Starting phenix.real_space_refine on Tue Feb 13 16:06:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7t_33047/02_2024/7x7t_33047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7t_33047/02_2024/7x7t_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7t_33047/02_2024/7x7t_33047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7t_33047/02_2024/7x7t_33047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7t_33047/02_2024/7x7t_33047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x7t_33047/02_2024/7x7t_33047.pdb" } 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 Residue "G ARG 357": "NH1" <-> "NH2" Residue "G ARG 408": "NH1" <-> "NH2" Residue "L GLU 85": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "A GLU 10": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.18, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 2.39 Conformation dependent library (CDL) restraints added in 1.4 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: 1.07 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: 1.99 Time building geometry restraints manager: 2.61 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: 93.91 - 102.00: 15 102.00 - 110.09: 1354 110.09 - 118.18: 3795 118.18 - 126.27: 4214 126.27 - 134.36: 118 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 2.440 nonbonded pdb=" OD2 ASP C 73 " pdb=" OG SER C 75 " model vdw 2.246 2.440 nonbonded pdb=" NE2 GLN B 38 " pdb=" OE1 GLN A 39 " model vdw 2.304 2.520 nonbonded pdb=" O SER D 60 " pdb=" OG SER D 60 " model vdw 2.323 2.440 nonbonded pdb=" OH TYR C 60 " pdb=" N LEU C 70 " model vdw 2.332 2.520 ... (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 ========== 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: 4.010 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: 13.600 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.050 Find NCS groups from input model: 0.240 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.960 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 0.783 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: 0.1973 time to fit residues: 51.3549 Evaluate side-chains 156 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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: 0.5980 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** B 34 ASN D 38 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6988 Z= 0.241 Angle : 0.627 11.613 9496 Z= 0.321 Chirality : 0.044 0.153 1018 Planarity : 0.004 0.045 1217 Dihedral : 5.858 38.318 980 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.18 % Allowed : 12.53 % Favored : 85.29 % 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: -3.88 (0.25), residues: 855 helix: -5.20 (0.24), residues: 26 sheet: -2.54 (0.26), residues: 319 loop : -2.50 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 35 HIS 0.003 0.001 HIS L 94 PHE 0.017 0.002 PHE G 490 TYR 0.017 0.001 TYR D 91 ARG 0.002 0.000 ARG A 63 *********************** 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 fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 1.027 Fit side-chains REVERT: G 472 ILE cc_start: 0.8226 (pt) cc_final: 0.7778 (mm) REVERT: G 519 HIS cc_start: 0.6455 (m-70) cc_final: 0.4670 (t-170) REVERT: L 111 LYS cc_start: 0.5581 (mtpp) cc_final: 0.5368 (mmmt) REVERT: H 51 PHE cc_start: 0.6534 (t80) cc_final: 0.5786 (t80) REVERT: B 3 GLN cc_start: 0.7825 (tt0) cc_final: 0.7352 (tp40) REVERT: B 17 ASP cc_start: 0.7803 (m-30) cc_final: 0.7378 (m-30) REVERT: A 25 SER cc_start: 0.7453 (t) cc_final: 0.7189 (p) REVERT: A 59 ARG cc_start: 0.5792 (mtt-85) cc_final: 0.5300 (mtm180) REVERT: D 105 GLU cc_start: 0.4057 (tp30) cc_final: 0.2995 (tp30) REVERT: C 46 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7005 (mt-10) REVERT: C 60 TYR cc_start: 0.7958 (m-80) cc_final: 0.7161 (m-80) REVERT: C 63 GLU cc_start: 0.8077 (mp0) cc_final: 0.7816 (mp0) outliers start: 16 outliers final: 12 residues processed: 158 average time/residue: 0.1951 time to fit residues: 41.9155 Evaluate side-chains 155 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 442 ASP 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 41 ASP 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 41 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 77 ASN D 38 GLN D 42 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 6988 Z= 0.371 Angle : 0.675 13.875 9496 Z= 0.343 Chirality : 0.045 0.143 1018 Planarity : 0.004 0.039 1217 Dihedral : 5.816 32.656 980 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.00 % Allowed : 16.62 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.63 (0.26), residues: 855 helix: -5.15 (0.23), residues: 27 sheet: -2.43 (0.25), residues: 351 loop : -2.19 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 436 HIS 0.007 0.002 HIS C 82 PHE 0.022 0.002 PHE G 377 TYR 0.017 0.002 TYR D 91 ARG 0.002 0.000 ARG G 466 *********************** 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 171 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 0.785 Fit side-chains REVERT: G 399 SER cc_start: 0.7570 (OUTLIER) cc_final: 0.7076 (p) REVERT: G 472 ILE cc_start: 0.8311 (pt) cc_final: 0.7815 (mm) REVERT: B 3 GLN cc_start: 0.7927 (tt0) cc_final: 0.7490 (tp40) REVERT: B 4 MET cc_start: 0.7088 (tpp) cc_final: 0.6628 (mmm) REVERT: B 17 ASP cc_start: 0.7729 (m-30) cc_final: 0.7245 (m-30) REVERT: B 61 ARG cc_start: 0.7243 (mtm-85) cc_final: 0.6977 (mtm-85) REVERT: B 90 GLN cc_start: 0.7124 (pp30) cc_final: 0.5820 (pp30) REVERT: A 25 SER cc_start: 0.7469 (t) cc_final: 0.7213 (p) REVERT: A 59 ARG cc_start: 0.5812 (mtt-85) cc_final: 0.5231 (mtm180) REVERT: A 103 ASN cc_start: 0.6815 (m-40) cc_final: 0.6363 (m-40) REVERT: D 39 LYS cc_start: 0.7135 (pttp) cc_final: 0.6656 (mtmm) REVERT: D 105 GLU cc_start: 0.3987 (tp30) cc_final: 0.2915 (tp30) REVERT: C 60 TYR cc_start: 0.7998 (m-80) cc_final: 0.7155 (m-80) outliers start: 22 outliers final: 19 residues processed: 159 average time/residue: 0.1826 time to fit residues: 38.8787 Evaluate side-chains 160 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 442 ASP Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 470 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 L residue 95 SER Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain C residue 30 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 80 optimal weight: 0.2980 chunk 71 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 394 ASN ** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 42 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.2098 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= 0.189 Angle : 0.577 10.665 9496 Z= 0.290 Chirality : 0.042 0.195 1018 Planarity : 0.004 0.041 1217 Dihedral : 5.290 29.114 980 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.27 % Allowed : 17.71 % Favored : 79.02 % 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: -3.07 (0.26), residues: 855 helix: -5.04 (0.29), residues: 26 sheet: -1.92 (0.27), residues: 334 loop : -1.94 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 436 HIS 0.006 0.001 HIS C 82 PHE 0.021 0.001 PHE A 29 TYR 0.019 0.001 TYR C 32 ARG 0.002 0.000 ARG G 408 *********************** 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 161 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 0.700 Fit side-chains REVERT: G 399 SER cc_start: 0.7420 (OUTLIER) cc_final: 0.7073 (p) REVERT: G 472 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7858 (mm) REVERT: L 111 LYS cc_start: 0.5580 (mtpp) cc_final: 0.5289 (mmmt) REVERT: H 51 PHE cc_start: 0.6581 (t80) cc_final: 0.5801 (t80) REVERT: B 3 GLN cc_start: 0.7997 (tt0) cc_final: 0.7604 (tp40) REVERT: B 4 MET cc_start: 0.7068 (tpp) cc_final: 0.6631 (mmm) REVERT: B 17 ASP cc_start: 0.7663 (m-30) cc_final: 0.7169 (m-30) REVERT: B 90 GLN cc_start: 0.7056 (pp30) cc_final: 0.5777 (pp30) REVERT: A 25 SER cc_start: 0.7533 (t) cc_final: 0.7320 (p) REVERT: A 59 ARG cc_start: 0.5749 (mtt-85) cc_final: 0.5206 (mtt180) REVERT: D 105 GLU cc_start: 0.3913 (tp30) cc_final: 0.2879 (tp30) REVERT: C 60 TYR cc_start: 0.7994 (m-80) cc_final: 0.7196 (m-80) outliers start: 24 outliers final: 17 residues processed: 148 average time/residue: 0.1764 time to fit residues: 35.3232 Evaluate side-chains 151 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 452 LEU Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN D 38 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 6988 Z= 0.372 Angle : 0.652 13.450 9496 Z= 0.331 Chirality : 0.044 0.175 1018 Planarity : 0.004 0.039 1217 Dihedral : 5.549 30.641 980 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.22 % Allowed : 17.71 % Favored : 78.07 % 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: -3.10 (0.26), residues: 855 helix: -5.05 (0.29), residues: 26 sheet: -2.00 (0.26), residues: 355 loop : -1.88 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 96 HIS 0.007 0.002 HIS C 82 PHE 0.026 0.002 PHE A 29 TYR 0.019 0.002 TYR C 32 ARG 0.002 0.000 ARG G 408 *********************** 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 169 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 0.811 Fit side-chains REVERT: G 399 SER cc_start: 0.7523 (OUTLIER) cc_final: 0.7027 (p) REVERT: L 111 LYS cc_start: 0.5628 (mtpp) cc_final: 0.5319 (mmmt) REVERT: B 3 GLN cc_start: 0.8084 (tt0) cc_final: 0.7645 (tp40) REVERT: B 4 MET cc_start: 0.7128 (tpp) cc_final: 0.6800 (mmm) REVERT: B 17 ASP cc_start: 0.7541 (m-30) cc_final: 0.7065 (m-30) REVERT: B 61 ARG cc_start: 0.7143 (mtm-85) cc_final: 0.6917 (mtm-85) REVERT: A 25 SER cc_start: 0.7544 (t) cc_final: 0.7318 (p) REVERT: A 59 ARG cc_start: 0.5724 (mtt-85) cc_final: 0.5149 (mtt180) REVERT: A 103 ASN cc_start: 0.6803 (m-40) cc_final: 0.6364 (m-40) REVERT: D 39 LYS cc_start: 0.7043 (pttp) cc_final: 0.6707 (mtmm) REVERT: D 105 GLU cc_start: 0.3951 (tp30) cc_final: 0.2966 (tp30) REVERT: C 60 TYR cc_start: 0.8040 (m-80) cc_final: 0.7220 (m-80) outliers start: 31 outliers final: 27 residues processed: 155 average time/residue: 0.1818 time to fit residues: 37.7154 Evaluate side-chains 162 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 398 ASP Chi-restraints excluded: chain G residue 399 SER Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 470 THR 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 95 SER 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 103 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 41 ASP 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 D residue 56 THR Chi-restraints excluded: chain C residue 30 THR 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 72 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 47 optimal weight: 7.9990 chunk 19 optimal weight: 0.0170 chunk 80 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN D 38 GLN C 6 GLN C 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6988 Z= 0.190 Angle : 0.571 10.608 9496 Z= 0.284 Chirality : 0.041 0.193 1018 Planarity : 0.004 0.041 1217 Dihedral : 5.144 27.559 980 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.09 % Allowed : 19.07 % Favored : 76.84 % 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: -2.74 (0.27), residues: 855 helix: -4.76 (0.47), residues: 26 sheet: -1.74 (0.27), residues: 349 loop : -1.66 (0.26), residues: 480 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 0.028 0.001 PHE G 456 TYR 0.017 0.001 TYR C 32 ARG 0.002 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 158 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 0.685 Fit side-chains REVERT: G 399 SER cc_start: 0.7465 (OUTLIER) cc_final: 0.7083 (p) REVERT: G 472 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7870 (mm) REVERT: G 523 THR cc_start: 0.6705 (m) cc_final: 0.6347 (p) REVERT: L 111 LYS cc_start: 0.5591 (mtpp) cc_final: 0.5284 (mmmt) REVERT: B 3 GLN cc_start: 0.8080 (tt0) cc_final: 0.7642 (tp40) REVERT: B 4 MET cc_start: 0.6983 (tpp) cc_final: 0.6743 (mmm) REVERT: B 17 ASP cc_start: 0.7508 (m-30) cc_final: 0.7032 (m-30) REVERT: B 61 ARG cc_start: 0.7182 (mtm-85) cc_final: 0.6946 (mtm-85) REVERT: B 90 GLN cc_start: 0.7300 (pp30) cc_final: 0.6587 (pp30) REVERT: A 25 SER cc_start: 0.7513 (t) cc_final: 0.7299 (p) REVERT: A 59 ARG cc_start: 0.5669 (mtt-85) cc_final: 0.5119 (mtt180) REVERT: D 79 GLN cc_start: 0.7034 (mt0) cc_final: 0.6408 (mp10) REVERT: D 92 TRP cc_start: 0.7648 (t-100) cc_final: 0.7209 (t-100) REVERT: D 105 GLU cc_start: 0.4026 (tp30) cc_final: 0.3050 (tp30) REVERT: C 60 TYR cc_start: 0.7989 (m-80) cc_final: 0.7145 (m-80) outliers start: 30 outliers final: 21 residues processed: 143 average time/residue: 0.1712 time to fit residues: 33.3101 Evaluate side-chains 151 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 452 LEU Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 472 ILE Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 0.0270 chunk 67 optimal weight: 0.0770 chunk 44 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 0.0870 chunk 49 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.1974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6988 Z= 0.135 Angle : 0.530 8.845 9496 Z= 0.262 Chirality : 0.040 0.205 1018 Planarity : 0.004 0.041 1217 Dihedral : 4.696 23.828 980 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.68 % Allowed : 19.62 % Favored : 76.70 % 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: -2.28 (0.28), residues: 855 helix: -4.18 (0.81), residues: 20 sheet: -1.39 (0.27), residues: 359 loop : -1.44 (0.27), residues: 476 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 0.032 0.001 PHE G 456 TYR 0.015 0.001 TYR C 32 ARG 0.002 0.000 ARG C 38 *********************** 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 162 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.282 Fit side-chains REVERT: G 420 ASP cc_start: 0.7276 (m-30) cc_final: 0.6863 (m-30) REVERT: G 452 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6719 (mt) REVERT: G 472 ILE cc_start: 0.8237 (pt) cc_final: 0.7944 (mm) REVERT: G 523 THR cc_start: 0.6886 (m) cc_final: 0.6572 (p) REVERT: L 111 LYS cc_start: 0.5603 (mtpp) cc_final: 0.5301 (mmmt) REVERT: B 3 GLN cc_start: 0.8036 (tt0) cc_final: 0.7622 (tp40) REVERT: B 4 MET cc_start: 0.6867 (tpp) cc_final: 0.6655 (mmm) REVERT: B 17 ASP cc_start: 0.7468 (m-30) cc_final: 0.6993 (m-30) REVERT: A 25 SER cc_start: 0.7430 (t) cc_final: 0.7228 (p) REVERT: A 43 GLN cc_start: 0.7249 (mp10) cc_final: 0.6785 (mp10) REVERT: A 59 ARG cc_start: 0.5539 (mtt-85) cc_final: 0.5142 (mtt180) REVERT: D 79 GLN cc_start: 0.7133 (mt0) cc_final: 0.6531 (mp10) REVERT: D 92 TRP cc_start: 0.7590 (t-100) cc_final: 0.7035 (t60) REVERT: D 105 GLU cc_start: 0.4056 (tp30) cc_final: 0.3103 (tp30) REVERT: C 60 TYR cc_start: 0.8063 (m-80) cc_final: 0.7196 (m-80) outliers start: 27 outliers final: 23 residues processed: 147 average time/residue: 0.1897 time to fit residues: 38.3264 Evaluate side-chains 153 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 402 ILE 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 95 SER 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 20 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 2 ILE 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 47 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.0170 chunk 50 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 0.0070 chunk 69 optimal weight: 5.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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** D 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6988 Z= 0.186 Angle : 0.554 9.642 9496 Z= 0.273 Chirality : 0.041 0.207 1018 Planarity : 0.004 0.038 1217 Dihedral : 4.719 24.234 980 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.54 % Allowed : 20.71 % Favored : 75.75 % 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: -2.13 (0.28), residues: 855 helix: -3.99 (0.87), residues: 20 sheet: -1.24 (0.26), residues: 363 loop : -1.38 (0.28), residues: 472 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 0.031 0.001 PHE G 456 TYR 0.015 0.001 TYR G 473 ARG 0.002 0.000 ARG G 408 *********************** 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 158 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 0.725 Fit side-chains REVERT: G 452 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6642 (mt) REVERT: G 472 ILE cc_start: 0.8234 (pt) cc_final: 0.7947 (mm) REVERT: G 523 THR cc_start: 0.6814 (m) cc_final: 0.6500 (p) REVERT: L 111 LYS cc_start: 0.5595 (mtpp) cc_final: 0.5299 (mmmt) REVERT: B 3 GLN cc_start: 0.8060 (tt0) cc_final: 0.7645 (tp40) REVERT: B 4 MET cc_start: 0.6928 (tpp) cc_final: 0.6643 (mmm) REVERT: B 17 ASP cc_start: 0.7434 (m-30) cc_final: 0.6955 (m-30) REVERT: A 25 SER cc_start: 0.7396 (t) cc_final: 0.7195 (p) REVERT: A 59 ARG cc_start: 0.5574 (mtt-85) cc_final: 0.5276 (mtm-85) REVERT: D 79 GLN cc_start: 0.7274 (mt0) cc_final: 0.6652 (mp10) REVERT: D 92 TRP cc_start: 0.7659 (t-100) cc_final: 0.7256 (t-100) REVERT: C 60 TYR cc_start: 0.8146 (m-80) cc_final: 0.7301 (m-80) REVERT: C 82 HIS cc_start: 0.6791 (t70) cc_final: 0.6474 (t70) outliers start: 26 outliers final: 23 residues processed: 142 average time/residue: 0.1745 time to fit residues: 33.5798 Evaluate side-chains 154 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 385 THR Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 470 THR 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 95 SER 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 20 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.1980 chunk 76 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 67 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 422 ASN D 42 ASN C 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6988 Z= 0.162 Angle : 0.540 9.213 9496 Z= 0.266 Chirality : 0.040 0.204 1018 Planarity : 0.004 0.038 1217 Dihedral : 4.613 24.152 980 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.41 % Allowed : 21.12 % Favored : 75.48 % 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: -1.94 (0.28), residues: 855 helix: -3.90 (0.86), residues: 20 sheet: -1.06 (0.27), residues: 360 loop : -1.29 (0.28), residues: 475 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 0.029 0.001 PHE G 456 TYR 0.015 0.001 TYR G 473 ARG 0.001 0.000 ARG G 408 *********************** 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 158 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 0.767 Fit side-chains REVERT: G 399 SER cc_start: 0.7486 (OUTLIER) cc_final: 0.7097 (p) REVERT: G 452 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6737 (mt) REVERT: G 472 ILE cc_start: 0.8209 (pt) cc_final: 0.7935 (mm) REVERT: G 523 THR cc_start: 0.6859 (m) cc_final: 0.6555 (p) REVERT: L 111 LYS cc_start: 0.5428 (mtpp) cc_final: 0.5109 (mmmt) REVERT: B 3 GLN cc_start: 0.8050 (tt0) cc_final: 0.7640 (tp40) REVERT: B 4 MET cc_start: 0.6868 (tpp) cc_final: 0.6597 (mmm) REVERT: B 17 ASP cc_start: 0.7430 (m-30) cc_final: 0.6960 (m-30) REVERT: A 25 SER cc_start: 0.7358 (t) cc_final: 0.7135 (p) REVERT: A 43 GLN cc_start: 0.7263 (mp10) cc_final: 0.6849 (mp10) REVERT: A 59 ARG cc_start: 0.5513 (mtt-85) cc_final: 0.5157 (mtt180) REVERT: D 4 MET cc_start: 0.5797 (mtm) cc_final: 0.5569 (mtm) REVERT: D 9 SER cc_start: 0.7035 (m) cc_final: 0.6187 (t) REVERT: D 79 GLN cc_start: 0.7274 (mt0) cc_final: 0.6678 (mp10) REVERT: C 60 TYR cc_start: 0.8137 (m-80) cc_final: 0.7729 (m-80) outliers start: 25 outliers final: 21 residues processed: 144 average time/residue: 0.1818 time to fit residues: 35.3235 Evaluate side-chains 153 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 402 ILE Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 470 THR 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 95 SER Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain C residue 52 VAL 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 54 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 moved from start: 0.2840 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= 0.190 Angle : 0.551 9.621 9496 Z= 0.272 Chirality : 0.041 0.153 1018 Planarity : 0.004 0.037 1217 Dihedral : 4.641 24.453 980 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.54 % Allowed : 21.12 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.28), residues: 855 helix: -3.82 (0.88), residues: 20 sheet: -1.08 (0.27), residues: 364 loop : -1.26 (0.28), residues: 471 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 0.037 0.002 PHE G 456 TYR 0.014 0.001 TYR G 473 ARG 0.001 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 157 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 0.705 Fit side-chains REVERT: G 399 SER cc_start: 0.7462 (OUTLIER) cc_final: 0.6998 (p) REVERT: G 452 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6635 (mt) REVERT: G 472 ILE cc_start: 0.8220 (pt) cc_final: 0.7937 (mm) REVERT: G 523 THR cc_start: 0.6889 (m) cc_final: 0.6605 (p) REVERT: L 111 LYS cc_start: 0.5365 (mtpp) cc_final: 0.5137 (mmmt) REVERT: B 3 GLN cc_start: 0.8065 (tt0) cc_final: 0.7660 (tp40) REVERT: B 4 MET cc_start: 0.6947 (tpp) cc_final: 0.6665 (mmm) REVERT: B 17 ASP cc_start: 0.7394 (m-30) cc_final: 0.6933 (m-30) REVERT: A 25 SER cc_start: 0.7324 (t) cc_final: 0.7060 (p) REVERT: A 43 GLN cc_start: 0.7162 (mp10) cc_final: 0.6751 (mp10) REVERT: A 59 ARG cc_start: 0.5526 (mtt-85) cc_final: 0.5271 (mtm-85) REVERT: D 9 SER cc_start: 0.7091 (m) cc_final: 0.6215 (t) REVERT: D 79 GLN cc_start: 0.7200 (mt0) cc_final: 0.6574 (mp10) REVERT: D 92 TRP cc_start: 0.7614 (t-100) cc_final: 0.7019 (t60) REVERT: C 60 TYR cc_start: 0.8140 (m-80) cc_final: 0.7770 (m-80) outliers start: 26 outliers final: 23 residues processed: 141 average time/residue: 0.1792 time to fit residues: 34.0720 Evaluate side-chains 152 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 402 ILE Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 460 ASN Chi-restraints excluded: chain G residue 470 THR 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 95 SER Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain D residue 30 ASN Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 0.0370 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.181597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.157208 restraints weight = 7541.203| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.10 r_work: 0.3674 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6988 Z= 0.166 Angle : 0.539 9.742 9496 Z= 0.266 Chirality : 0.041 0.213 1018 Planarity : 0.004 0.039 1217 Dihedral : 4.557 24.272 980 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.41 % Allowed : 21.12 % Favored : 75.48 % 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: -1.83 (0.28), residues: 855 helix: -3.76 (0.88), residues: 20 sheet: -0.98 (0.27), residues: 362 loop : -1.23 (0.28), residues: 473 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 0.015 0.001 PHE B 87 TYR 0.013 0.001 TYR C 32 ARG 0.002 0.000 ARG G 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2109.57 seconds wall clock time: 39 minutes 2.29 seconds (2342.29 seconds total)