855 helix: -5.09 (0.32), residues: 26 sheet: -1.75 (0.27), residues: 351 loop : -1.51 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 408 TYR 0.018 0.001 TYR C 32 PHE 0.027 0.002 PHE G 456 TRP 0.013 0.002 TRP G 436 HIS 0.006 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 6988) covalent geometry : angle 0.61583 / 0.31 ( 9496) SS BOND : bond 0.00269 / 0.13 ( 8) SS BOND : angle 0.65585 / 0.35 ( 16) hydrogen bonds : bond 0.02839 / 1.81 ( 155) hydrogen bonds : angle 5.93203 / 4.24 ( 363) link_NAG-ASN : bond 0.00144 / 0.08 ( 1) link_NAG-ASN : angle 3.38515 / 1.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: G 399 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8347 (p) REVERT: G 405 ASP cc_start: 0.8618 (t0) cc_final: 0.8401 (t0) REVERT: G 501 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7746 (m110) REVERT: G 516 GLU cc_start: 0.5135 (tp30) cc_final: 0.4853 (tp30) REVERT: L 111 LYS cc_start: 0.6524 (mtpp) cc_final: 0.6154 (mmmt) REVERT: H 19 LYS cc_start: 0.8458 (mtpt) cc_final: 0.7917 (mtpt) REVERT: B 90 GLN cc_start: 0.8948 (pp30) cc_final: 0.8730 (pp30) REVERT: A 103 ASN cc_start: 0.8776 (m-40) cc_final: 0.8450 (m-40) REVERT: D 79 GLN cc_start: 0.8117 (mt0) cc_final: 0.7638 (mp10) REVERT: C 60 TYR cc_start: 0.9099 (m-80) cc_final: 0.8804 (m-80) outliers start: 27 outliers final: 21 residues processed: 146 average time/residue: 0.0719 time to fit residues: 14.3361 Evaluate side-chains 147 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 445 VAL Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain C residue 2 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 52 optimal weight: 0.0970 chunk 17 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.181136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.155873 restraints weight = 7691.591| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.92 r_work: 0.3233 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6997 Z= 0.130 Angle : 0.603 9.496 9515 Z= 0.302 Chirality : 0.042 0.202 1018 Planarity : 0.004 0.043 1217 Dihedral : 5.128 27.470 959 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.41 % Allowed : 19.21 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.28), residues: 855 helix: -4.90 (0.42), residues: 20 sheet: -1.64 (0.26), residues: 366 loop : -1.33 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 408 TYR 0.021 0.001 TYR C 32 PHE 0.030 0.002 PHE G 456 TRP 0.013 0.001 TRP G 436 HIS 0.006 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 6988) covalent geometry : angle 0.60048 / 0.30 ( 9496) SS BOND : bond 0.00249 / 0.13 ( 8) SS BOND : angle 0.60278 / 0.32 ( 16) hydrogen bonds : bond 0.02691 / 1.71 ( 155) hydrogen bonds : angle 5.65106 / 4.02 ( 363) link_NAG-ASN : bond 0.00085 / 0.04 ( 1) link_NAG-ASN : angle 3.33728 / 1.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.231 Fit side-chains REVERT: G 399 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8368 (p) REVERT: G 405 ASP cc_start: 0.8596 (t0) cc_final: 0.8357 (t0) REVERT: G 501 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7670 (m110) REVERT: G 516 GLU cc_start: 0.5206 (tp30) cc_final: 0.4917 (tp30) REVERT: L 111 LYS cc_start: 0.6386 (mtpp) cc_final: 0.6022 (mmmt) REVERT: H 19 LYS cc_start: 0.8545 (mtpt) cc_final: 0.7941 (mtpt) REVERT: B 90 GLN cc_start: 0.8949 (pp30) cc_final: 0.8681 (pp30) REVERT: A 43 GLN cc_start: 0.8406 (mp10) cc_final: 0.8058 (mp10) REVERT: D 79 GLN cc_start: 0.8122 (mt0) cc_final: 0.7610 (mp10) REVERT: C 60 TYR cc_start: 0.9119 (m-80) cc_final: 0.8812 (m-80) outliers start: 25 outliers final: 19 residues processed: 141 average time/residue: 0.0672 time to fit residues: 13.0685 Evaluate side-chains 141 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 445 VAL Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 34 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.183195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.157695 restraints weight = 7689.645| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.27 r_work: 0.3657 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6997 Z= 0.116 Angle : 0.581 8.816 9515 Z= 0.290 Chirality : 0.042 0.206 1018 Planarity : 0.004 0.042 1217 Dihedral : 4.904 24.666 959 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.00 % Allowed : 20.84 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.28), residues: 855 helix: -4.78 (0.47), residues: 20 sheet: -1.46 (0.26), residues: 375 loop : -1.21 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 408 TYR 0.018 0.001 TYR C 32 PHE 0.035 0.001 PHE G 456 TRP 0.012 0.001 TRP G 436 HIS 0.010 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 6988) covalent geometry : angle 0.57858 / 0.29 ( 9496) SS BOND : bond 0.00227 / 0.11 ( 8) SS BOND : angle 0.52510 / 0.28 ( 16) hydrogen bonds : bond 0.02580 / 1.64 ( 155) hydrogen bonds : angle 5.40045 / 3.84 ( 363) link_NAG-ASN : bond 0.00115 / 0.06 ( 1) link_NAG-ASN : angle 3.20667 / 1.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 405 ASP cc_start: 0.8676 (t0) cc_final: 0.8378 (t0) REVERT: G 516 GLU cc_start: 0.5151 (tp30) cc_final: 0.4851 (tp30) REVERT: L 111 LYS cc_start: 0.6529 (mtpp) cc_final: 0.6182 (mmmt) REVERT: H 19 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8129 (mttp) REVERT: D 9 SER cc_start: 0.8429 (m) cc_final: 0.7700 (t) REVERT: D 79 GLN cc_start: 0.8225 (mt0) cc_final: 0.7888 (mp10) REVERT: C 60 TYR cc_start: 0.9046 (m-80) cc_final: 0.8818 (m-80) outliers start: 22 outliers final: 18 residues processed: 141 average time/residue: 0.0685 time to fit residues: 13.4509 Evaluate side-chains 142 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 445 VAL Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain C residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 23 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 64 optimal weight: 3.9990 chunk 77 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.182138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.156730 restraints weight = 7656.006| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.25 r_work: 0.3233 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6997 Z= 0.140 Angle : 0.596 9.419 9515 Z= 0.299 Chirality : 0.042 0.213 1018 Planarity : 0.004 0.042 1217 Dihedral : 4.963 24.785 959 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.72 % Allowed : 21.93 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.28), residues: 855 helix: -4.76 (0.45), residues: 20 sheet: -1.42 (0.26), residues: 376 loop : -1.20 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 408 TYR 0.019 0.001 TYR C 32 PHE 0.040 0.002 PHE G 456 TRP 0.012 0.001 TRP G 436 HIS 0.010 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 6988) covalent geometry : angle 0.59313 / 0.30 ( 9496) SS BOND : bond 0.00224 / 0.11 ( 8) SS BOND : angle 0.57440 / 0.31 ( 16) hydrogen bonds : bond 0.02613 / 1.65 ( 155) hydrogen bonds : angle 5.38628 / 3.82 ( 363) link_NAG-ASN : bond 0.00108 / 0.06 ( 1) link_NAG-ASN : angle 3.22411 / 1.67 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 399 SER cc_start: 0.8682 (OUTLIER) cc_final: 0.8276 (p) REVERT: G 405 ASP cc_start: 0.8597 (t0) cc_final: 0.8335 (t0) REVERT: G 516 GLU cc_start: 0.5205 (tp30) cc_final: 0.4932 (tp30) REVERT: G 519 HIS cc_start: 0.8120 (m-70) cc_final: 0.6667 (t-170) REVERT: L 111 LYS cc_start: 0.6444 (mtpp) cc_final: 0.6098 (mmmt) REVERT: H 19 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8092 (mttp) REVERT: D 9 SER cc_start: 0.8404 (m) cc_final: 0.7615 (t) REVERT: D 79 GLN cc_start: 0.8098 (mt0) cc_final: 0.7689 (mp10) REVERT: C 60 TYR cc_start: 0.9084 (m-80) cc_final: 0.8822 (m-80) outliers start: 20 outliers final: 18 residues processed: 142 average time/residue: 0.0654 time to fit residues: 12.9487 Evaluate side-chains 147 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 445 VAL Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain C residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 6 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.183881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158624 restraints weight = 7660.421| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.25 r_work: 0.3243 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6997 Z= 0.124 Angle : 0.585 9.833 9515 Z= 0.292 Chirality : 0.042 0.206 1018 Planarity : 0.004 0.042 1217 Dihedral : 4.869 24.660 959 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.86 % Allowed : 21.93 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.28), residues: 855 helix: -4.70 (0.47), residues: 20 sheet: -1.30 (0.26), residues: 374 loop : -1.18 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 408 TYR 0.018 0.001 TYR C 32 PHE 0.039 0.002 PHE G 456 TRP 0.012 0.001 TRP G 436 HIS 0.010 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.12 ( 6988) covalent geometry : angle 0.58303 / 0.29 ( 9496) SS BOND : bond 0.00207 / 0.10 ( 8) SS BOND : angle 0.50831 / 0.28 ( 16) hydrogen bonds : bond 0.02567 / 1.63 ( 155) hydrogen bonds : angle 5.27610 / 3.74 ( 363) link_NAG-ASN : bond 0.00116 / 0.06 ( 1) link_NAG-ASN : angle 3.09536 / 1.61 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1779.38 seconds wall clock time: 31 minutes 17.71 seconds (1877.71 seconds total)