Starting phenix.real_space_refine on Sat Apr 6 07:31:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhc_36262/04_2024/8jhc_36262.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhc_36262/04_2024/8jhc_36262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhc_36262/04_2024/8jhc_36262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhc_36262/04_2024/8jhc_36262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhc_36262/04_2024/8jhc_36262.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhc_36262/04_2024/8jhc_36262.pdb" } resolution = 3.3 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= 0.001 sd= 0.025 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 37 5.16 5 C 4857 2.51 5 N 1254 2.21 5 O 1415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7563 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3346 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 16, 'TRANS': 412} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 76 Chain: "H" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1678 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 915 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1624 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 4.42, per 1000 atoms: 0.58 Number of scatterers: 7563 At special positions: 0 Unit cell: (78.208, 99.84, 158.08, 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 37 16.00 O 1415 8.00 N 1254 7.00 C 4857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS R 165 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 189 " - pdb=" SG CYS R 264 " distance=2.03 Simple disulfide: pdb=" SG CYS R 286 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 458 " - pdb=" SG CYS R 465 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 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: 2.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 14 sheets defined 34.4% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'R' and resid 195 through 227 removed outlier: 3.745A pdb=" N ILE R 212 " --> pdb=" O LEU R 208 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP R 227 " --> pdb=" O THR R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 259 removed outlier: 3.791A pdb=" N PHE R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE R 256 " --> pdb=" O PHE R 252 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 314 Processing helix chain 'R' and resid 327 through 336 Processing helix chain 'R' and resid 337 through 349 Processing helix chain 'R' and resid 367 through 374 removed outlier: 3.597A pdb=" N LEU R 371 " --> pdb=" O ASP R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 399 Processing helix chain 'R' and resid 1002 through 1024 removed outlier: 3.793A pdb=" N ASN R1018 " --> pdb=" O THR R1014 " (cutoff:3.500A) Processing helix chain 'R' and resid 1029 through 1049 removed outlier: 4.290A pdb=" N LYS R1037 " --> pdb=" O ASP R1033 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA R1040 " --> pdb=" O THR R1036 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA R1048 " --> pdb=" O ASP R1044 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR R1049 " --> pdb=" O ALA R1045 " (cutoff:3.500A) Processing helix chain 'R' and resid 1064 through 1086 removed outlier: 4.944A pdb=" N PHE R1070 " --> pdb=" O PHE R1066 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU R1083 " --> pdb=" O ASP R1079 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU R1086 " --> pdb=" O LYS R1082 " (cutoff:3.500A) Processing helix chain 'R' and resid 1088 through 1097 removed outlier: 3.885A pdb=" N ALA R1092 " --> pdb=" O LYS R1088 " (cutoff:3.500A) Processing helix chain 'R' and resid 1098 through 1107 removed outlier: 3.977A pdb=" N THR R1102 " --> pdb=" O GLN R1098 " (cutoff:3.500A) Processing helix chain 'R' and resid 1109 through 1118 Processing helix chain 'R' and resid 413 through 445 removed outlier: 4.304A pdb=" N VAL R 430 " --> pdb=" O ILE R 426 " (cutoff:3.500A) Proline residue: R 431 - end of helix removed outlier: 3.547A pdb=" N TYR R 445 " --> pdb=" O TYR R 441 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 457 Processing helix chain 'R' and resid 476 through 487 removed outlier: 3.761A pdb=" N PHE R 480 " --> pdb=" O ASP R 476 " (cutoff:3.500A) Processing helix chain 'R' and resid 488 through 491 Processing helix chain 'R' and resid 492 through 499 removed outlier: 4.242A pdb=" N PHE R 496 " --> pdb=" O ILE R 492 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TRP R 497 " --> pdb=" O PRO R 493 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 4.056A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 202 through 206 removed outlier: 4.132A pdb=" N GLN H 206 " --> pdb=" O LEU H 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 98 removed outlier: 4.228A pdb=" N VAL L 98 " --> pdb=" O TYR L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 179 Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA3, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.222A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR H 53 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 137 removed outlier: 6.132A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 134 through 137 removed outlier: 6.132A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 165 through 168 removed outlier: 3.862A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.762A pdb=" N THR K 69 " --> pdb=" O GLN K 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.999A pdb=" N GLY K 10 " --> pdb=" O THR K 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.716A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE K 98 " --> pdb=" O TYR K 110 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR K 110 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.448A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.448A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 118 through 120 removed outlier: 3.731A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 146 through 151 380 hydrogen bonds defined for protein. 1056 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: 2.55 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2372 1.34 - 1.46: 1863 1.46 - 1.58: 3457 1.58 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 7744 Sorted by residual: bond pdb=" C GLU H 162 " pdb=" N PRO H 163 " ideal model delta sigma weight residual 1.333 1.360 -0.026 1.01e-02 9.80e+03 6.74e+00 bond pdb=" CG1 ILE R 338 " pdb=" CD1 ILE R 338 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.50e+00 bond pdb=" CA ILE R1107 " pdb=" CB ILE R1107 " ideal model delta sigma weight residual 1.540 1.558 -0.018 1.36e-02 5.41e+03 1.80e+00 bond pdb=" C VAL R 316 " pdb=" N PRO R 317 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.71e+00 bond pdb=" CA ILE R1107 " pdb=" C ILE R1107 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.27e-02 6.20e+03 1.67e+00 ... (remaining 7739 not shown) Histogram of bond angle deviations from ideal: 93.02 - 101.22: 15 101.22 - 109.43: 694 109.43 - 117.63: 4980 117.63 - 125.84: 4703 125.84 - 134.05: 146 Bond angle restraints: 10538 Sorted by residual: angle pdb=" CG1 ILE R1107 " pdb=" CB ILE R1107 " pdb=" CG2 ILE R1107 " ideal model delta sigma weight residual 110.70 93.02 17.68 3.00e+00 1.11e-01 3.48e+01 angle pdb=" CA ILE R 338 " pdb=" CB ILE R 338 " pdb=" CG1 ILE R 338 " ideal model delta sigma weight residual 110.40 116.37 -5.97 1.70e+00 3.46e-01 1.24e+01 angle pdb=" C GLY H 204 " pdb=" N THR H 205 " pdb=" CA THR H 205 " ideal model delta sigma weight residual 121.54 127.94 -6.40 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N LYS R1109 " pdb=" CA LYS R1109 " pdb=" C LYS R1109 " ideal model delta sigma weight residual 113.50 109.72 3.78 1.23e+00 6.61e-01 9.45e+00 angle pdb=" C PRO R 173 " pdb=" N ASP R 174 " pdb=" CA ASP R 174 " ideal model delta sigma weight residual 122.08 126.54 -4.46 1.47e+00 4.63e-01 9.20e+00 ... (remaining 10533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4108 17.94 - 35.88: 375 35.88 - 53.83: 76 53.83 - 71.77: 10 71.77 - 89.71: 4 Dihedral angle restraints: 4573 sinusoidal: 1707 harmonic: 2866 Sorted by residual: dihedral pdb=" CB CYS R 458 " pdb=" SG CYS R 458 " pdb=" SG CYS R 465 " pdb=" CB CYS R 465 " ideal model delta sinusoidal sigma weight residual -86.00 -125.99 39.99 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CA GLN R1108 " pdb=" C GLN R1108 " pdb=" N LYS R1109 " pdb=" CA LYS R1109 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CB CYS R 286 " pdb=" SG CYS R 286 " pdb=" SG CYS R 361 " pdb=" CB CYS R 361 " ideal model delta sinusoidal sigma weight residual -86.00 -120.01 34.01 1 1.00e+01 1.00e-02 1.64e+01 ... (remaining 4570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 933 0.054 - 0.108: 223 0.108 - 0.162: 38 0.162 - 0.216: 2 0.216 - 0.271: 1 Chirality restraints: 1197 Sorted by residual: chirality pdb=" CB ILE R1107 " pdb=" CA ILE R1107 " pdb=" CG1 ILE R1107 " pdb=" CG2 ILE R1107 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ILE R1107 " pdb=" N ILE R1107 " pdb=" C ILE R1107 " pdb=" CB ILE R1107 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CA TYR R 233 " pdb=" N TYR R 233 " pdb=" C TYR R 233 " pdb=" CB TYR R 233 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 1194 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR R 233 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.06e+00 pdb=" N PRO R 234 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO R 234 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 234 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R1107 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C ILE R1107 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE R1107 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN R1108 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO H 109 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " 0.025 5.00e-02 4.00e+02 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1230 2.76 - 3.30: 7178 3.30 - 3.83: 12464 3.83 - 4.37: 14426 4.37 - 4.90: 24844 Nonbonded interactions: 60142 Sorted by model distance: nonbonded pdb=" O TYR L 188 " pdb=" OH TYR L 194 " model vdw 2.227 2.440 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.260 2.440 nonbonded pdb=" O ILE R 206 " pdb=" OG SER R 210 " model vdw 2.265 2.440 nonbonded pdb=" OG SER H 200 " pdb=" N SER H 201 " model vdw 2.273 2.520 nonbonded pdb=" OH TYR R 241 " pdb=" O VAL R 490 " model vdw 2.286 2.440 ... (remaining 60137 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: 1.220 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: 5.100 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.950 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 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 : 0.004 0.062 7744 Z= 0.263 Angle : 0.702 17.685 10538 Z= 0.365 Chirality : 0.046 0.271 1197 Planarity : 0.005 0.075 1325 Dihedral : 14.173 89.710 2706 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.38 (0.27), residues: 972 helix: -0.81 (0.28), residues: 319 sheet: 0.05 (0.33), residues: 255 loop : -1.55 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 111 HIS 0.003 0.001 HIS L 191 PHE 0.013 0.002 PHE R 362 TYR 0.023 0.002 TYR R 241 ARG 0.003 0.000 ARG K 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 265 ASN cc_start: 0.8071 (m110) cc_final: 0.7477 (m110) REVERT: R 292 ILE cc_start: 0.8351 (tt) cc_final: 0.7986 (pt) REVERT: R 382 TYR cc_start: 0.7851 (m-10) cc_final: 0.7536 (m-10) REVERT: R 1002 ARG cc_start: 0.7487 (ttm170) cc_final: 0.7172 (ttm170) REVERT: R 1004 GLN cc_start: 0.7049 (pp30) cc_final: 0.6801 (pp30) REVERT: R 1019 LEU cc_start: 0.8410 (tp) cc_final: 0.8203 (tp) REVERT: R 1072 ILE cc_start: 0.8836 (tp) cc_final: 0.8613 (pt) REVERT: H 185 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7706 (mm-40) REVERT: K 104 TYR cc_start: 0.8164 (m-10) cc_final: 0.7958 (m-10) REVERT: L 5 MET cc_start: 0.8332 (mmm) cc_final: 0.7821 (mmt) REVERT: L 55 LEU cc_start: 0.8714 (mm) cc_final: 0.8513 (mp) REVERT: L 109 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8678 (tttp) REVERT: L 149 GLN cc_start: 0.8088 (mt0) cc_final: 0.7650 (mt0) REVERT: L 158 SER cc_start: 0.8714 (m) cc_final: 0.8314 (t) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2019 time to fit residues: 54.8687 Evaluate side-chains 191 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 56 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN K 77 ASN ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7744 Z= 0.346 Angle : 0.652 8.956 10538 Z= 0.336 Chirality : 0.044 0.176 1197 Planarity : 0.005 0.068 1325 Dihedral : 4.952 21.616 1065 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.34 % Allowed : 13.37 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.88 (0.27), residues: 972 helix: -0.01 (0.29), residues: 325 sheet: 0.11 (0.33), residues: 254 loop : -1.48 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 497 HIS 0.006 0.001 HIS L 191 PHE 0.018 0.002 PHE R 290 TYR 0.027 0.002 TYR R 241 ARG 0.003 0.000 ARG R1103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 195 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: R 265 ASN cc_start: 0.8006 (m110) cc_final: 0.7540 (m110) REVERT: R 1003 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.7190 (ptt90) REVERT: R 1019 LEU cc_start: 0.8369 (tp) cc_final: 0.8165 (tp) REVERT: R 1033 ASP cc_start: 0.7998 (t0) cc_final: 0.7632 (t0) REVERT: R 1072 ILE cc_start: 0.8650 (tp) cc_final: 0.8432 (pt) REVERT: R 1097 GLU cc_start: 0.7715 (pp20) cc_final: 0.7167 (pp20) REVERT: H 86 MET cc_start: 0.7420 (mtm) cc_final: 0.6636 (mtm) REVERT: H 121 THR cc_start: 0.8215 (t) cc_final: 0.7988 (m) REVERT: H 185 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7909 (mm-40) REVERT: L 5 MET cc_start: 0.8399 (mmm) cc_final: 0.7776 (mmt) REVERT: L 23 THR cc_start: 0.8760 (t) cc_final: 0.8530 (m) REVERT: L 109 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8730 (tttt) REVERT: L 147 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8168 (pttp) REVERT: L 149 GLN cc_start: 0.7921 (mt0) cc_final: 0.7595 (mt0) REVERT: L 158 SER cc_start: 0.8816 (m) cc_final: 0.8439 (t) REVERT: L 160 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7759 (p0) REVERT: L 188 TYR cc_start: 0.7535 (t80) cc_final: 0.7222 (t80) REVERT: L 211 PHE cc_start: 0.8618 (p90) cc_final: 0.8258 (p90) outliers start: 27 outliers final: 10 residues processed: 204 average time/residue: 0.1958 time to fit residues: 53.4827 Evaluate side-chains 204 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1031 VAL Chi-restraints excluded: chain R residue 477 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 59 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 0.0010 chunk 95 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 443 GLN H 85 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7744 Z= 0.188 Angle : 0.582 7.463 10538 Z= 0.297 Chirality : 0.041 0.142 1197 Planarity : 0.005 0.067 1325 Dihedral : 4.653 21.211 1065 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.35 % Allowed : 16.83 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.49 (0.28), residues: 972 helix: 0.52 (0.30), residues: 323 sheet: 0.17 (0.34), residues: 252 loop : -1.31 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 36 HIS 0.004 0.001 HIS L 191 PHE 0.019 0.001 PHE R 224 TYR 0.020 0.001 TYR R 241 ARG 0.006 0.000 ARG K 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 192 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 174 ASP cc_start: 0.7390 (t0) cc_final: 0.7151 (t0) REVERT: R 265 ASN cc_start: 0.7899 (m110) cc_final: 0.7407 (m110) REVERT: R 291 MET cc_start: 0.7890 (mmm) cc_final: 0.7484 (mmm) REVERT: R 382 TYR cc_start: 0.7516 (m-80) cc_final: 0.6580 (m-10) REVERT: R 1003 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.7164 (ptm160) REVERT: R 1019 LEU cc_start: 0.8327 (tp) cc_final: 0.8080 (tp) REVERT: R 1033 ASP cc_start: 0.7993 (t0) cc_final: 0.7632 (t0) REVERT: R 1097 GLU cc_start: 0.7709 (pp20) cc_final: 0.7158 (pp20) REVERT: H 21 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7796 (tt) REVERT: H 86 MET cc_start: 0.7394 (mtm) cc_final: 0.6712 (mtm) REVERT: H 124 THR cc_start: 0.7765 (p) cc_final: 0.7282 (t) REVERT: H 185 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7866 (mm-40) REVERT: K 104 TYR cc_start: 0.8169 (m-10) cc_final: 0.7821 (m-10) REVERT: L 5 MET cc_start: 0.8364 (mmm) cc_final: 0.7804 (mmm) REVERT: L 109 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8686 (ttmt) REVERT: L 158 SER cc_start: 0.8774 (m) cc_final: 0.8385 (t) REVERT: L 188 TYR cc_start: 0.7301 (t80) cc_final: 0.7018 (t80) REVERT: L 211 PHE cc_start: 0.8570 (p90) cc_final: 0.8209 (p90) outliers start: 19 outliers final: 12 residues processed: 199 average time/residue: 0.2023 time to fit residues: 53.7181 Evaluate side-chains 199 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1031 VAL Chi-restraints excluded: chain R residue 445 TYR Chi-restraints excluded: chain R residue 482 MET Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 443 GLN H 85 GLN K 77 ASN ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7744 Z= 0.216 Angle : 0.577 7.562 10538 Z= 0.295 Chirality : 0.041 0.145 1197 Planarity : 0.005 0.067 1325 Dihedral : 4.552 20.622 1065 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.34 % Allowed : 15.84 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.38 (0.28), residues: 972 helix: 0.69 (0.30), residues: 325 sheet: 0.22 (0.33), residues: 267 loop : -1.38 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R1012 HIS 0.005 0.001 HIS L 191 PHE 0.022 0.002 PHE R 224 TYR 0.021 0.001 TYR R 241 ARG 0.007 0.000 ARG K 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 174 ASP cc_start: 0.7336 (t0) cc_final: 0.7068 (t0) REVERT: R 265 ASN cc_start: 0.7919 (m110) cc_final: 0.7487 (m110) REVERT: R 292 ILE cc_start: 0.8290 (tt) cc_final: 0.7913 (pt) REVERT: R 1003 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7187 (ptt90) REVERT: R 1019 LEU cc_start: 0.8331 (tp) cc_final: 0.8108 (tp) REVERT: R 1033 ASP cc_start: 0.8063 (t0) cc_final: 0.7723 (t0) REVERT: R 1097 GLU cc_start: 0.7782 (pp20) cc_final: 0.7188 (pp20) REVERT: R 1112 GLU cc_start: 0.6832 (pm20) cc_final: 0.6534 (pm20) REVERT: H 21 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7726 (tt) REVERT: H 86 MET cc_start: 0.7381 (mtm) cc_final: 0.6780 (mtm) REVERT: H 124 THR cc_start: 0.7816 (p) cc_final: 0.7325 (t) REVERT: H 185 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7909 (mm-40) REVERT: K 104 TYR cc_start: 0.8146 (m-10) cc_final: 0.7922 (m-10) REVERT: L 5 MET cc_start: 0.8365 (mmm) cc_final: 0.7782 (mmt) REVERT: L 95 TYR cc_start: 0.8421 (m-10) cc_final: 0.8102 (m-10) REVERT: L 109 LYS cc_start: 0.8934 (ttmm) cc_final: 0.8692 (ttmt) REVERT: L 149 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7631 (mt0) REVERT: L 158 SER cc_start: 0.8787 (m) cc_final: 0.8397 (t) REVERT: L 188 TYR cc_start: 0.7304 (t80) cc_final: 0.6983 (t80) REVERT: L 211 PHE cc_start: 0.8559 (p90) cc_final: 0.8198 (p90) outliers start: 27 outliers final: 17 residues processed: 208 average time/residue: 0.1926 time to fit residues: 53.7821 Evaluate side-chains 211 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 192 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1031 VAL Chi-restraints excluded: chain R residue 1044 ASP Chi-restraints excluded: chain R residue 1081 LEU Chi-restraints excluded: chain R residue 445 TYR Chi-restraints excluded: chain R residue 477 LEU Chi-restraints excluded: chain R residue 482 MET Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain L residue 198 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 443 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 7744 Z= 0.420 Angle : 0.676 8.834 10538 Z= 0.348 Chirality : 0.045 0.166 1197 Planarity : 0.005 0.067 1325 Dihedral : 5.071 21.777 1065 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 5.07 % Allowed : 15.10 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.65 (0.28), residues: 972 helix: 0.52 (0.30), residues: 325 sheet: 0.02 (0.32), residues: 280 loop : -1.60 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R1012 HIS 0.008 0.001 HIS L 191 PHE 0.029 0.002 PHE R 224 TYR 0.028 0.002 TYR R 241 ARG 0.007 0.000 ARG K 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 188 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: R 174 ASP cc_start: 0.7455 (t0) cc_final: 0.7171 (t0) REVERT: R 265 ASN cc_start: 0.8046 (m110) cc_final: 0.7668 (m110) REVERT: R 291 MET cc_start: 0.7964 (mmm) cc_final: 0.7572 (mmm) REVERT: R 325 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6914 (tm-30) REVERT: R 1003 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7203 (ptt90) REVERT: R 1009 GLU cc_start: 0.7822 (tp30) cc_final: 0.7408 (tp30) REVERT: R 1019 LEU cc_start: 0.8320 (tp) cc_final: 0.8096 (tp) REVERT: R 1033 ASP cc_start: 0.8118 (t0) cc_final: 0.7779 (t0) REVERT: R 1082 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.8027 (tttp) REVERT: R 1097 GLU cc_start: 0.7926 (pp20) cc_final: 0.7386 (pp20) REVERT: H 21 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7758 (tt) REVERT: H 86 MET cc_start: 0.7422 (mtm) cc_final: 0.6821 (mtm) REVERT: H 124 THR cc_start: 0.7945 (p) cc_final: 0.7547 (t) REVERT: H 185 GLN cc_start: 0.8240 (mm-40) cc_final: 0.8018 (mm-40) REVERT: K 27 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7504 (mtt90) REVERT: K 104 TYR cc_start: 0.8150 (m-10) cc_final: 0.7880 (m-10) REVERT: L 5 MET cc_start: 0.8420 (mmm) cc_final: 0.7762 (mmt) REVERT: L 109 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8720 (tttt) REVERT: L 158 SER cc_start: 0.8846 (m) cc_final: 0.8490 (t) REVERT: L 160 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7828 (p0) REVERT: L 188 TYR cc_start: 0.7440 (t80) cc_final: 0.7099 (t80) REVERT: L 211 PHE cc_start: 0.8662 (p90) cc_final: 0.8334 (p90) outliers start: 41 outliers final: 26 residues processed: 210 average time/residue: 0.1943 time to fit residues: 54.8867 Evaluate side-chains 221 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 177 TYR Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1031 VAL Chi-restraints excluded: chain R residue 1044 ASP Chi-restraints excluded: chain R residue 1076 GLN Chi-restraints excluded: chain R residue 1081 LEU Chi-restraints excluded: chain R residue 1082 LYS Chi-restraints excluded: chain R residue 1109 LYS Chi-restraints excluded: chain R residue 477 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 179 THR Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 443 GLN K 77 ASN ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7744 Z= 0.286 Angle : 0.641 7.906 10538 Z= 0.326 Chirality : 0.043 0.158 1197 Planarity : 0.005 0.076 1325 Dihedral : 4.931 22.534 1065 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.69 % Favored : 93.21 % Rotamer: Outliers : 4.95 % Allowed : 18.44 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.61 (0.28), residues: 972 helix: 0.63 (0.30), residues: 325 sheet: -0.04 (0.32), residues: 281 loop : -1.59 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R1012 HIS 0.003 0.001 HIS L 191 PHE 0.027 0.002 PHE R 224 TYR 0.021 0.002 TYR R 241 ARG 0.005 0.000 ARG K 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 200 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: R 174 ASP cc_start: 0.7432 (t0) cc_final: 0.7087 (t0) REVERT: R 265 ASN cc_start: 0.7992 (m110) cc_final: 0.7622 (m110) REVERT: R 291 MET cc_start: 0.7915 (mmm) cc_final: 0.7528 (mmm) REVERT: R 321 SER cc_start: 0.8321 (p) cc_final: 0.7928 (p) REVERT: R 325 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6936 (tm-30) REVERT: R 1003 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.7188 (ptm160) REVERT: R 1009 GLU cc_start: 0.7776 (tp30) cc_final: 0.7370 (tp30) REVERT: R 1019 LEU cc_start: 0.8322 (tp) cc_final: 0.8081 (tp) REVERT: R 1033 ASP cc_start: 0.8107 (t0) cc_final: 0.7798 (t0) REVERT: R 1082 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8040 (tttp) REVERT: R 1097 GLU cc_start: 0.7924 (pp20) cc_final: 0.7411 (pp20) REVERT: H 21 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7765 (tt) REVERT: H 86 MET cc_start: 0.7414 (mtm) cc_final: 0.6885 (mtm) REVERT: H 124 THR cc_start: 0.7927 (p) cc_final: 0.7535 (t) REVERT: H 185 GLN cc_start: 0.8225 (mm-40) cc_final: 0.8014 (mm-40) REVERT: H 206 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.6387 (pp30) REVERT: K 27 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7481 (mtt90) REVERT: K 104 TYR cc_start: 0.8133 (m-10) cc_final: 0.7873 (m-10) REVERT: L 2 ASP cc_start: 0.8068 (t0) cc_final: 0.7832 (t0) REVERT: L 5 MET cc_start: 0.8368 (mmm) cc_final: 0.7753 (mmt) REVERT: L 94 TYR cc_start: 0.8604 (t80) cc_final: 0.8404 (t80) REVERT: L 109 LYS cc_start: 0.8928 (ttmm) cc_final: 0.8698 (tttt) REVERT: L 147 LYS cc_start: 0.8369 (pttp) cc_final: 0.8107 (pttp) REVERT: L 149 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7552 (mt0) REVERT: L 158 SER cc_start: 0.8848 (m) cc_final: 0.8466 (t) REVERT: L 160 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7787 (p0) REVERT: L 188 TYR cc_start: 0.7443 (t80) cc_final: 0.7134 (t80) REVERT: L 190 LYS cc_start: 0.8489 (pptt) cc_final: 0.8248 (pptt) REVERT: L 211 PHE cc_start: 0.8668 (p90) cc_final: 0.8364 (p90) outliers start: 40 outliers final: 28 residues processed: 223 average time/residue: 0.1924 time to fit residues: 57.8017 Evaluate side-chains 230 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 197 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1031 VAL Chi-restraints excluded: chain R residue 1044 ASP Chi-restraints excluded: chain R residue 1076 GLN Chi-restraints excluded: chain R residue 1081 LEU Chi-restraints excluded: chain R residue 1082 LYS Chi-restraints excluded: chain R residue 1109 LYS Chi-restraints excluded: chain R residue 477 LEU Chi-restraints excluded: chain R residue 482 MET Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 0.0060 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 443 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7744 Z= 0.236 Angle : 0.626 7.889 10538 Z= 0.315 Chirality : 0.042 0.151 1197 Planarity : 0.005 0.082 1325 Dihedral : 4.778 21.994 1065 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.38 % Favored : 93.52 % Rotamer: Outliers : 5.07 % Allowed : 19.06 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.44 (0.28), residues: 972 helix: 0.74 (0.30), residues: 321 sheet: 0.05 (0.32), residues: 280 loop : -1.43 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R1012 HIS 0.001 0.000 HIS H 214 PHE 0.029 0.002 PHE R 224 TYR 0.031 0.001 TYR L 50 ARG 0.005 0.000 ARG K 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 193 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: R 174 ASP cc_start: 0.7415 (t0) cc_final: 0.7052 (t0) REVERT: R 265 ASN cc_start: 0.7991 (m110) cc_final: 0.7615 (m110) REVERT: R 291 MET cc_start: 0.7836 (mmm) cc_final: 0.7395 (mmm) REVERT: R 292 ILE cc_start: 0.8336 (tt) cc_final: 0.7992 (pt) REVERT: R 321 SER cc_start: 0.8321 (p) cc_final: 0.7926 (p) REVERT: R 325 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6979 (tm-30) REVERT: R 1003 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7197 (ptt90) REVERT: R 1009 GLU cc_start: 0.7731 (tp30) cc_final: 0.7395 (tp30) REVERT: R 1019 LEU cc_start: 0.8358 (tp) cc_final: 0.8104 (tp) REVERT: R 1030 GLN cc_start: 0.7409 (pm20) cc_final: 0.7187 (pm20) REVERT: R 1033 ASP cc_start: 0.8102 (t0) cc_final: 0.7815 (t0) REVERT: R 1082 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.8029 (tttp) REVERT: R 1097 GLU cc_start: 0.7924 (pp20) cc_final: 0.7410 (pp20) REVERT: H 21 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7750 (tt) REVERT: H 86 MET cc_start: 0.7388 (mtm) cc_final: 0.6894 (mtm) REVERT: H 124 THR cc_start: 0.7903 (p) cc_final: 0.7569 (t) REVERT: H 185 GLN cc_start: 0.8203 (mm-40) cc_final: 0.8000 (mm-40) REVERT: K 27 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7452 (mtt90) REVERT: K 104 TYR cc_start: 0.8133 (m-10) cc_final: 0.7895 (m-10) REVERT: L 5 MET cc_start: 0.8341 (mmm) cc_final: 0.7735 (mmt) REVERT: L 109 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8693 (ttmt) REVERT: L 158 SER cc_start: 0.8838 (m) cc_final: 0.8450 (t) REVERT: L 160 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7789 (p0) REVERT: L 188 TYR cc_start: 0.7384 (t80) cc_final: 0.7052 (t80) REVERT: L 190 LYS cc_start: 0.8489 (pptt) cc_final: 0.8284 (pptt) REVERT: L 211 PHE cc_start: 0.8641 (p90) cc_final: 0.8336 (p90) outliers start: 41 outliers final: 31 residues processed: 217 average time/residue: 0.1949 time to fit residues: 57.1835 Evaluate side-chains 227 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 192 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 193 TYR Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1031 VAL Chi-restraints excluded: chain R residue 1044 ASP Chi-restraints excluded: chain R residue 1076 GLN Chi-restraints excluded: chain R residue 1082 LYS Chi-restraints excluded: chain R residue 1109 LYS Chi-restraints excluded: chain R residue 477 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 208 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7744 Z= 0.241 Angle : 0.632 8.440 10538 Z= 0.317 Chirality : 0.042 0.153 1197 Planarity : 0.005 0.088 1325 Dihedral : 4.699 22.029 1065 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.48 % Favored : 93.42 % Rotamer: Outliers : 5.07 % Allowed : 19.43 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.36 (0.28), residues: 972 helix: 0.81 (0.30), residues: 321 sheet: 0.05 (0.32), residues: 280 loop : -1.35 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R1012 HIS 0.001 0.000 HIS H 214 PHE 0.032 0.002 PHE R 224 TYR 0.029 0.001 TYR L 50 ARG 0.004 0.000 ARG K 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 201 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 174 ASP cc_start: 0.7416 (t0) cc_final: 0.7037 (t0) REVERT: R 265 ASN cc_start: 0.8024 (m110) cc_final: 0.7657 (m110) REVERT: R 291 MET cc_start: 0.7848 (mmm) cc_final: 0.7390 (mmm) REVERT: R 292 ILE cc_start: 0.8343 (tt) cc_final: 0.8000 (pt) REVERT: R 321 SER cc_start: 0.8342 (p) cc_final: 0.7951 (p) REVERT: R 325 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7011 (tm-30) REVERT: R 1003 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7200 (ptt90) REVERT: R 1009 GLU cc_start: 0.7730 (tp30) cc_final: 0.7377 (tp30) REVERT: R 1019 LEU cc_start: 0.8375 (tp) cc_final: 0.8108 (tp) REVERT: R 1033 ASP cc_start: 0.8132 (t0) cc_final: 0.7881 (t0) REVERT: R 1082 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8031 (tttp) REVERT: H 21 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7740 (tt) REVERT: H 86 MET cc_start: 0.7396 (mtm) cc_final: 0.6911 (mtm) REVERT: H 124 THR cc_start: 0.7831 (p) cc_final: 0.7419 (t) REVERT: K 27 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7458 (mtt90) REVERT: K 104 TYR cc_start: 0.8151 (m-10) cc_final: 0.7945 (m-10) REVERT: L 5 MET cc_start: 0.8354 (mmm) cc_final: 0.7737 (mmt) REVERT: L 109 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8706 (ttmt) REVERT: L 147 LYS cc_start: 0.8246 (pttp) cc_final: 0.7945 (ptmm) REVERT: L 158 SER cc_start: 0.8839 (m) cc_final: 0.8442 (t) REVERT: L 160 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7752 (p0) REVERT: L 211 PHE cc_start: 0.8641 (p90) cc_final: 0.8338 (p90) outliers start: 41 outliers final: 32 residues processed: 224 average time/residue: 0.1890 time to fit residues: 56.9234 Evaluate side-chains 235 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 199 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 193 TYR Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 1003 ARG Chi-restraints excluded: chain R residue 1031 VAL Chi-restraints excluded: chain R residue 1044 ASP Chi-restraints excluded: chain R residue 1076 GLN Chi-restraints excluded: chain R residue 1078 ASP Chi-restraints excluded: chain R residue 1082 LYS Chi-restraints excluded: chain R residue 1109 LYS Chi-restraints excluded: chain R residue 445 TYR Chi-restraints excluded: chain R residue 482 MET Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 98 ILE Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.8008 > 50: distance: 42 - 110: 3.372 distance: 45 - 107: 4.302 distance: 55 - 95: 4.743 distance: 58 - 92: 5.138 distance: 77 - 82: 7.259 distance: 82 - 83: 9.316 distance: 83 - 84: 10.926 distance: 84 - 85: 17.039 distance: 84 - 86: 17.167 distance: 86 - 224: 7.604 distance: 87 - 88: 10.605 distance: 87 - 90: 9.510 distance: 88 - 89: 3.236 distance: 88 - 92: 5.694 distance: 89 - 221: 4.010 distance: 90 - 91: 18.305 distance: 91 - 234: 15.433 distance: 93 - 96: 5.139 distance: 96 - 97: 6.916 distance: 97 - 98: 7.214 distance: 97 - 99: 4.503 distance: 100 - 210: 5.143 distance: 101 - 102: 5.258 distance: 102 - 103: 3.098 distance: 102 - 107: 4.843 distance: 103 - 207: 3.658 distance: 104 - 105: 3.084 distance: 104 - 106: 3.705 distance: 107 - 108: 5.438 distance: 108 - 109: 6.124 distance: 108 - 111: 4.018 distance: 109 - 110: 6.179 distance: 109 - 116: 6.729 distance: 111 - 112: 5.724 distance: 112 - 113: 5.644 distance: 113 - 114: 3.882 distance: 114 - 115: 8.730 distance: 116 - 117: 10.000 distance: 116 - 192: 9.583 distance: 117 - 120: 3.040 distance: 118 - 119: 5.727 distance: 118 - 124: 8.476 distance: 120 - 121: 7.964 distance: 121 - 122: 3.838 distance: 121 - 123: 8.596 distance: 124 - 125: 6.060 distance: 125 - 126: 6.055 distance: 126 - 127: 6.359 distance: 126 - 136: 5.378 distance: 128 - 129: 3.209 distance: 129 - 130: 10.620 distance: 129 - 131: 8.451 distance: 130 - 132: 5.301 distance: 131 - 133: 5.298 distance: 133 - 134: 6.881 distance: 134 - 135: 7.795 distance: 136 - 137: 16.474 distance: 137 - 138: 11.817 distance: 137 - 140: 17.800 distance: 138 - 139: 4.754 distance: 138 - 147: 21.280 distance: 140 - 141: 16.498 distance: 141 - 142: 7.890 distance: 141 - 143: 7.984 distance: 142 - 144: 8.133 distance: 143 - 145: 3.560 distance: 144 - 146: 11.291 distance: 145 - 146: 10.967 distance: 147 - 148: 19.571 distance: 147 - 153: 13.059 distance: 148 - 149: 6.414 distance: 148 - 151: 6.271 distance: 149 - 150: 12.519 distance: 149 - 154: 16.353 distance: 151 - 152: 10.357 distance: 152 - 153: 11.296 distance: 154 - 155: 11.136 distance: 155 - 156: 20.236 distance: 155 - 158: 12.441 distance: 156 - 157: 28.391 distance: 156 - 159: 5.000