Starting phenix.real_space_refine on Wed Mar 12 00:40:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x7t_33047/03_2025/7x7t_33047.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x7t_33047/03_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_33047/03_2025/7x7t_33047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x7t_33047/03_2025/7x7t_33047.map" model { file = "/net/cci-nas-00/data/ceres_data/7x7t_33047/03_2025/7x7t_33047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x7t_33047/03_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-5624/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: 5.08, per 1000 atoms: 0.75 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: 1.53 Conformation dependent library (CDL) restraints added in 915.4 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: 0.84 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: 1.67 Time building geometry restraints manager: 1.85 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: 5.140 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.550 Find NCS groups from input model: 0.110 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- 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 : 0.640 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: 0.1782 time to fit residues: 46.4873 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 : 0.681 ------------------------------------------------------------------------------- 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: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.183698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.157734 restraints weight = 7504.848| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.32 r_work: 0.3661 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 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 = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6988 Z= 0.215 Angle : 0.626 11.139 9496 Z= 0.322 Chirality : 0.044 0.153 1018 Planarity : 0.005 0.045 1217 Dihedral : 5.894 44.779 980 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.12 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 (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: -3.78 (0.25), residues: 855 helix: -5.17 (0.27), residues: 26 sheet: -2.50 (0.26), residues: 334 loop : -2.37 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 35 HIS 0.002 0.001 HIS H 41 PHE 0.019 0.002 PHE G 456 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 168 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.698 Fit side-chains REVERT: G 405 ASP cc_start: 0.8774 (t0) cc_final: 0.8552 (t0) REVERT: G 519 HIS cc_start: 0.8415 (m-70) cc_final: 0.7034 (t-170) REVERT: H 19 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7731 (mtpt) REVERT: H 51 PHE cc_start: 0.8218 (t80) cc_final: 0.7636 (t80) REVERT: D 105 GLU cc_start: 0.5208 (tp30) cc_final: 0.3300 (tp30) outliers start: 12 outliers final: 9 residues processed: 159 average time/residue: 0.1761 time to fit residues: 38.0481 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 : 0.735 ------------------------------------------------------------------------------- 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: 2.9990 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.177891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152152 restraints weight = 7710.862| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.95 r_work: 0.3598 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 6988 Z= 0.369 Angle : 0.680 13.592 9496 Z= 0.347 Chirality : 0.045 0.141 1018 Planarity : 0.005 0.039 1217 Dihedral : 5.926 38.390 980 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.59 % Allowed : 14.99 % 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 (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: -3.52 (0.26), residues: 855 helix: -5.10 (0.28), residues: 27 sheet: -2.36 (0.25), residues: 350 loop : -2.11 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 47 HIS 0.007 0.002 HIS L 38 PHE 0.023 0.002 PHE G 377 TYR 0.019 0.002 TYR D 91 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 165 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.668 Fit side-chains REVERT: G 399 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8412 (p) REVERT: G 405 ASP cc_start: 0.8748 (t0) cc_final: 0.8502 (t0) REVERT: H 19 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8093 (mtpt) REVERT: A 103 ASN cc_start: 0.8839 (m-40) cc_final: 0.8544 (m-40) REVERT: D 39 LYS cc_start: 0.8557 (pttp) cc_final: 0.8226 (mtmm) REVERT: D 105 GLU cc_start: 0.5291 (tp30) cc_final: 0.3287 (tp30) REVERT: C 60 TYR cc_start: 0.9117 (m-80) cc_final: 0.8837 (m-80) outliers start: 19 outliers final: 16 residues processed: 155 average time/residue: 0.1774 time to fit residues: 36.9691 Evaluate side-chains 153 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 0.0470 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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** D 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.182312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.156863 restraints weight = 7669.641| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.95 r_work: 0.3640 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6988 Z= 0.202 Angle : 0.594 11.027 9496 Z= 0.300 Chirality : 0.042 0.134 1018 Planarity : 0.004 0.040 1217 Dihedral : 5.441 29.699 980 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.86 % Allowed : 17.03 % Favored : 80.11 % 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: -2.97 (0.27), residues: 855 helix: -5.08 (0.33), residues: 26 sheet: -1.90 (0.27), residues: 339 loop : -1.81 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 436 HIS 0.006 0.001 HIS C 82 PHE 0.019 0.001 PHE G 456 TYR 0.020 0.001 TYR C 32 ARG 0.004 0.000 ARG A 63 *********************** 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 156 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.678 Fit side-chains REVERT: G 399 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8336 (p) REVERT: G 405 ASP cc_start: 0.8726 (t0) cc_final: 0.8459 (t0) REVERT: H 19 LYS cc_start: 0.8422 (mtpt) cc_final: 0.8126 (mtpt) REVERT: D 105 GLU cc_start: 0.5204 (tp30) cc_final: 0.3261 (tp30) outliers start: 21 outliers final: 16 residues processed: 146 average time/residue: 0.1667 time to fit residues: 33.3782 Evaluate side-chains 148 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 28 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 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 62 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 5 optimal weight: 0.0030 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 13 optimal weight: 0.0170 chunk 15 optimal weight: 0.0270 chunk 72 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 overall best weight: 0.1286 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.186447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.161238 restraints weight = 7613.045| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.15 r_work: 0.3709 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6988 Z= 0.140 Angle : 0.542 8.285 9496 Z= 0.273 Chirality : 0.040 0.136 1018 Planarity : 0.004 0.040 1217 Dihedral : 4.822 23.947 980 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.68 % Allowed : 16.08 % 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: -2.47 (0.27), residues: 855 helix: -5.03 (0.33), residues: 26 sheet: -1.46 (0.28), residues: 336 loop : -1.54 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 436 HIS 0.006 0.001 HIS C 82 PHE 0.020 0.001 PHE G 456 TYR 0.018 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 161 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.746 Fit side-chains REVERT: G 405 ASP cc_start: 0.8419 (t0) cc_final: 0.8163 (t0) REVERT: H 19 LYS cc_start: 0.8423 (mtpt) cc_final: 0.7993 (mttp) REVERT: D 105 GLU cc_start: 0.5038 (tp30) cc_final: 0.3260 (tp30) outliers start: 27 outliers final: 19 residues processed: 147 average time/residue: 0.1640 time to fit residues: 33.5360 Evaluate side-chains 141 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 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 H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 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 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 42 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 79 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 0.0170 chunk 36 optimal weight: 4.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.183569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.157874 restraints weight = 7587.923| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.23 r_work: 0.3647 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6988 Z= 0.217 Angle : 0.586 10.168 9496 Z= 0.290 Chirality : 0.041 0.131 1018 Planarity : 0.004 0.039 1217 Dihedral : 4.899 24.561 980 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.00 % Allowed : 18.26 % Favored : 78.75 % 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 (0.28), residues: 855 helix: -4.97 (0.34), residues: 26 sheet: -1.53 (0.27), residues: 363 loop : -1.36 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.011 0.002 HIS C 82 PHE 0.033 0.002 PHE G 456 TYR 0.015 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 145 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: G 399 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8295 (p) REVERT: G 405 ASP cc_start: 0.8717 (t0) cc_final: 0.8415 (t0) REVERT: H 19 LYS cc_start: 0.8491 (mtpt) cc_final: 0.8103 (mtpp) outliers start: 22 outliers final: 19 residues processed: 134 average time/residue: 0.1579 time to fit residues: 29.7266 Evaluate side-chains 140 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 399 SER 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 28 THR Chi-restraints excluded: chain H residue 87 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 19 VAL Chi-restraints excluded: chain D residue 30 ASN 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 15 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 75 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.184089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.159362 restraints weight = 7491.105| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.11 r_work: 0.3716 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6988 Z= 0.197 Angle : 0.567 10.187 9496 Z= 0.282 Chirality : 0.041 0.128 1018 Planarity : 0.004 0.039 1217 Dihedral : 4.835 24.733 980 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.68 % Allowed : 17.57 % Favored : 78.75 % 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: -2.21 (0.28), residues: 855 helix: -4.83 (0.42), residues: 26 sheet: -1.38 (0.26), residues: 376 loop : -1.23 (0.29), residues: 453 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 0.030 0.002 PHE G 456 TYR 0.018 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 149 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.685 Fit side-chains REVERT: G 405 ASP cc_start: 0.8641 (t0) cc_final: 0.8363 (t0) REVERT: H 19 LYS cc_start: 0.8489 (mtpt) cc_final: 0.8095 (mtpp) REVERT: D 79 GLN cc_start: 0.8174 (mt0) cc_final: 0.7911 (mp10) REVERT: D 92 TRP cc_start: 0.8476 (t-100) cc_final: 0.8086 (t-100) REVERT: C 44 SER cc_start: 0.8384 (t) cc_final: 0.7939 (p) outliers start: 27 outliers final: 21 residues processed: 139 average time/residue: 0.1598 time to fit residues: 30.9566 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 : 0.756 ------------------------------------------------------------------------------- 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 452 LEU Chi-restraints excluded: chain G residue 462 LYS 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 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 27 optimal weight: 0.0170 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 21 optimal weight: 0.0770 chunk 15 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.183317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158795 restraints weight = 7581.100| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.85 r_work: 0.3673 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- 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 = 0.49 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 = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6988 Z= 0.187 Angle : 0.566 9.851 9496 Z= 0.280 Chirality : 0.040 0.128 1018 Planarity : 0.004 0.039 1217 Dihedral : 4.778 24.554 980 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.41 % Allowed : 17.30 % 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: -2.06 (0.28), residues: 855 helix: -4.72 (0.43), residues: 26 sheet: -1.26 (0.26), residues: 375 loop : -1.15 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 436 HIS 0.010 0.001 HIS C 82 PHE 0.039 0.002 PHE G 456 TYR 0.017 0.001 TYR C 32 ARG 0.005 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: 25 poor density : 124 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 399 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8287 (p) REVERT: G 405 ASP cc_start: 0.8651 (t0) cc_final: 0.8373 (t0) REVERT: G 519 HIS cc_start: 0.8311 (m-70) cc_final: 0.6788 (t-170) REVERT: H 19 LYS cc_start: 0.8511 (mtpt) cc_final: 0.8105 (mtpp) REVERT: A 43 GLN cc_start: 0.8385 (mp10) cc_final: 0.8155 (mp10) REVERT: D 79 GLN cc_start: 0.8182 (mt0) cc_final: 0.7893 (mp10) REVERT: D 92 TRP cc_start: 0.8510 (t-100) cc_final: 0.8056 (t-100) REVERT: C 44 SER cc_start: 0.8350 (t) cc_final: 0.7890 (p) outliers start: 25 outliers final: 23 residues processed: 139 average time/residue: 0.1659 time to fit residues: 31.8311 Evaluate side-chains 145 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 452 LEU Chi-restraints excluded: chain G residue 462 LYS 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 H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 SER 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 34 MET Chi-restraints excluded: chain C residue 119 THR 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: 0.8980 chunk 41 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.179252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.154439 restraints weight = 7638.453| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.14 r_work: 0.3195 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 6988 Z= 0.348 Angle : 0.635 12.381 9496 Z= 0.321 Chirality : 0.042 0.132 1018 Planarity : 0.004 0.036 1217 Dihedral : 5.173 25.973 980 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.95 % Allowed : 17.17 % Favored : 78.88 % 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: -2.23 (0.28), residues: 855 helix: -4.86 (0.37), residues: 26 sheet: -1.37 (0.26), residues: 372 loop : -1.28 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 96 HIS 0.010 0.002 HIS C 82 PHE 0.022 0.002 PHE G 377 TYR 0.019 0.002 TYR G 473 ARG 0.005 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 151 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: G 399 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8239 (p) REVERT: G 420 ASP cc_start: 0.8483 (m-30) cc_final: 0.8140 (m-30) REVERT: G 501 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7605 (m110) REVERT: G 516 GLU cc_start: 0.5140 (tp30) cc_final: 0.4871 (tp30) REVERT: H 19 LYS cc_start: 0.8550 (mtpt) cc_final: 0.8091 (mtpp) REVERT: A 43 GLN cc_start: 0.8402 (mp10) cc_final: 0.8106 (mp10) REVERT: A 103 ASN cc_start: 0.8771 (m-40) cc_final: 0.8483 (m-40) REVERT: D 79 GLN cc_start: 0.8120 (mt0) cc_final: 0.7727 (mp10) outliers start: 29 outliers final: 23 residues processed: 139 average time/residue: 0.1673 time to fit residues: 32.0376 Evaluate side-chains 147 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 452 LEU Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 462 LYS 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 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 30 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 52 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.183909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.158555 restraints weight = 7802.516| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.31 r_work: 0.3231 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6988 Z= 0.190 Angle : 0.575 10.437 9496 Z= 0.286 Chirality : 0.040 0.128 1018 Planarity : 0.004 0.038 1217 Dihedral : 4.863 25.141 980 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.68 % Allowed : 17.98 % 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: -1.99 (0.28), residues: 855 helix: -4.56 (0.45), residues: 20 sheet: -1.21 (0.27), residues: 372 loop : -1.18 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 92 HIS 0.010 0.001 HIS C 82 PHE 0.032 0.001 PHE G 456 TYR 0.019 0.001 TYR C 32 ARG 0.005 0.000 ARG A 63 ********************** 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 149 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 399 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8294 (p) REVERT: G 516 GLU cc_start: 0.5086 (tp30) cc_final: 0.4860 (tp30) REVERT: G 519 HIS cc_start: 0.8177 (m-70) cc_final: 0.6514 (t-170) REVERT: H 19 LYS cc_start: 0.8481 (mtpt) cc_final: 0.8027 (mtpp) REVERT: H 33 THR cc_start: 0.9033 (p) cc_final: 0.8816 (t) REVERT: D 9 SER cc_start: 0.8311 (m) cc_final: 0.7562 (t) REVERT: D 79 GLN cc_start: 0.8061 (mt0) cc_final: 0.7682 (mp10) REVERT: D 92 TRP cc_start: 0.8533 (t-100) cc_final: 0.8016 (t-100) outliers start: 27 outliers final: 24 residues processed: 137 average time/residue: 0.1690 time to fit residues: 31.9008 Evaluate side-chains 144 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 452 LEU Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 462 LYS 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 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 100 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 36 optimal weight: 0.0170 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 overall best weight: 0.6020 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.183311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.157515 restraints weight = 7697.501| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.43 r_work: 0.3432 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6988 Z= 0.209 Angle : 0.580 10.454 9496 Z= 0.290 Chirality : 0.041 0.128 1018 Planarity : 0.004 0.038 1217 Dihedral : 4.852 24.848 980 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.41 % Allowed : 18.80 % Favored : 77.79 % 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: -1.96 (0.28), residues: 855 helix: -4.36 (0.53), residues: 20 sheet: -1.21 (0.27), residues: 367 loop : -1.14 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 92 HIS 0.011 0.001 HIS C 82 PHE 0.036 0.002 PHE G 456 TYR 0.018 0.001 TYR C 32 ARG 0.003 0.000 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3912.70 seconds wall clock time: 67 minutes 50.73 seconds (4070.73 seconds total)