Starting phenix.real_space_refine on Sun Mar 10 23:18:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey0_31374/03_2024/7ey0_31374.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey0_31374/03_2024/7ey0_31374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey0_31374/03_2024/7ey0_31374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey0_31374/03_2024/7ey0_31374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey0_31374/03_2024/7ey0_31374.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ey0_31374/03_2024/7ey0_31374.pdb" } resolution = 3.2 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= 0.042 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 24 5.16 5 C 3824 2.51 5 N 994 2.21 5 O 1121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 6": "OE1" <-> "OE2" Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "H PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 340": "OE1" <-> "OE2" Residue "R ARG 357": "NH1" <-> "NH2" Residue "R TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 405": "OD1" <-> "OD2" Residue "R GLU 406": "OE1" <-> "OE2" Residue "R PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 224": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5963 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 905 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 903 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 767 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "R" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "B" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 564 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 7, 'TRANS': 65} Chain breaks: 4 Chain: "N" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1359 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain breaks: 7 Time building chain proxies: 3.68, per 1000 atoms: 0.62 Number of scatterers: 5963 At special positions: 0 Unit cell: (79.92, 117.72, 123.12, 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 24 16.00 O 1121 8.00 N 994 7.00 C 3824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 86 " distance=2.07 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 166 " distance=2.04 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 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.0 seconds 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 17 sheets defined 8.2% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.623A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.526A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.561A pdb=" N THR H 90 " --> pdb=" O VAL H 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 343 removed outlier: 3.511A pdb=" N VAL R 341 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 364 through 370 removed outlier: 4.452A pdb=" N LEU R 368 " --> pdb=" O ASP R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 390 removed outlier: 3.584A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU R 390 " --> pdb=" O LEU R 387 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.473A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 4 through 7 current: chain 'A' and resid 78 through 83 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 50 removed outlier: 6.678A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 35 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 97 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 93 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 104 through 108 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.526A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N THR L 69 " --> pdb=" O THR L 25 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.366A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.413A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 36 through 38 Processing sheet with id=AA8, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA9, first strand: chain 'L' and resid 91 through 92 removed outlier: 3.874A pdb=" N LEU L 96 " --> pdb=" O ASP L 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 354 through 358 removed outlier: 4.256A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL R 433 " --> pdb=" O LYS R 378 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB5, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.595A pdb=" N SER B 61 " --> pdb=" O ILE B 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.577A pdb=" N VAL B 88 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 97 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 90 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 50 through 55 removed outlier: 3.774A pdb=" N ASP N 53 " --> pdb=" O ARG N 273 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP N 287 " --> pdb=" O LYS N 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 63 through 64 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 63 through 64 current: chain 'N' and resid 116 through 121 removed outlier: 3.767A pdb=" N ASN N 164 " --> pdb=" O GLU N 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 163 through 164 current: chain 'N' and resid 200 through 205 removed outlier: 5.953A pdb=" N SER N 205 " --> pdb=" O PRO N 225 " (cutoff:3.500A) 111 hydrogen bonds defined for protein. 255 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: 1.53 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 949 1.31 - 1.45: 2124 1.45 - 1.59: 3010 1.59 - 1.74: 0 1.74 - 1.88: 31 Bond restraints: 6114 Sorted by residual: bond pdb=" C PRO B 96 " pdb=" O PRO B 96 " ideal model delta sigma weight residual 1.233 1.172 0.060 1.16e-02 7.43e+03 2.71e+01 bond pdb=" C PRO B 6 " pdb=" O PRO B 6 " ideal model delta sigma weight residual 1.246 1.204 0.041 8.50e-03 1.38e+04 2.37e+01 bond pdb=" C PRO B 42 " pdb=" O PRO B 42 " ideal model delta sigma weight residual 1.235 1.184 0.051 1.30e-02 5.92e+03 1.54e+01 bond pdb=" N PRO B 96 " pdb=" CA PRO B 96 " ideal model delta sigma weight residual 1.467 1.420 0.047 1.21e-02 6.83e+03 1.53e+01 bond pdb=" CA PRO B 96 " pdb=" CB PRO B 96 " ideal model delta sigma weight residual 1.532 1.490 0.042 1.34e-02 5.57e+03 9.76e+00 ... (remaining 6109 not shown) Histogram of bond angle deviations from ideal: 97.27 - 104.65: 104 104.65 - 112.03: 2823 112.03 - 119.41: 2001 119.41 - 126.79: 3286 126.79 - 134.16: 79 Bond angle restraints: 8293 Sorted by residual: angle pdb=" C PRO B 96 " pdb=" CA PRO B 96 " pdb=" CB PRO B 96 " ideal model delta sigma weight residual 111.46 100.25 11.21 1.29e+00 6.01e-01 7.55e+01 angle pdb=" C PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta sigma weight residual 110.29 97.27 13.02 1.64e+00 3.72e-01 6.30e+01 angle pdb=" C GLN B 87 " pdb=" CA GLN B 87 " pdb=" CB GLN B 87 " ideal model delta sigma weight residual 111.74 99.57 12.17 1.59e+00 3.96e-01 5.86e+01 angle pdb=" CA CYS R 379 " pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 114.40 129.86 -15.46 2.30e+00 1.89e-01 4.52e+01 angle pdb=" C GLN B 95 " pdb=" CA GLN B 95 " pdb=" CB GLN B 95 " ideal model delta sigma weight residual 109.45 99.97 9.48 1.45e+00 4.76e-01 4.27e+01 ... (remaining 8288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3172 17.35 - 34.70: 290 34.70 - 52.05: 59 52.05 - 69.41: 15 69.41 - 86.76: 10 Dihedral angle restraints: 3546 sinusoidal: 1375 harmonic: 2171 Sorted by residual: dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual -86.00 -13.29 -72.71 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" C PHE B 98 " pdb=" N PHE B 98 " pdb=" CA PHE B 98 " pdb=" CB PHE B 98 " ideal model delta harmonic sigma weight residual -122.60 -102.26 -20.34 0 2.50e+00 1.60e-01 6.62e+01 dihedral pdb=" CA THR H 101 " pdb=" C THR H 101 " pdb=" N TYR H 102 " pdb=" CA TYR H 102 " ideal model delta harmonic sigma weight residual 180.00 139.58 40.42 0 5.00e+00 4.00e-02 6.54e+01 ... (remaining 3543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 788 0.092 - 0.183: 84 0.183 - 0.275: 14 0.275 - 0.367: 4 0.367 - 0.458: 2 Chirality restraints: 892 Sorted by residual: chirality pdb=" CA PHE B 98 " pdb=" N PHE B 98 " pdb=" C PHE B 98 " pdb=" CB PHE B 98 " both_signs ideal model delta sigma weight residual False 2.51 2.97 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA GLN B 5 " pdb=" N GLN B 5 " pdb=" C GLN B 5 " pdb=" CB GLN B 5 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA GLN B 95 " pdb=" N GLN B 95 " pdb=" C GLN B 95 " pdb=" CB GLN B 95 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 889 not shown) Planarity restraints: 1058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " 0.064 5.00e-02 4.00e+02 9.70e-02 1.50e+01 pdb=" N PRO L 80 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 97 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C VAL B 97 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL B 97 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE B 98 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 33 " -0.015 2.00e-02 2.50e+03 2.09e-02 8.71e+00 pdb=" CG TYR H 33 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR H 33 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR H 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR H 33 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR H 33 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR H 33 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 33 " 0.003 2.00e-02 2.50e+03 ... (remaining 1055 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 185 2.66 - 3.22: 5667 3.22 - 3.78: 8987 3.78 - 4.34: 12996 4.34 - 4.90: 21645 Nonbonded interactions: 49480 Sorted by model distance: nonbonded pdb=" OE2 GLU H 6 " pdb=" N GLY H 111 " model vdw 2.105 2.520 nonbonded pdb=" OH TYR N 37 " pdb=" O LEU N 54 " model vdw 2.149 2.440 nonbonded pdb=" OG SER R 469 " pdb=" OE1 GLU R 471 " model vdw 2.170 2.440 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.196 2.440 nonbonded pdb=" NE2 GLN B 5 " pdb=" SG CYS B 21 " model vdw 2.199 2.880 ... (remaining 49475 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=1.00 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: 3.880 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: 13.680 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.800 Find NCS groups from input model: 0.200 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 0.068 6114 Z= 0.471 Angle : 1.007 15.464 8293 Z= 0.614 Chirality : 0.064 0.458 892 Planarity : 0.007 0.097 1058 Dihedral : 14.511 86.758 2138 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.24 % Favored : 87.34 % Rotamer: Outliers : 3.08 % Allowed : 0.62 % Favored : 96.31 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.42 (0.31), residues: 719 helix: -2.18 (1.14), residues: 21 sheet: -1.17 (0.36), residues: 217 loop : -1.88 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 47 HIS 0.012 0.002 HIS B 32 PHE 0.030 0.002 PHE B 98 TYR 0.048 0.002 TYR H 33 ARG 0.018 0.001 ARG N 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 194 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 471 GLU cc_start: 0.7604 (mp0) cc_final: 0.7357 (mp0) REVERT: B 38 PRO cc_start: 0.8488 (OUTLIER) cc_final: 0.8284 (Cg_endo) REVERT: B 40 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7686 (mm110) REVERT: B 47 TYR cc_start: 0.4554 (OUTLIER) cc_final: 0.4258 (p90) REVERT: B 87 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: B 88 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8696 (t) REVERT: B 95 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7919 (pt0) REVERT: N 43 PHE cc_start: 0.5948 (p90) cc_final: 0.5165 (p90) REVERT: N 84 LEU cc_start: 0.7640 (mt) cc_final: 0.7405 (mp) REVERT: N 111 ASP cc_start: 0.8045 (t70) cc_final: 0.7562 (p0) REVERT: N 129 LYS cc_start: 0.7819 (mtmt) cc_final: 0.7553 (ttpp) REVERT: N 132 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7793 (mt-10) REVERT: N 133 PHE cc_start: 0.7780 (m-80) cc_final: 0.7492 (m-10) REVERT: N 171 VAL cc_start: 0.8677 (t) cc_final: 0.8441 (p) REVERT: N 202 LYS cc_start: 0.8234 (mttt) cc_final: 0.7936 (mttp) REVERT: N 231 ILE cc_start: 0.8945 (mm) cc_final: 0.8556 (pt) REVERT: N 237 ARG cc_start: 0.8228 (ptm160) cc_final: 0.7905 (ptp90) outliers start: 20 outliers final: 3 residues processed: 206 average time/residue: 0.2292 time to fit residues: 58.5168 Evaluate side-chains 173 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 38 PRO Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 42 PRO Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 95 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 37 optimal weight: 0.0010 chunk 29 optimal weight: 0.0570 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 overall best weight: 0.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6114 Z= 0.209 Angle : 0.624 10.337 8293 Z= 0.327 Chirality : 0.045 0.169 892 Planarity : 0.005 0.068 1058 Dihedral : 8.536 89.554 845 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.08 % Allowed : 9.38 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.93 (0.32), residues: 719 helix: -1.94 (1.21), residues: 21 sheet: -0.60 (0.37), residues: 209 loop : -1.65 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 64 HIS 0.005 0.002 HIS B 32 PHE 0.016 0.001 PHE R 456 TYR 0.020 0.001 TYR H 33 ARG 0.005 0.001 ARG N 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 31 THR cc_start: 0.8446 (p) cc_final: 0.8116 (t) REVERT: L 38 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7946 (tm-30) REVERT: R 471 GLU cc_start: 0.7478 (mp0) cc_final: 0.7231 (mp0) REVERT: B 5 GLN cc_start: 0.6108 (tp40) cc_final: 0.5739 (tp40) REVERT: B 47 TYR cc_start: 0.4699 (OUTLIER) cc_final: 0.4203 (p90) REVERT: B 95 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7332 (pt0) REVERT: B 103 LYS cc_start: 0.8826 (tttt) cc_final: 0.8621 (tptp) REVERT: N 32 PHE cc_start: 0.5208 (p90) cc_final: 0.4995 (p90) REVERT: N 43 PHE cc_start: 0.6328 (p90) cc_final: 0.5045 (p90) REVERT: N 62 VAL cc_start: 0.7967 (t) cc_final: 0.7381 (p) REVERT: N 111 ASP cc_start: 0.8446 (t70) cc_final: 0.7680 (p0) REVERT: N 129 LYS cc_start: 0.7725 (mtmt) cc_final: 0.7289 (ttpp) REVERT: N 132 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7849 (mt-10) REVERT: N 202 LYS cc_start: 0.8340 (mttt) cc_final: 0.8076 (mttp) REVERT: N 237 ARG cc_start: 0.8071 (ptm160) cc_final: 0.7744 (ptp90) REVERT: N 241 LEU cc_start: 0.6254 (tt) cc_final: 0.6004 (tt) outliers start: 20 outliers final: 11 residues processed: 202 average time/residue: 0.2056 time to fit residues: 52.0430 Evaluate side-chains 180 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 167 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 173 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6114 Z= 0.259 Angle : 0.616 9.677 8293 Z= 0.325 Chirality : 0.045 0.149 892 Planarity : 0.004 0.057 1058 Dihedral : 6.287 64.009 827 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.46 % Allowed : 13.38 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.85 (0.31), residues: 719 helix: -2.53 (0.96), residues: 21 sheet: -0.54 (0.36), residues: 222 loop : -1.58 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 64 HIS 0.006 0.001 HIS N 49 PHE 0.029 0.002 PHE H 67 TYR 0.014 0.001 TYR L 49 ARG 0.004 0.001 ARG N 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 177 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8317 (tm-30) cc_final: 0.8066 (tm-30) REVERT: R 434 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7962 (pt) REVERT: R 471 GLU cc_start: 0.7497 (mp0) cc_final: 0.7191 (mp0) REVERT: B 47 TYR cc_start: 0.4325 (OUTLIER) cc_final: 0.4042 (p90) REVERT: B 94 ASP cc_start: 0.7922 (t0) cc_final: 0.7623 (t70) REVERT: B 95 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7551 (pt0) REVERT: N 31 SER cc_start: 0.7027 (p) cc_final: 0.6767 (t) REVERT: N 32 PHE cc_start: 0.5447 (p90) cc_final: 0.5209 (p90) REVERT: N 43 PHE cc_start: 0.6331 (p90) cc_final: 0.5038 (p90) REVERT: N 111 ASP cc_start: 0.8418 (t70) cc_final: 0.7957 (p0) REVERT: N 112 SER cc_start: 0.9044 (p) cc_final: 0.8742 (t) REVERT: N 129 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7335 (mtpp) REVERT: N 132 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7947 (mt-10) REVERT: N 190 ARG cc_start: 0.6161 (mtp-110) cc_final: 0.5316 (mpt180) REVERT: N 202 LYS cc_start: 0.8609 (mttt) cc_final: 0.8377 (mttp) REVERT: N 237 ARG cc_start: 0.8124 (ptm160) cc_final: 0.7783 (ptp90) outliers start: 29 outliers final: 21 residues processed: 191 average time/residue: 0.2078 time to fit residues: 50.0366 Evaluate side-chains 189 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 173 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.0050 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN B 36 GLN N 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6114 Z= 0.208 Angle : 0.589 9.609 8293 Z= 0.306 Chirality : 0.044 0.160 892 Planarity : 0.004 0.052 1058 Dihedral : 5.724 48.651 827 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.77 % Allowed : 15.38 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.67 (0.31), residues: 719 helix: -2.57 (0.97), residues: 21 sheet: -0.25 (0.37), residues: 214 loop : -1.53 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 64 HIS 0.004 0.001 HIS L 34 PHE 0.035 0.001 PHE H 67 TYR 0.014 0.001 TYR N 170 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.8490 (m-80) cc_final: 0.8279 (m-80) REVERT: L 38 GLN cc_start: 0.8291 (tm-30) cc_final: 0.8069 (tm-30) REVERT: R 434 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7950 (pt) REVERT: R 442 ASP cc_start: 0.7803 (m-30) cc_final: 0.7601 (m-30) REVERT: R 471 GLU cc_start: 0.7411 (mp0) cc_final: 0.7194 (mp0) REVERT: B 46 MET cc_start: 0.5414 (ttp) cc_final: 0.5203 (ttp) REVERT: B 47 TYR cc_start: 0.4516 (OUTLIER) cc_final: 0.4053 (p90) REVERT: B 94 ASP cc_start: 0.7963 (t0) cc_final: 0.7674 (t70) REVERT: N 43 PHE cc_start: 0.6301 (p90) cc_final: 0.5036 (p90) REVERT: N 111 ASP cc_start: 0.8466 (t70) cc_final: 0.8107 (p0) REVERT: N 129 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7337 (mtpp) REVERT: N 132 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8088 (mt-10) REVERT: N 190 ARG cc_start: 0.6235 (mtp-110) cc_final: 0.5319 (mpt180) REVERT: N 202 LYS cc_start: 0.8666 (mttt) cc_final: 0.8418 (mttp) REVERT: N 237 ARG cc_start: 0.8198 (ptm160) cc_final: 0.7855 (ptp90) outliers start: 31 outliers final: 26 residues processed: 184 average time/residue: 0.1995 time to fit residues: 46.3129 Evaluate side-chains 190 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain R residue 361 CYS Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 28 TYR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain N residue 221 SER Chi-restraints excluded: chain N residue 239 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.0060 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN B 36 GLN N 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6114 Z= 0.304 Angle : 0.625 9.558 8293 Z= 0.325 Chirality : 0.044 0.159 892 Planarity : 0.004 0.047 1058 Dihedral : 5.441 47.846 824 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 5.69 % Allowed : 15.69 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.68 (0.31), residues: 719 helix: -2.54 (0.99), residues: 21 sheet: -0.32 (0.36), residues: 221 loop : -1.52 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 64 HIS 0.005 0.001 HIS N 49 PHE 0.021 0.002 PHE N 32 TYR 0.015 0.001 TYR L 49 ARG 0.004 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 167 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8301 (tm-30) cc_final: 0.8086 (tm-30) REVERT: R 434 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7908 (pt) REVERT: R 471 GLU cc_start: 0.7441 (mp0) cc_final: 0.7131 (mp0) REVERT: B 47 TYR cc_start: 0.4577 (OUTLIER) cc_final: 0.4073 (p90) REVERT: B 94 ASP cc_start: 0.8008 (t0) cc_final: 0.7741 (t0) REVERT: N 43 PHE cc_start: 0.6374 (p90) cc_final: 0.5068 (p90) REVERT: N 111 ASP cc_start: 0.8463 (t70) cc_final: 0.8156 (p0) REVERT: N 129 LYS cc_start: 0.7744 (mtmt) cc_final: 0.7362 (mtpp) REVERT: N 132 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8124 (mt-10) REVERT: N 202 LYS cc_start: 0.8655 (mttt) cc_final: 0.8353 (mttp) REVERT: N 237 ARG cc_start: 0.8216 (ptm160) cc_final: 0.7875 (ptp90) outliers start: 37 outliers final: 27 residues processed: 186 average time/residue: 0.2007 time to fit residues: 47.6512 Evaluate side-chains 188 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain R residue 361 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain N residue 28 TYR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 172 SER Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain N residue 221 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6114 Z= 0.267 Angle : 0.607 9.158 8293 Z= 0.319 Chirality : 0.044 0.178 892 Planarity : 0.004 0.044 1058 Dihedral : 5.441 46.290 824 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.92 % Allowed : 17.85 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.57 (0.32), residues: 719 helix: -2.55 (0.99), residues: 21 sheet: -0.33 (0.35), residues: 228 loop : -1.39 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 64 HIS 0.004 0.001 HIS L 34 PHE 0.046 0.002 PHE H 67 TYR 0.014 0.001 TYR L 49 ARG 0.003 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8300 (tm-30) cc_final: 0.8085 (tm-30) REVERT: R 434 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.7984 (pt) REVERT: R 471 GLU cc_start: 0.7436 (mp0) cc_final: 0.7112 (mp0) REVERT: B 46 MET cc_start: 0.5556 (ttp) cc_final: 0.5340 (ttp) REVERT: B 47 TYR cc_start: 0.4541 (OUTLIER) cc_final: 0.3924 (p90) REVERT: N 43 PHE cc_start: 0.6254 (p90) cc_final: 0.4915 (p90) REVERT: N 111 ASP cc_start: 0.8508 (t70) cc_final: 0.8178 (p0) REVERT: N 129 LYS cc_start: 0.7706 (mtmt) cc_final: 0.7326 (mtpp) REVERT: N 132 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8077 (mt-10) REVERT: N 202 LYS cc_start: 0.8538 (mttt) cc_final: 0.8278 (mttp) REVERT: N 237 ARG cc_start: 0.8264 (ptm160) cc_final: 0.7908 (ptp90) outliers start: 32 outliers final: 26 residues processed: 180 average time/residue: 0.2053 time to fit residues: 46.8502 Evaluate side-chains 188 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain R residue 361 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain N residue 28 TYR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 172 SER Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain N residue 221 SER Chi-restraints excluded: chain N residue 282 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 0.0000 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 70 optimal weight: 0.0270 chunk 44 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6114 Z= 0.208 Angle : 0.584 8.754 8293 Z= 0.306 Chirality : 0.044 0.185 892 Planarity : 0.004 0.043 1058 Dihedral : 5.309 45.246 824 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 5.54 % Allowed : 18.00 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.44 (0.32), residues: 719 helix: -2.57 (0.98), residues: 21 sheet: -0.21 (0.36), residues: 222 loop : -1.30 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 64 HIS 0.004 0.001 HIS L 34 PHE 0.014 0.001 PHE H 67 TYR 0.015 0.001 TYR L 49 ARG 0.003 0.000 ARG N 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8281 (tm-30) cc_final: 0.8064 (tm-30) REVERT: R 434 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7948 (pt) REVERT: R 442 ASP cc_start: 0.7836 (m-30) cc_final: 0.7603 (m-30) REVERT: R 471 GLU cc_start: 0.7436 (mp0) cc_final: 0.7123 (mp0) REVERT: B 46 MET cc_start: 0.5489 (ttp) cc_final: 0.5226 (ttp) REVERT: B 47 TYR cc_start: 0.4446 (OUTLIER) cc_final: 0.4081 (p90) REVERT: N 43 PHE cc_start: 0.6318 (p90) cc_final: 0.4961 (p90) REVERT: N 111 ASP cc_start: 0.8510 (t70) cc_final: 0.8199 (p0) REVERT: N 129 LYS cc_start: 0.7706 (mtmt) cc_final: 0.7347 (mtpp) REVERT: N 237 ARG cc_start: 0.8274 (ptm160) cc_final: 0.7926 (ptp90) outliers start: 36 outliers final: 26 residues processed: 188 average time/residue: 0.2133 time to fit residues: 50.4416 Evaluate side-chains 187 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain R residue 361 CYS Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 28 TYR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain N residue 172 SER Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain N residue 221 SER Chi-restraints excluded: chain N residue 282 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6114 Z= 0.259 Angle : 0.611 8.981 8293 Z= 0.320 Chirality : 0.044 0.195 892 Planarity : 0.004 0.041 1058 Dihedral : 5.362 44.245 824 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 5.23 % Allowed : 18.15 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.40 (0.32), residues: 719 helix: -2.52 (1.00), residues: 21 sheet: -0.24 (0.36), residues: 228 loop : -1.25 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 33 HIS 0.004 0.001 HIS L 34 PHE 0.017 0.001 PHE H 67 TYR 0.014 0.001 TYR L 49 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: H 67 PHE cc_start: 0.8781 (m-10) cc_final: 0.8544 (m-80) REVERT: L 38 GLN cc_start: 0.8292 (tm-30) cc_final: 0.8077 (tm-30) REVERT: R 434 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7895 (pt) REVERT: R 471 GLU cc_start: 0.7427 (mp0) cc_final: 0.7109 (mp0) REVERT: B 46 MET cc_start: 0.5526 (ttp) cc_final: 0.5210 (ttp) REVERT: B 47 TYR cc_start: 0.4433 (OUTLIER) cc_final: 0.4091 (p90) REVERT: N 43 PHE cc_start: 0.6346 (p90) cc_final: 0.4966 (p90) REVERT: N 111 ASP cc_start: 0.8515 (t70) cc_final: 0.8215 (p0) REVERT: N 129 LYS cc_start: 0.7704 (mtmt) cc_final: 0.7337 (mtpp) REVERT: N 132 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7669 (mt-10) REVERT: N 237 ARG cc_start: 0.8249 (ptm160) cc_final: 0.7878 (ptp90) outliers start: 34 outliers final: 28 residues processed: 183 average time/residue: 0.2235 time to fit residues: 51.9662 Evaluate side-chains 188 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain R residue 361 CYS Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 465 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 28 TYR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 172 SER Chi-restraints excluded: chain N residue 221 SER Chi-restraints excluded: chain N residue 282 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6114 Z= 0.221 Angle : 0.598 9.058 8293 Z= 0.313 Chirality : 0.044 0.200 892 Planarity : 0.004 0.041 1058 Dihedral : 5.246 43.243 824 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.62 % Allowed : 19.54 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.36 (0.32), residues: 719 helix: -2.34 (1.07), residues: 21 sheet: -0.28 (0.35), residues: 234 loop : -1.19 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 436 HIS 0.004 0.001 HIS L 34 PHE 0.013 0.001 PHE R 456 TYR 0.015 0.001 TYR H 107 ARG 0.006 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8299 (tm-30) cc_final: 0.8086 (tm-30) REVERT: R 434 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7950 (pt) REVERT: R 442 ASP cc_start: 0.7850 (m-30) cc_final: 0.7636 (m-30) REVERT: R 471 GLU cc_start: 0.7404 (mp0) cc_final: 0.7093 (mp0) REVERT: B 47 TYR cc_start: 0.4323 (OUTLIER) cc_final: 0.4075 (p90) REVERT: N 43 PHE cc_start: 0.6312 (p90) cc_final: 0.4930 (p90) REVERT: N 111 ASP cc_start: 0.8521 (t70) cc_final: 0.8215 (p0) REVERT: N 129 LYS cc_start: 0.7678 (mtmt) cc_final: 0.7331 (mtpp) REVERT: N 132 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7642 (mt-10) REVERT: N 170 TYR cc_start: 0.8208 (t80) cc_final: 0.7865 (t80) REVERT: N 237 ARG cc_start: 0.8258 (ptm160) cc_final: 0.7887 (ptp90) outliers start: 30 outliers final: 25 residues processed: 182 average time/residue: 0.1925 time to fit residues: 44.8828 Evaluate side-chains 188 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain R residue 361 CYS Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 28 TYR Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 172 SER Chi-restraints excluded: chain N residue 221 SER Chi-restraints excluded: chain N residue 282 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 0.0870 chunk 66 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6114 Z= 0.195 Angle : 0.596 10.383 8293 Z= 0.309 Chirality : 0.044 0.212 892 Planarity : 0.004 0.041 1058 Dihedral : 5.133 42.465 824 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.00 % Allowed : 19.85 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.26 (0.32), residues: 719 helix: -2.26 (1.11), residues: 21 sheet: -0.18 (0.36), residues: 236 loop : -1.15 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.005 0.001 HIS L 34 PHE 0.013 0.001 PHE R 456 TYR 0.014 0.001 TYR L 49 ARG 0.005 0.000 ARG H 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8306 (tm-30) cc_final: 0.8085 (tm-30) REVERT: L 104 LYS cc_start: 0.8745 (mtpt) cc_final: 0.8376 (mppt) REVERT: R 434 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7937 (pt) REVERT: R 442 ASP cc_start: 0.7834 (m-30) cc_final: 0.7614 (m-30) REVERT: R 471 GLU cc_start: 0.7386 (mp0) cc_final: 0.7086 (mp0) REVERT: B 46 MET cc_start: 0.5818 (ttp) cc_final: 0.5370 (ttt) REVERT: B 47 TYR cc_start: 0.4325 (OUTLIER) cc_final: 0.3925 (p90) REVERT: N 111 ASP cc_start: 0.8485 (t70) cc_final: 0.8167 (p0) REVERT: N 129 LYS cc_start: 0.7670 (mtmt) cc_final: 0.7346 (mtpp) REVERT: N 132 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7757 (mt-10) REVERT: N 237 ARG cc_start: 0.8277 (ptm160) cc_final: 0.7890 (ptp90) outliers start: 26 outliers final: 22 residues processed: 185 average time/residue: 0.2016 time to fit residues: 48.3648 Evaluate side-chains 191 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain R residue 361 CYS Chi-restraints excluded: chain R residue 379 CYS Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 391 CYS Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain N residue 28 TYR Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 172 SER Chi-restraints excluded: chain N residue 221 SER Chi-restraints excluded: chain N residue 282 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.0370 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.154413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127024 restraints weight = 9674.636| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.75 r_work: 0.3435 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6114 Z= 0.207 Angle : 0.597 9.999 8293 Z= 0.311 Chirality : 0.044 0.201 892 Planarity : 0.004 0.040 1058 Dihedral : 5.127 42.463 824 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.00 % Allowed : 20.46 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.26 (0.32), residues: 719 helix: -2.76 (0.94), residues: 27 sheet: -0.19 (0.35), residues: 238 loop : -1.09 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 64 HIS 0.005 0.001 HIS L 34 PHE 0.013 0.001 PHE R 456 TYR 0.014 0.001 TYR H 107 ARG 0.005 0.000 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2075.37 seconds wall clock time: 37 minutes 43.98 seconds (2263.98 seconds total)