Starting phenix.real_space_refine on Wed Feb 12 01:02:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x7t_33047/02_2025/7x7t_33047.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x7t_33047/02_2025/7x7t_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_33047/02_2025/7x7t_33047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x7t_33047/02_2025/7x7t_33047.map" model { file = "/net/cci-nas-00/data/ceres_data/7x7t_33047/02_2025/7x7t_33047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x7t_33047/02_2025/7x7t_33047.cif" } resolution = 3.48 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= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.18, per 1000 atoms: 0.76 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: 1.47 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.92 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: 1.87 Time building geometry restraints manager: 1.77 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: 3682 17.03 - 34.06: 320 34.06 - 51.09: 48 51.09 - 68.12: 15 68.12 - 85.15: 7 Dihedral angle restraints: 4072 sinusoidal: 1566 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 4069 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: 0.000 Normalize map: mean=0, sd=1: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.870 Find NCS groups from input model: 0.120 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 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 : 0.007 0.075 6988 Z= 0.442 Angle : 1.038 14.279 9496 Z= 0.644 Chirality : 0.063 0.451 1018 Planarity : 0.006 0.058 1217 Dihedral : 13.408 85.150 2468 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 (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: -4.53 (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 TRP 0.020 0.003 TRP C 47 HIS 0.003 0.001 HIS B 55 PHE 0.027 0.002 PHE A 29 TYR 0.025 0.002 TYR D 91 ARG 0.002 0.000 ARG G 466 *********************** 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 : 0.765 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: 0.7251 (mtpp) REVERT: H 109 ASP cc_start: 0.7730 (m-30) cc_final: 0.7494 (m-30) REVERT: B 17 ASP cc_start: 0.7873 (m-30) cc_final: 0.7461 (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: 0.1860 time to fit residues: 48.4401 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 : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 0.0030 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.183692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157560 restraints weight = 7497.572| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.30 r_work: 0.3257 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 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 = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 0.056 6988 Z= 0.214 Angle : 0.627 11.071 9496 Z= 0.322 Chirality : 0.044 0.155 1018 Planarity : 0.005 0.045 1217 Dihedral : 5.898 44.792 980 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.50 % Allowed : 12.67 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.25), residues: 855 helix: -5.18 (0.26), residues: 26 sheet: -2.50 (0.26), residues: 334 loop : -2.39 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 47 HIS 0.002 0.001 HIS H 41 PHE 0.017 0.002 PHE G 490 TYR 0.019 0.001 TYR D 91 ARG 0.002 0.000 ARG B 61 *********************** 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: 11 poor density : 156 time to evaluate : 0.873 Fit side-chains REVERT: G 384 PRO cc_start: 0.8488 (Cg_endo) cc_final: 0.8285 (Cg_exo) REVERT: G 490 PHE cc_start: 0.8319 (m-80) cc_final: 0.8013 (m-10) REVERT: G 519 HIS cc_start: 0.8247 (m-70) cc_final: 0.6757 (t-170) REVERT: H 19 LYS cc_start: 0.8242 (mtpt) cc_final: 0.7662 (mtpt) REVERT: H 51 PHE cc_start: 0.8190 (t80) cc_final: 0.7528 (t80) REVERT: B 61 ARG cc_start: 0.8218 (mtm110) cc_final: 0.7991 (mtm-85) REVERT: D 105 GLU cc_start: 0.5217 (tp30) cc_final: 0.3280 (tp30) outliers start: 11 outliers final: 9 residues processed: 159 average time/residue: 0.1765 time to fit residues: 37.6941 Evaluate side-chains 150 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 3 VAL 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 82 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 47 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.0270 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4125 r_free = 0.4125 target = 0.183972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.158478 restraints weight = 7631.322| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.27 r_work: 0.3668 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6988 Z= 0.192 Angle : 0.591 10.680 9496 Z= 0.298 Chirality : 0.042 0.140 1018 Planarity : 0.004 0.039 1217 Dihedral : 5.584 44.302 980 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.04 % Allowed : 14.31 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.26), residues: 855 helix: -5.11 (0.28), residues: 26 sheet: -2.05 (0.27), residues: 337 loop : -1.98 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 436 HIS 0.007 0.001 HIS C 82 PHE 0.016 0.001 PHE G 490 TYR 0.020 0.001 TYR C 32 ARG 0.004 0.000 ARG A 63 *********************** 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 160 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.722 Fit side-chains REVERT: G 399 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8339 (p) REVERT: G 519 HIS cc_start: 0.8366 (m-70) cc_final: 0.6955 (t-170) REVERT: H 19 LYS cc_start: 0.8353 (mtpt) cc_final: 0.7921 (mttp) REVERT: H 51 PHE cc_start: 0.8090 (t80) cc_final: 0.7519 (t80) REVERT: D 92 TRP cc_start: 0.8384 (t-100) cc_final: 0.8082 (t-100) REVERT: D 105 GLU cc_start: 0.5040 (tp30) cc_final: 0.3113 (tp30) outliers start: 15 outliers final: 11 residues processed: 151 average time/residue: 0.1696 time to fit residues: 34.7927 Evaluate side-chains 151 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 399 SER Chi-restraints excluded: chain G residue 445 VAL 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 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 3 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.0050 overall best weight: 0.3952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4125 r_free = 0.4125 target = 0.184323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.157960 restraints weight = 7695.456| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.44 r_work: 0.3594 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6988 Z= 0.164 Angle : 0.563 9.581 9496 Z= 0.285 Chirality : 0.041 0.203 1018 Planarity : 0.004 0.040 1217 Dihedral : 5.336 44.811 980 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.72 % Allowed : 15.80 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.71 (0.27), residues: 855 helix: -5.01 (0.30), residues: 26 sheet: -1.68 (0.28), residues: 338 loop : -1.67 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 436 HIS 0.006 0.001 HIS C 82 PHE 0.018 0.001 PHE G 456 TYR 0.020 0.001 TYR C 32 ARG 0.005 0.000 ARG B 61 *********************** 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 158 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.744 Fit side-chains REVERT: G 399 SER cc_start: 0.8452 (OUTLIER) cc_final: 0.8224 (p) REVERT: H 19 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7947 (mttp) REVERT: D 92 TRP cc_start: 0.8264 (t-100) cc_final: 0.7932 (t-100) REVERT: D 105 GLU cc_start: 0.4909 (tp30) cc_final: 0.3065 (tp30) outliers start: 20 outliers final: 15 residues processed: 147 average time/residue: 0.1646 time to fit residues: 33.3558 Evaluate side-chains 149 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 460 ASN Chi-restraints excluded: chain G residue 489 TYR 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 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 30 ASN Chi-restraints excluded: chain C residue 34 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.0370 chunk 15 optimal weight: 0.0060 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.7276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.181835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155945 restraints weight = 7681.611| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.29 r_work: 0.3637 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6988 Z= 0.229 Angle : 0.597 10.643 9496 Z= 0.298 Chirality : 0.042 0.204 1018 Planarity : 0.004 0.039 1217 Dihedral : 5.354 42.101 980 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.54 % Allowed : 16.21 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.60 (0.27), residues: 855 helix: -4.92 (0.33), residues: 26 sheet: -1.65 (0.27), residues: 352 loop : -1.53 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.007 0.001 HIS C 82 PHE 0.018 0.002 PHE G 456 TYR 0.020 0.001 TYR C 32 ARG 0.004 0.000 ARG A 63 *********************** 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 155 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.747 Fit side-chains REVERT: G 399 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8299 (p) REVERT: G 420 ASP cc_start: 0.8361 (m-30) cc_final: 0.8053 (m-30) REVERT: H 19 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8116 (mtpp) REVERT: D 92 TRP cc_start: 0.8453 (t-100) cc_final: 0.8106 (t-100) REVERT: D 105 GLU cc_start: 0.5143 (tp30) cc_final: 0.3238 (tp30) outliers start: 26 outliers final: 18 residues processed: 142 average time/residue: 0.1600 time to fit residues: 31.3792 Evaluate side-chains 146 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 341 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 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 H residue 2 VAL 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 30 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 0.0270 chunk 65 optimal weight: 0.9980 chunk 55 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4120 r_free = 0.4120 target = 0.183933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.158100 restraints weight = 7591.131| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.26 r_work: 0.3646 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6988 Z= 0.195 Angle : 0.570 9.930 9496 Z= 0.287 Chirality : 0.041 0.205 1018 Planarity : 0.004 0.040 1217 Dihedral : 5.185 36.815 980 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.27 % Allowed : 17.17 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.41 (0.27), residues: 855 helix: -4.74 (0.44), residues: 26 sheet: -1.54 (0.27), residues: 347 loop : -1.40 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 436 HIS 0.010 0.001 HIS C 82 PHE 0.025 0.001 PHE G 456 TYR 0.017 0.001 TYR C 32 ARG 0.004 0.000 ARG A 63 *********************** 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 159 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.675 Fit side-chains REVERT: G 399 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.8270 (p) REVERT: G 420 ASP cc_start: 0.8344 (m-30) cc_final: 0.8104 (m-30) REVERT: G 519 HIS cc_start: 0.8401 (m-70) cc_final: 0.6933 (t-170) REVERT: H 19 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8129 (mtpp) REVERT: D 92 TRP cc_start: 0.8460 (t-100) cc_final: 0.8086 (t-100) REVERT: C 60 TYR cc_start: 0.9027 (m-80) cc_final: 0.8734 (m-80) outliers start: 24 outliers final: 21 residues processed: 146 average time/residue: 0.1816 time to fit residues: 36.0323 Evaluate side-chains 149 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 460 ASN Chi-restraints excluded: chain G residue 489 TYR 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 106 THR Chi-restraints excluded: chain H residue 2 VAL 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 2 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 15 optimal weight: 0.0570 chunk 72 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 75 optimal weight: 0.0970 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.185649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.161441 restraints weight = 7500.081| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.21 r_work: 0.3550 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6988 Z= 0.168 Angle : 0.561 9.224 9496 Z= 0.279 Chirality : 0.041 0.208 1018 Planarity : 0.004 0.041 1217 Dihedral : 4.825 24.360 980 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.00 % Allowed : 17.17 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.09 (0.28), residues: 855 helix: -4.56 (0.52), residues: 26 sheet: -1.28 (0.27), residues: 362 loop : -1.19 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 92 HIS 0.010 0.001 HIS C 82 PHE 0.022 0.001 PHE G 456 TYR 0.017 0.001 TYR C 32 ARG 0.005 0.000 ARG A 63 *********************** 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 150 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: G 420 ASP cc_start: 0.8341 (m-30) cc_final: 0.8117 (m-30) REVERT: G 519 HIS cc_start: 0.8299 (m-70) cc_final: 0.6847 (t-170) REVERT: L 83 GLU cc_start: 0.7670 (pp20) cc_final: 0.7444 (pp20) REVERT: H 19 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8055 (mtpp) REVERT: D 92 TRP cc_start: 0.8449 (t-100) cc_final: 0.8198 (t-100) REVERT: C 60 TYR cc_start: 0.9018 (m-80) cc_final: 0.8725 (m-80) outliers start: 22 outliers final: 19 residues processed: 138 average time/residue: 0.1629 time to fit residues: 31.4630 Evaluate side-chains 144 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 445 VAL Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU 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 H residue 2 VAL 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 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 2 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4113 r_free = 0.4113 target = 0.182916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.156749 restraints weight = 7605.724| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.32 r_work: 0.3231 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6988 Z= 0.234 Angle : 0.590 10.511 9496 Z= 0.296 Chirality : 0.042 0.210 1018 Planarity : 0.004 0.040 1217 Dihedral : 4.915 24.955 980 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.27 % Allowed : 17.44 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.07 (0.28), residues: 855 helix: -4.47 (0.56), residues: 26 sheet: -1.29 (0.26), residues: 375 loop : -1.16 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 96 HIS 0.009 0.001 HIS C 82 PHE 0.032 0.002 PHE G 456 TYR 0.020 0.001 TYR C 32 ARG 0.004 0.000 ARG A 63 *********************** 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 149 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: G 399 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8221 (p) REVERT: G 420 ASP cc_start: 0.8472 (m-30) cc_final: 0.8102 (m-30) REVERT: G 519 HIS cc_start: 0.8193 (m-70) cc_final: 0.6594 (t-170) REVERT: L 83 GLU cc_start: 0.7667 (pp20) cc_final: 0.7434 (pp20) REVERT: H 19 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8049 (mtpp) REVERT: D 92 TRP cc_start: 0.8576 (t-100) cc_final: 0.8124 (t-100) REVERT: C 44 SER cc_start: 0.8441 (t) cc_final: 0.8036 (p) REVERT: C 60 TYR cc_start: 0.9099 (m-80) cc_final: 0.8730 (m-80) outliers start: 24 outliers final: 20 residues processed: 137 average time/residue: 0.1700 time to fit residues: 31.8853 Evaluate side-chains 143 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 398 ASP Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 445 VAL Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU 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 2 VAL 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4049 r_free = 0.4049 target = 0.176473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.153063 restraints weight = 7651.900| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.93 r_work: 0.3189 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- 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 = 0.57 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 = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 6988 Z= 0.421 Angle : 0.701 13.678 9496 Z= 0.353 Chirality : 0.046 0.218 1018 Planarity : 0.005 0.037 1217 Dihedral : 5.486 27.186 980 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.54 % Allowed : 17.85 % 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 (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: -2.35 (0.28), residues: 855 helix: -4.62 (0.50), residues: 26 sheet: -1.51 (0.26), residues: 375 loop : -1.31 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 47 HIS 0.008 0.002 HIS C 82 PHE 0.043 0.003 PHE G 456 TYR 0.020 0.002 TYR C 32 ARG 0.004 0.000 ARG A 63 *********************** 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 155 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: G 399 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8197 (p) REVERT: G 420 ASP cc_start: 0.8495 (m-30) cc_final: 0.8156 (m-30) REVERT: G 501 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7760 (m110) REVERT: G 516 GLU cc_start: 0.5084 (tp30) cc_final: 0.4843 (tp30) REVERT: L 83 GLU cc_start: 0.7793 (pp20) cc_final: 0.7565 (pp20) REVERT: H 19 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8063 (mtpp) REVERT: A 103 ASN cc_start: 0.8803 (m-40) cc_final: 0.8474 (m-40) REVERT: C 60 TYR cc_start: 0.9156 (m-80) cc_final: 0.8798 (m-80) outliers start: 26 outliers final: 22 residues processed: 144 average time/residue: 0.1812 time to fit residues: 35.5002 Evaluate side-chains 147 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 398 ASP 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 G residue 501 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU 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 2 VAL 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 70 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 30 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 76 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4097 r_free = 0.4097 target = 0.181366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156223 restraints weight = 7777.352| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.91 r_work: 0.3228 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6988 Z= 0.226 Angle : 0.609 11.640 9496 Z= 0.303 Chirality : 0.042 0.197 1018 Planarity : 0.004 0.039 1217 Dihedral : 5.147 26.324 980 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.00 % Allowed : 18.53 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.18 (0.28), residues: 855 helix: -4.47 (0.54), residues: 27 sheet: -1.41 (0.26), residues: 370 loop : -1.17 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 92 HIS 0.010 0.001 HIS C 82 PHE 0.018 0.002 PHE A 29 TYR 0.020 0.001 TYR C 32 ARG 0.003 0.000 ARG G 408 ********************** 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 144 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: G 399 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8267 (p) REVERT: G 420 ASP cc_start: 0.8507 (m-30) cc_final: 0.8139 (m-30) REVERT: G 501 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7660 (m110) REVERT: G 516 GLU cc_start: 0.5116 (tp30) cc_final: 0.4856 (tp30) REVERT: L 83 GLU cc_start: 0.7764 (pp20) cc_final: 0.7545 (pp20) REVERT: H 19 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8010 (mtpp) REVERT: D 9 SER cc_start: 0.8348 (m) cc_final: 0.7566 (t) REVERT: C 60 TYR cc_start: 0.9125 (m-80) cc_final: 0.8770 (m-80) outliers start: 22 outliers final: 20 residues processed: 134 average time/residue: 0.1906 time to fit residues: 35.3838 Evaluate side-chains 142 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 398 ASP 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 G residue 501 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU 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 2 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 52 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 65 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4119 r_free = 0.4119 target = 0.183543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.157741 restraints weight = 7686.724| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.30 r_work: 0.3575 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6988 Z= 0.201 Angle : 0.585 10.390 9496 Z= 0.292 Chirality : 0.042 0.203 1018 Planarity : 0.004 0.039 1217 Dihedral : 4.959 25.211 980 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.41 % Allowed : 18.26 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.02 (0.28), residues: 855 helix: -4.15 (0.75), residues: 20 sheet: -1.31 (0.26), residues: 370 loop : -1.14 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 92 HIS 0.010 0.001 HIS C 82 PHE 0.025 0.002 PHE D 98 TYR 0.020 0.001 TYR C 32 ARG 0.003 0.000 ARG G 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3971.98 seconds wall clock time: 71 minutes 17.90 seconds (4277.90 seconds total)