Starting phenix.real_space_refine on Wed Feb 14 00:42:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2t_27149/02_2024/8d2t_27149_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2t_27149/02_2024/8d2t_27149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2t_27149/02_2024/8d2t_27149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2t_27149/02_2024/8d2t_27149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2t_27149/02_2024/8d2t_27149_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2t_27149/02_2024/8d2t_27149_updated.pdb" } resolution = 3.4 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= 0.003 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1606 atoms to isotropic. 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 33 5.16 5 C 4322 2.51 5 N 1015 2.21 5 O 1239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6609 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 460, 3380 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 134 Conformer: "B" Number of residues, atoms: 460, 3380 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 134 bond proxies already assigned to first conformer: 3432 Chain: "B" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1395 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1412 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 350 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 9, 315 Unusual residues: {'LMT': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Conformer: "B" Number of residues, atoms: 9, 315 Unusual residues: {'LMT': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} bond proxies already assigned to first conformer: 288 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AARG A 323 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 323 " occ=0.50 residue: pdb=" N APHE A 396 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 396 " occ=0.50 residue: pdb=" N APHE A 449 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 449 " occ=0.50 residue: pdb=" C1 ALMT A 603 " occ=0.50 ... (68 atoms not shown) pdb=" O6BBLMT A 603 " occ=0.50 Time building chain proxies: 5.75, per 1000 atoms: 0.87 Number of scatterers: 6609 At special positions: 0 Unit cell: (69.208, 72.584, 141.792, 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 33 16.00 O 1239 8.00 N 1015 7.00 C 4322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS A 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 186 " 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 1.9 seconds 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1570 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 11 sheets defined 40.6% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 37 through 67 removed outlier: 3.630A pdb=" N GLY A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Proline residue: A 49 - end of helix removed outlier: 5.636A pdb=" N GLN A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 removed outlier: 3.646A pdb=" N ILE A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 110 through 127 Proline residue: A 118 - end of helix removed outlier: 3.521A pdb=" N LEU A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 166 removed outlier: 3.778A pdb=" N PHE A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Proline residue: A 158 - end of helix removed outlier: 4.050A pdb=" N THR A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N MET A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 196 removed outlier: 3.520A pdb=" N THR A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.694A pdb=" N ALA A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 289 through 310 removed outlier: 4.062A pdb=" N GLY A 310 " --> pdb=" O MET A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 325 through 350 removed outlier: 3.740A pdb=" N VAL A 329 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU A 330 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE A 341 " --> pdb=" O THR A 338 " (cutoff:3.500A) Proline residue: A 342 - end of helix Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.694A pdb=" N THR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 362 " --> pdb=" O TYR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 379 through 413 removed outlier: 3.619A pdb=" N ALA A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Proline residue: A 399 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 422 through 450 Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 497 through 506 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.679A pdb=" N LYS B 100 " --> pdb=" O LYS B 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 18 through 23 Processing sheet with id= C, first strand: chain 'B' and resid 83 through 88 removed outlier: 3.502A pdb=" N THR B 47 " --> pdb=" O TRP B 34 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASN B 36 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU B 45 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 112 through 114 Processing sheet with id= E, first strand: chain 'B' and resid 140 through 144 Processing sheet with id= F, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.531A pdb=" N ALA C 18 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN C 76 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 33 through 36 removed outlier: 3.838A pdb=" N ALA C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 37 through 39 Processing sheet with id= I, first strand: chain 'C' and resid 121 through 123 removed outlier: 6.042A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 149 through 152 Processing sheet with id= K, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.878A pdb=" N LEU C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 881 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: 1.84 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1947 1.34 - 1.46: 1719 1.46 - 1.58: 3055 1.58 - 1.70: 22 1.70 - 1.81: 46 Bond restraints: 6789 Sorted by residual: bond pdb=" C1B LMT A 601 " pdb=" O5B LMT A 601 " ideal model delta sigma weight residual 1.393 1.515 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C1B LMT A 602 " pdb=" O5B LMT A 602 " ideal model delta sigma weight residual 1.393 1.514 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" C1B LMT A 609 " pdb=" O5B LMT A 609 " ideal model delta sigma weight residual 1.393 1.513 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C1BALMT A 603 " pdb=" O5BALMT A 603 " ideal model delta sigma weight residual 1.393 1.513 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C1BBLMT A 603 " pdb=" O5BBLMT A 603 " ideal model delta sigma weight residual 1.393 1.512 -0.119 2.00e-02 2.50e+03 3.55e+01 ... (remaining 6784 not shown) Histogram of bond angle deviations from ideal: 98.98 - 106.00: 185 106.00 - 113.03: 3791 113.03 - 120.05: 2242 120.05 - 127.07: 2963 127.07 - 134.10: 93 Bond angle restraints: 9274 Sorted by residual: angle pdb=" C THR A 90 " pdb=" N ASP A 91 " pdb=" CA ASP A 91 " ideal model delta sigma weight residual 121.80 112.97 8.83 2.44e+00 1.68e-01 1.31e+01 angle pdb=" N GLY B 97 " pdb=" CA GLY B 97 " pdb=" C GLY B 97 " ideal model delta sigma weight residual 113.18 121.74 -8.56 2.37e+00 1.78e-01 1.30e+01 angle pdb=" N TRP C 95 " pdb=" CA TRP C 95 " pdb=" C TRP C 95 " ideal model delta sigma weight residual 109.24 103.88 5.36 1.67e+00 3.59e-01 1.03e+01 angle pdb=" C1B LMT A 606 " pdb=" O1B LMT A 606 " pdb=" C4' LMT A 606 " ideal model delta sigma weight residual 117.87 108.34 9.53 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N ASP A 235 " pdb=" CA ASP A 235 " pdb=" C ASP A 235 " ideal model delta sigma weight residual 112.89 108.96 3.93 1.24e+00 6.50e-01 1.00e+01 ... (remaining 9269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.38: 3866 23.38 - 46.76: 229 46.76 - 70.14: 86 70.14 - 93.52: 52 93.52 - 116.90: 96 Dihedral angle restraints: 4329 sinusoidal: 1865 harmonic: 2464 Sorted by residual: dihedral pdb=" CA ARG A 455 " pdb=" C ARG A 455 " pdb=" N GLY A 456 " pdb=" CA GLY A 456 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" C1B LMT A 602 " pdb=" C2B LMT A 602 " pdb=" C3B LMT A 602 " pdb=" O3B LMT A 602 " ideal model delta sinusoidal sigma weight residual -175.52 -58.62 -116.90 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" O2B LMT A 606 " pdb=" C2B LMT A 606 " pdb=" C3B LMT A 606 " pdb=" O3B LMT A 606 " ideal model delta sinusoidal sigma weight residual 63.73 -179.47 -116.80 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 4326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 825 0.050 - 0.100: 219 0.100 - 0.150: 56 0.150 - 0.200: 10 0.200 - 0.250: 2 Chirality restraints: 1112 Sorted by residual: chirality pdb=" C1B LMT B 301 " pdb=" C2B LMT B 301 " pdb=" O1B LMT B 301 " pdb=" O5B LMT B 301 " both_signs ideal model delta sigma weight residual False -2.20 -2.45 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C4' LMT B 301 " pdb=" C3' LMT B 301 " pdb=" C5' LMT B 301 " pdb=" O1B LMT B 301 " both_signs ideal model delta sigma weight residual False -2.55 -2.35 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" C1B LMT A 608 " pdb=" C2B LMT A 608 " pdb=" O1B LMT A 608 " pdb=" O5B LMT A 608 " both_signs ideal model delta sigma weight residual False -2.20 -2.40 0.19 2.00e-01 2.50e+01 9.48e-01 ... (remaining 1109 not shown) Planarity restraints: 1119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 251 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C TYR A 251 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR A 251 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 252 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 103 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO C 104 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 46 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO C 47 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " 0.030 5.00e-02 4.00e+02 ... (remaining 1116 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1520 2.79 - 3.31: 6098 3.31 - 3.84: 11210 3.84 - 4.37: 12385 4.37 - 4.90: 22193 Nonbonded interactions: 53406 Sorted by model distance: nonbonded pdb=" O TRP A 86 " pdb=" OG1 THR A 90 " model vdw 2.257 2.440 nonbonded pdb=" O TYR A 452 " pdb=" ND2 ASN C 99 " model vdw 2.275 2.520 nonbonded pdb=" OD1 ASP A 67 " pdb=" OH TYR A 452 " model vdw 2.281 2.440 nonbonded pdb=" O GLN A 135 " pdb=" O6' LMT A 608 " model vdw 2.301 2.440 nonbonded pdb=" NZ LYS B 11 " pdb=" O ARG B 19 " model vdw 2.304 2.520 ... (remaining 53401 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 8.710 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: 12.080 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 25.080 Find NCS groups from input model: 0.190 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.011 0.122 6789 Z= 0.704 Angle : 1.101 9.528 9274 Z= 0.457 Chirality : 0.050 0.250 1112 Planarity : 0.006 0.055 1119 Dihedral : 27.925 116.897 2744 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.51 % Allowed : 8.22 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.28), residues: 865 helix: 0.61 (0.26), residues: 376 sheet: -0.59 (0.40), residues: 180 loop : -2.26 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 33 HIS 0.004 0.002 HIS A 156 PHE 0.029 0.002 PHE C 38 TYR 0.008 0.001 TYR A 251 ARG 0.002 0.000 ARG C 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7700 (m-80) cc_final: 0.7475 (m-10) REVERT: A 109 MET cc_start: 0.8205 (mmt) cc_final: 0.7884 (mmt) REVERT: A 181 MET cc_start: 0.7940 (mtt) cc_final: 0.7675 (mtp) REVERT: A 189 LEU cc_start: 0.8416 (tp) cc_final: 0.8213 (tt) REVERT: A 427 PHE cc_start: 0.8184 (t80) cc_final: 0.7954 (t80) REVERT: B 60 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.6816 (mt0) outliers start: 3 outliers final: 0 residues processed: 151 average time/residue: 0.1986 time to fit residues: 39.1603 Evaluate side-chains 123 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 50 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 195 GLN B 36 ASN B 37 GLN C 50 ASN C 57 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6789 Z= 0.263 Angle : 0.860 11.245 9274 Z= 0.370 Chirality : 0.052 0.318 1112 Planarity : 0.005 0.051 1119 Dihedral : 18.763 77.224 1587 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.91 % Allowed : 10.62 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 865 helix: 1.13 (0.27), residues: 377 sheet: -0.50 (0.40), residues: 174 loop : -2.29 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 PHE 0.023 0.002 PHE A 343 TYR 0.009 0.001 TYR A 251 ARG 0.007 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7703 (m-80) cc_final: 0.7500 (m-10) REVERT: A 109 MET cc_start: 0.8374 (mmt) cc_final: 0.8062 (mmt) REVERT: A 181 MET cc_start: 0.7912 (mtt) cc_final: 0.7551 (mtp) REVERT: A 189 LEU cc_start: 0.8399 (tp) cc_final: 0.8191 (tt) REVERT: A 206 CYS cc_start: 0.5148 (m) cc_final: 0.4473 (m) REVERT: A 291 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.5460 (t80) REVERT: B 60 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.6848 (mt0) REVERT: B 198 MET cc_start: 0.7779 (mmm) cc_final: 0.7204 (mmt) outliers start: 17 outliers final: 8 residues processed: 130 average time/residue: 0.1925 time to fit residues: 33.0184 Evaluate side-chains 121 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN C 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6789 Z= 0.245 Angle : 0.748 10.867 9274 Z= 0.337 Chirality : 0.047 0.346 1112 Planarity : 0.005 0.050 1119 Dihedral : 13.924 64.354 1587 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.23 % Allowed : 13.01 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.29), residues: 865 helix: 1.27 (0.27), residues: 376 sheet: -0.58 (0.39), residues: 181 loop : -2.26 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 103 HIS 0.002 0.001 HIS A 156 PHE 0.023 0.002 PHE C 38 TYR 0.009 0.001 TYR A 251 ARG 0.006 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 106 PHE cc_start: 0.7727 (m-80) cc_final: 0.7522 (m-10) REVERT: A 109 MET cc_start: 0.8391 (mmt) cc_final: 0.8056 (mmt) REVERT: A 181 MET cc_start: 0.7898 (mtt) cc_final: 0.7531 (mtp) REVERT: A 189 LEU cc_start: 0.8392 (tp) cc_final: 0.8188 (tt) REVERT: A 291 TYR cc_start: 0.7577 (OUTLIER) cc_final: 0.5428 (t80) REVERT: A 303 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8185 (mt) REVERT: B 60 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.6883 (mt0) outliers start: 13 outliers final: 6 residues processed: 121 average time/residue: 0.2008 time to fit residues: 31.7052 Evaluate side-chains 118 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 163 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 22 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6789 Z= 0.217 Angle : 0.704 10.221 9274 Z= 0.322 Chirality : 0.045 0.281 1112 Planarity : 0.005 0.049 1119 Dihedral : 12.366 59.720 1587 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.60 % Allowed : 13.01 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 865 helix: 1.43 (0.27), residues: 377 sheet: -0.58 (0.39), residues: 181 loop : -2.23 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 103 HIS 0.001 0.001 HIS A 156 PHE 0.022 0.002 PHE A 427 TYR 0.009 0.001 TYR A 251 ARG 0.006 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8344 (mmt) cc_final: 0.8046 (mmt) REVERT: A 181 MET cc_start: 0.7877 (mtt) cc_final: 0.7551 (mtp) REVERT: A 189 LEU cc_start: 0.8407 (tp) cc_final: 0.8194 (tt) REVERT: A 291 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.5129 (t80) REVERT: B 60 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.6863 (mt0) REVERT: B 198 MET cc_start: 0.7688 (mmm) cc_final: 0.7332 (mmt) outliers start: 21 outliers final: 14 residues processed: 122 average time/residue: 0.1979 time to fit residues: 31.6575 Evaluate side-chains 127 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 188 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 0.3980 chunk 57 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6789 Z= 0.267 Angle : 0.707 11.791 9274 Z= 0.328 Chirality : 0.044 0.243 1112 Planarity : 0.005 0.051 1119 Dihedral : 11.145 59.320 1587 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.42 % Allowed : 13.36 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.29), residues: 865 helix: 1.47 (0.27), residues: 378 sheet: -0.59 (0.40), residues: 174 loop : -2.24 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 103 HIS 0.003 0.001 HIS A 156 PHE 0.025 0.002 PHE C 38 TYR 0.009 0.001 TYR A 251 ARG 0.004 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8343 (mmt) cc_final: 0.7960 (mmt) REVERT: A 181 MET cc_start: 0.7888 (mtt) cc_final: 0.7626 (mtp) REVERT: A 189 LEU cc_start: 0.8418 (tp) cc_final: 0.8200 (tt) REVERT: A 291 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.5070 (t80) REVERT: B 60 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7114 (mt0) REVERT: B 198 MET cc_start: 0.7768 (mmm) cc_final: 0.7474 (mmt) outliers start: 20 outliers final: 13 residues processed: 126 average time/residue: 0.1963 time to fit residues: 32.3518 Evaluate side-chains 134 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 48 optimal weight: 0.0870 chunk 20 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6789 Z= 0.239 Angle : 0.676 11.432 9274 Z= 0.318 Chirality : 0.042 0.198 1112 Planarity : 0.005 0.051 1119 Dihedral : 10.479 59.416 1587 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.94 % Allowed : 13.53 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.29), residues: 865 helix: 1.54 (0.27), residues: 378 sheet: -0.56 (0.40), residues: 174 loop : -2.30 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 103 HIS 0.002 0.001 HIS A 156 PHE 0.023 0.002 PHE C 38 TYR 0.009 0.001 TYR A 251 ARG 0.006 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8273 (mmt) cc_final: 0.7855 (mmt) REVERT: A 181 MET cc_start: 0.7841 (mtt) cc_final: 0.7510 (mtp) REVERT: A 189 LEU cc_start: 0.8401 (tp) cc_final: 0.8175 (tt) REVERT: A 291 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.5090 (t80) REVERT: B 60 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7287 (mt0) REVERT: B 198 MET cc_start: 0.7715 (mmm) cc_final: 0.7473 (mmt) outliers start: 23 outliers final: 15 residues processed: 127 average time/residue: 0.1936 time to fit residues: 32.2923 Evaluate side-chains 133 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 188 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.0060 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 0.0040 chunk 51 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 234 GLN A 328 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN C 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6789 Z= 0.182 Angle : 0.646 11.436 9274 Z= 0.304 Chirality : 0.041 0.176 1112 Planarity : 0.004 0.050 1119 Dihedral : 9.850 59.698 1587 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.60 % Allowed : 15.41 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.30), residues: 865 helix: 1.64 (0.27), residues: 377 sheet: -0.53 (0.39), residues: 180 loop : -2.21 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 103 HIS 0.001 0.001 HIS A 156 PHE 0.026 0.002 PHE A 367 TYR 0.008 0.001 TYR A 251 ARG 0.007 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8283 (mmt) cc_final: 0.7918 (mmt) REVERT: A 181 MET cc_start: 0.7767 (mtt) cc_final: 0.7474 (mtp) REVERT: A 189 LEU cc_start: 0.8363 (tp) cc_final: 0.8154 (tt) REVERT: A 291 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.5101 (t80) REVERT: B 60 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7372 (mt0) REVERT: B 198 MET cc_start: 0.7654 (mmm) cc_final: 0.7442 (mmt) outliers start: 21 outliers final: 15 residues processed: 125 average time/residue: 0.1908 time to fit residues: 31.5780 Evaluate side-chains 132 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 190 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6789 Z= 0.265 Angle : 0.670 9.607 9274 Z= 0.320 Chirality : 0.042 0.181 1112 Planarity : 0.004 0.050 1119 Dihedral : 9.828 59.913 1587 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.60 % Allowed : 15.58 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 865 helix: 1.58 (0.27), residues: 378 sheet: -0.60 (0.41), residues: 162 loop : -2.31 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 344 HIS 0.003 0.001 HIS A 156 PHE 0.025 0.002 PHE C 38 TYR 0.009 0.001 TYR B 48 ARG 0.003 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8288 (mmt) cc_final: 0.7895 (mmt) REVERT: A 181 MET cc_start: 0.7850 (mtt) cc_final: 0.7537 (mtp) REVERT: A 189 LEU cc_start: 0.8400 (tp) cc_final: 0.8170 (tt) REVERT: A 291 TYR cc_start: 0.7594 (OUTLIER) cc_final: 0.5179 (t80) REVERT: A 303 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8033 (mt) REVERT: B 60 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7565 (mt0) REVERT: B 198 MET cc_start: 0.7697 (mmm) cc_final: 0.7489 (mmt) outliers start: 21 outliers final: 16 residues processed: 118 average time/residue: 0.1896 time to fit residues: 29.5066 Evaluate side-chains 129 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 188 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 chunk 23 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 81 optimal weight: 0.1980 chunk 49 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6789 Z= 0.225 Angle : 0.649 9.792 9274 Z= 0.309 Chirality : 0.042 0.181 1112 Planarity : 0.004 0.050 1119 Dihedral : 9.488 59.821 1587 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.60 % Allowed : 15.58 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.29), residues: 865 helix: 1.59 (0.27), residues: 378 sheet: -0.54 (0.39), residues: 178 loop : -2.27 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 PHE 0.023 0.002 PHE A 427 TYR 0.009 0.001 TYR A 251 ARG 0.007 0.001 ARG B 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8274 (mmt) cc_final: 0.7869 (mmt) REVERT: A 181 MET cc_start: 0.7844 (mtt) cc_final: 0.7529 (mtp) REVERT: A 189 LEU cc_start: 0.8379 (tp) cc_final: 0.8142 (tt) REVERT: A 291 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.5031 (t80) REVERT: A 303 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8068 (mt) REVERT: B 60 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7827 (mt0) outliers start: 21 outliers final: 18 residues processed: 121 average time/residue: 0.1900 time to fit residues: 30.5734 Evaluate side-chains 135 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 190 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 78 optimal weight: 0.0470 chunk 68 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6789 Z= 0.248 Angle : 0.663 9.650 9274 Z= 0.317 Chirality : 0.042 0.181 1112 Planarity : 0.004 0.050 1119 Dihedral : 9.437 59.848 1587 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.94 % Allowed : 15.41 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.29), residues: 865 helix: 1.57 (0.27), residues: 378 sheet: -0.51 (0.42), residues: 160 loop : -2.31 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 344 HIS 0.002 0.001 HIS A 156 PHE 0.024 0.002 PHE C 38 TYR 0.009 0.001 TYR A 251 ARG 0.006 0.001 ARG B 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8264 (mmt) cc_final: 0.7818 (mmt) REVERT: A 181 MET cc_start: 0.7856 (mtt) cc_final: 0.7536 (mtp) REVERT: A 189 LEU cc_start: 0.8393 (tp) cc_final: 0.8162 (tt) REVERT: A 291 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.5170 (t80) REVERT: A 303 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8047 (mt) REVERT: B 60 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7904 (mt0) outliers start: 23 outliers final: 17 residues processed: 120 average time/residue: 0.1890 time to fit residues: 30.0816 Evaluate side-chains 131 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 291 TYR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 60 GLN Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 190 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 68 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 0.0020 chunk 49 optimal weight: 0.7980 overall best weight: 0.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.168224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.143801 restraints weight = 20988.632| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.47 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6789 Z= 0.174 Angle : 0.641 13.589 9274 Z= 0.302 Chirality : 0.040 0.175 1112 Planarity : 0.004 0.051 1119 Dihedral : 9.016 59.594 1587 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.49 % Favored : 94.39 % Rotamer: Outliers : 2.40 % Allowed : 17.64 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.30), residues: 865 helix: 1.71 (0.27), residues: 378 sheet: -0.40 (0.39), residues: 180 loop : -2.24 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 344 HIS 0.001 0.000 HIS A 156 PHE 0.023 0.001 PHE A 427 TYR 0.007 0.001 TYR A 179 ARG 0.007 0.001 ARG B 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1880.33 seconds wall clock time: 35 minutes 55.56 seconds (2155.56 seconds total)