Starting phenix.real_space_refine on Sat Apr 6 06:30:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mew_23805/04_2024/7mew_23805_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mew_23805/04_2024/7mew_23805.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mew_23805/04_2024/7mew_23805_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mew_23805/04_2024/7mew_23805_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mew_23805/04_2024/7mew_23805_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mew_23805/04_2024/7mew_23805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mew_23805/04_2024/7mew_23805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mew_23805/04_2024/7mew_23805_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mew_23805/04_2024/7mew_23805_updated.pdb" } resolution = 3.9 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians S 42 5.16 5 Cl 4 4.86 5 C 4632 2.51 5 N 1320 2.21 5 O 1376 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 325": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7376 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 3658 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 13, 'TRANS': 558} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1024 Unresolved non-hydrogen dihedrals: 631 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 13, 'ASP:plan': 18, 'PHE:plan': 6, 'GLU:plan': 23, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 458 Chain: "B" Number of atoms: 3658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 3658 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 13, 'TRANS': 558} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 802 Unresolved non-hydrogen angles: 1024 Unresolved non-hydrogen dihedrals: 631 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 7, 'ASN:plan1': 13, 'ASP:plan': 18, 'PHE:plan': 6, 'GLU:plan': 23, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 458 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Z5Y': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Z5Y': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.47, per 1000 atoms: 0.61 Number of scatterers: 7376 At special positions: 0 Unit cell: (102.09, 84.87, 137.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 42 16.00 F 2 9.00 O 1376 8.00 N 1320 7.00 C 4632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 4 sheets defined 64.2% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 25 through 56 removed outlier: 3.550A pdb=" N ILE A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 45 " --> pdb=" O ASP A 41 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 60 through 109 removed outlier: 3.705A pdb=" N VAL A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TRP A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Proline residue: A 68 - end of helix Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.586A pdb=" N LYS A 118 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 162 removed outlier: 4.565A pdb=" N ARG A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 188 removed outlier: 3.587A pdb=" N LEU A 174 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.628A pdb=" N THR A 204 " --> pdb=" O MET A 200 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 220 Processing helix chain 'A' and resid 224 through 271 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 281 through 323 removed outlier: 3.840A pdb=" N MET A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 4.682A pdb=" N ASN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 389 Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 497 Processing helix chain 'A' and resid 517 through 529 removed outlier: 4.047A pdb=" N ASN A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 562 through 568 Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'B' and resid 10 through 14 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 25 through 54 removed outlier: 3.617A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 60 through 109 removed outlier: 4.488A pdb=" N VAL B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 121 through 162 Processing helix chain 'B' and resid 165 through 188 Proline residue: B 176 - end of helix Processing helix chain 'B' and resid 197 through 208 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 224 through 271 removed outlier: 4.136A pdb=" N ASP B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 281 through 323 removed outlier: 4.468A pdb=" N ARG B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Proline residue: B 297 - end of helix Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 412 through 417 Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.531A pdb=" N ALA B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 497 Processing helix chain 'B' and resid 517 through 529 removed outlier: 4.036A pdb=" N ASN B 529 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 562 through 568 Processing helix chain 'B' and resid 571 through 578 Processing sheet with id= A, first strand: chain 'A' and resid 372 through 375 removed outlier: 7.438A pdb=" N GLU A 547 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N VAL A 375 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL A 549 " --> pdb=" O VAL A 375 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 419 through 422 removed outlier: 6.587A pdb=" N ILE A 501 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL A 422 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE A 503 " --> pdb=" O VAL A 422 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 372 through 375 removed outlier: 7.383A pdb=" N GLU B 547 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL B 375 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 549 " --> pdb=" O VAL B 375 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 419 through 422 removed outlier: 6.596A pdb=" N ILE B 501 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL B 422 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 503 " --> pdb=" O VAL B 422 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 505 hydrogen bonds defined for protein. 1503 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: 2.28 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2532 1.35 - 1.46: 1689 1.46 - 1.58: 3159 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 7464 Sorted by residual: bond pdb=" C11 Z5Y A 601 " pdb=" C12 Z5Y A 601 " ideal model delta sigma weight residual 1.534 1.384 0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" C11 Z5Y B 601 " pdb=" C13 Z5Y B 601 " ideal model delta sigma weight residual 1.534 1.385 0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" C11 Z5Y B 601 " pdb=" C12 Z5Y B 601 " ideal model delta sigma weight residual 1.534 1.386 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C11 Z5Y A 601 " pdb=" C13 Z5Y A 601 " ideal model delta sigma weight residual 1.534 1.386 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C12 Z5Y B 601 " pdb=" C13 Z5Y B 601 " ideal model delta sigma weight residual 1.528 1.386 0.142 2.00e-02 2.50e+03 5.07e+01 ... (remaining 7459 not shown) Histogram of bond angle deviations from ideal: 59.92 - 78.03: 6 78.03 - 96.14: 0 96.14 - 114.25: 4519 114.25 - 132.36: 5667 132.36 - 150.46: 14 Bond angle restraints: 10206 Sorted by residual: angle pdb=" C14 Z5Y B 601 " pdb=" C15 Z5Y B 601 " pdb=" C16 Z5Y B 601 " ideal model delta sigma weight residual 152.65 118.71 33.94 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C14 Z5Y A 601 " pdb=" C15 Z5Y A 601 " pdb=" C16 Z5Y A 601 " ideal model delta sigma weight residual 152.65 119.25 33.40 3.00e+00 1.11e-01 1.24e+02 angle pdb=" C14 Z5Y B 601 " pdb=" C9 Z5Y B 601 " pdb=" C8 Z5Y B 601 " ideal model delta sigma weight residual 96.93 120.88 -23.95 3.00e+00 1.11e-01 6.37e+01 angle pdb=" C14 Z5Y A 601 " pdb=" C9 Z5Y A 601 " pdb=" C8 Z5Y A 601 " ideal model delta sigma weight residual 96.93 120.62 -23.69 3.00e+00 1.11e-01 6.23e+01 angle pdb=" C10 Z5Y A 601 " pdb=" C11 Z5Y A 601 " pdb=" C13 Z5Y A 601 " ideal model delta sigma weight residual 127.45 149.75 -22.30 3.00e+00 1.11e-01 5.53e+01 ... (remaining 10201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 4056 15.07 - 30.13: 268 30.13 - 45.20: 73 45.20 - 60.27: 17 60.27 - 75.34: 4 Dihedral angle restraints: 4418 sinusoidal: 1124 harmonic: 3294 Sorted by residual: dihedral pdb=" CA LYS A 118 " pdb=" C LYS A 118 " pdb=" N GLN A 119 " pdb=" CA GLN A 119 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA LYS B 118 " pdb=" C LYS B 118 " pdb=" N GLN B 119 " pdb=" CA GLN B 119 " ideal model delta harmonic sigma weight residual 180.00 152.52 27.48 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA LEU A 48 " pdb=" C LEU A 48 " pdb=" N LYS A 49 " pdb=" CA LYS A 49 " ideal model delta harmonic sigma weight residual -180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 4415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.417: 1282 0.417 - 0.834: 0 0.834 - 1.251: 0 1.251 - 1.667: 0 1.667 - 2.084: 2 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C11 Z5Y A 601 " pdb=" C10 Z5Y A 601 " pdb=" C12 Z5Y A 601 " pdb=" C13 Z5Y A 601 " both_signs ideal model delta sigma weight residual True 2.09 -0.01 2.08 2.00e-01 2.50e+01 1.09e+02 chirality pdb=" C11 Z5Y B 601 " pdb=" C10 Z5Y B 601 " pdb=" C12 Z5Y B 601 " pdb=" C13 Z5Y B 601 " both_signs ideal model delta sigma weight residual True 2.09 -0.01 2.08 2.00e-01 2.50e+01 1.08e+02 chirality pdb=" CA LYS A 49 " pdb=" N LYS A 49 " pdb=" C LYS A 49 " pdb=" CB LYS A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 1281 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 111 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO B 112 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 296 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 297 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 297 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 297 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 43 " 0.016 2.00e-02 2.50e+03 1.48e-02 3.82e+00 pdb=" CG PHE A 43 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 43 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 43 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 43 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 43 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 43 " 0.004 2.00e-02 2.50e+03 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1298 2.76 - 3.30: 7783 3.30 - 3.83: 12364 3.83 - 4.37: 11739 4.37 - 4.90: 20960 Nonbonded interactions: 54144 Sorted by model distance: nonbonded pdb=" O VAL B 287 " pdb=" OG SER B 290 " model vdw 2.229 2.440 nonbonded pdb=" O GLY A 213 " pdb=" N VAL A 217 " model vdw 2.268 2.520 nonbonded pdb=" O ALA A 281 " pdb=" OG1 THR A 285 " model vdw 2.278 2.440 nonbonded pdb=" OG SER A 206 " pdb=" OE2 GLU A 226 " model vdw 2.292 2.440 nonbonded pdb=" NH1 ARG B 190 " pdb=" O ASN B 191 " model vdw 2.299 2.520 ... (remaining 54139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 0.040 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: 0.720 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.720 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 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 : 0.005 0.150 7464 Z= 0.348 Angle : 1.006 33.937 10206 Z= 0.434 Chirality : 0.093 2.084 1284 Planarity : 0.004 0.061 1326 Dihedral : 12.294 75.337 2278 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: 2.11 (0.26), residues: 1140 helix: 1.90 (0.19), residues: 772 sheet: 1.25 (0.70), residues: 60 loop : 0.24 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 91 HIS 0.002 0.001 HIS A 107 PHE 0.034 0.002 PHE A 43 TYR 0.017 0.001 TYR B 162 ARG 0.008 0.001 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: A 90 SER cc_start: 0.9291 (t) cc_final: 0.8858 (p) REVERT: A 109 MET cc_start: 0.8024 (mmm) cc_final: 0.7714 (tpp) REVERT: A 159 MET cc_start: 0.8192 (ttt) cc_final: 0.7901 (ttp) REVERT: A 188 ARG cc_start: 0.7499 (ttp-170) cc_final: 0.6833 (tpp-160) REVERT: B 83 TYR cc_start: 0.9199 (t80) cc_final: 0.8771 (t80) REVERT: B 119 GLN cc_start: 0.7031 (mm110) cc_final: 0.6708 (mp10) REVERT: B 183 ARG cc_start: 0.7364 (tpp-160) cc_final: 0.6186 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2285 time to fit residues: 58.2850 Evaluate side-chains 187 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 40.0000 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 40.0000 chunk 29 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 40.0000 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.1980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7464 Z= 0.256 Angle : 0.599 7.335 10206 Z= 0.311 Chirality : 0.044 0.161 1284 Planarity : 0.004 0.051 1326 Dihedral : 5.234 74.760 1200 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.72 % Allowed : 17.94 % Favored : 80.34 % 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: 2.08 (0.26), residues: 1140 helix: 1.94 (0.19), residues: 754 sheet: 1.07 (0.68), residues: 60 loop : 0.22 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 66 HIS 0.002 0.001 HIS B 107 PHE 0.016 0.002 PHE A 230 TYR 0.006 0.001 TYR B 83 ARG 0.005 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 202 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 43 PHE cc_start: 0.7450 (t80) cc_final: 0.7099 (t80) REVERT: A 78 ARG cc_start: 0.7571 (ttp80) cc_final: 0.7154 (ttt-90) REVERT: A 111 MET cc_start: 0.8277 (ppp) cc_final: 0.8038 (ppp) REVERT: A 149 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7820 (mm-30) REVERT: A 319 PHE cc_start: 0.6540 (m-10) cc_final: 0.6197 (m-80) REVERT: A 325 GLU cc_start: 0.8214 (tp30) cc_final: 0.7999 (tp30) REVERT: B 43 PHE cc_start: 0.7533 (t80) cc_final: 0.7193 (t80) REVERT: B 83 TYR cc_start: 0.9240 (t80) cc_final: 0.8799 (t80) REVERT: B 118 LYS cc_start: 0.8523 (ptmm) cc_final: 0.8215 (pptt) REVERT: B 159 MET cc_start: 0.8237 (ttt) cc_final: 0.7936 (ttp) REVERT: B 319 PHE cc_start: 0.5782 (m-80) cc_final: 0.5112 (m-80) outliers start: 9 outliers final: 8 residues processed: 206 average time/residue: 0.2256 time to fit residues: 59.2935 Evaluate side-chains 196 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 50.0000 chunk 112 optimal weight: 7.9990 chunk 92 optimal weight: 50.0000 chunk 102 optimal weight: 40.0000 chunk 35 optimal weight: 50.0000 chunk 83 optimal weight: 0.5980 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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: 0.7091 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7464 Z= 0.218 Angle : 0.555 8.051 10206 Z= 0.292 Chirality : 0.043 0.157 1284 Planarity : 0.004 0.051 1326 Dihedral : 5.377 85.509 1200 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.77 % Allowed : 19.47 % Favored : 75.76 % 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: 2.16 (0.25), residues: 1140 helix: 2.00 (0.19), residues: 752 sheet: 1.03 (0.67), residues: 60 loop : 0.27 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 66 HIS 0.002 0.001 HIS A 107 PHE 0.014 0.001 PHE A 23 TYR 0.017 0.001 TYR B 162 ARG 0.006 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7573 (ttp80) cc_final: 0.7359 (ttt-90) REVERT: A 149 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7963 (mm-30) REVERT: A 196 MET cc_start: 0.7452 (pmm) cc_final: 0.7225 (pmm) REVERT: A 319 PHE cc_start: 0.6434 (m-10) cc_final: 0.6176 (m-80) REVERT: B 174 LEU cc_start: 0.8641 (mt) cc_final: 0.8357 (mt) REVERT: B 319 PHE cc_start: 0.5813 (m-80) cc_final: 0.5082 (m-80) outliers start: 25 outliers final: 15 residues processed: 200 average time/residue: 0.2167 time to fit residues: 56.4711 Evaluate side-chains 197 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 182 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7464 Z= 0.367 Angle : 0.686 8.336 10206 Z= 0.359 Chirality : 0.047 0.205 1284 Planarity : 0.005 0.051 1326 Dihedral : 5.863 81.430 1200 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.30 % Allowed : 23.09 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.81 (0.26), residues: 1140 helix: 1.64 (0.19), residues: 752 sheet: 0.89 (0.66), residues: 60 loop : 0.40 (0.38), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 66 HIS 0.004 0.002 HIS B 107 PHE 0.023 0.002 PHE A 23 TYR 0.015 0.002 TYR A 162 ARG 0.006 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7924 (mm-30) REVERT: A 196 MET cc_start: 0.7485 (pmm) cc_final: 0.7266 (pmm) REVERT: A 319 PHE cc_start: 0.6594 (m-10) cc_final: 0.6330 (m-80) REVERT: B 41 ASP cc_start: 0.8048 (t0) cc_final: 0.7555 (t0) REVERT: B 43 PHE cc_start: 0.7775 (t80) cc_final: 0.7556 (t80) REVERT: B 83 TYR cc_start: 0.9193 (t80) cc_final: 0.8851 (t80) REVERT: B 174 LEU cc_start: 0.8867 (mt) cc_final: 0.8634 (mt) REVERT: B 236 ARG cc_start: 0.7780 (ttm-80) cc_final: 0.7454 (tpp80) REVERT: B 309 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7789 (tp40) outliers start: 33 outliers final: 20 residues processed: 200 average time/residue: 0.2388 time to fit residues: 60.2632 Evaluate side-chains 200 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 324 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 30.0000 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 98 optimal weight: 40.0000 chunk 27 optimal weight: 9.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7464 Z= 0.162 Angle : 0.532 7.015 10206 Z= 0.280 Chirality : 0.043 0.171 1284 Planarity : 0.003 0.050 1326 Dihedral : 5.377 88.403 1200 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.39 % Allowed : 25.57 % Favored : 70.04 % 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: 2.19 (0.26), residues: 1140 helix: 1.99 (0.19), residues: 764 sheet: 1.03 (0.65), residues: 60 loop : 0.31 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 66 HIS 0.002 0.001 HIS B 107 PHE 0.019 0.001 PHE B 43 TYR 0.017 0.001 TYR A 162 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7304 (tpt) cc_final: 0.5160 (tpt) REVERT: A 149 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7909 (mm-30) REVERT: A 162 TYR cc_start: 0.8435 (t80) cc_final: 0.8209 (t80) REVERT: A 319 PHE cc_start: 0.6334 (m-10) cc_final: 0.5804 (m-10) REVERT: B 78 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7323 (ttp80) outliers start: 23 outliers final: 14 residues processed: 201 average time/residue: 0.2343 time to fit residues: 60.9691 Evaluate side-chains 199 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 20.0000 chunk 99 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 91 optimal weight: 0.3980 chunk 51 optimal weight: 40.0000 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 50.0000 chunk 57 optimal weight: 20.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7464 Z= 0.282 Angle : 0.627 7.530 10206 Z= 0.324 Chirality : 0.046 0.189 1284 Planarity : 0.004 0.050 1326 Dihedral : 5.479 83.958 1200 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.77 % Allowed : 25.95 % Favored : 69.27 % 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: 2.06 (0.26), residues: 1140 helix: 1.87 (0.19), residues: 762 sheet: 0.97 (0.64), residues: 60 loop : 0.35 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 66 HIS 0.003 0.002 HIS B 107 PHE 0.018 0.002 PHE B 230 TYR 0.011 0.001 TYR A 162 ARG 0.005 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 83 TYR cc_start: 0.9260 (t80) cc_final: 0.8927 (t80) REVERT: A 89 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8063 (mm) REVERT: A 149 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7989 (mm-30) REVERT: A 319 PHE cc_start: 0.6467 (m-10) cc_final: 0.6207 (m-10) REVERT: B 118 LYS cc_start: 0.8662 (ptmm) cc_final: 0.8319 (ptpt) REVERT: B 119 GLN cc_start: 0.7279 (mm-40) cc_final: 0.6915 (mm-40) REVERT: B 309 GLN cc_start: 0.7994 (tp-100) cc_final: 0.7621 (tp40) outliers start: 25 outliers final: 15 residues processed: 195 average time/residue: 0.2240 time to fit residues: 56.1804 Evaluate side-chains 193 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 177 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 324 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 50.0000 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 50.0000 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 50.0000 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN B 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7464 Z= 0.211 Angle : 0.597 8.106 10206 Z= 0.306 Chirality : 0.045 0.161 1284 Planarity : 0.004 0.050 1326 Dihedral : 5.310 79.699 1200 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.01 % Allowed : 27.10 % Favored : 68.89 % 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: 2.12 (0.25), residues: 1140 helix: 1.92 (0.19), residues: 762 sheet: 1.05 (0.64), residues: 60 loop : 0.34 (0.38), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 66 HIS 0.002 0.001 HIS B 107 PHE 0.019 0.001 PHE B 43 TYR 0.017 0.001 TYR A 162 ARG 0.006 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 181 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7631 (ttp80) cc_final: 0.7424 (ttt-90) REVERT: A 149 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7975 (mm-30) REVERT: A 319 PHE cc_start: 0.6361 (m-10) cc_final: 0.5908 (m-10) REVERT: B 78 ARG cc_start: 0.7561 (ttp80) cc_final: 0.7205 (ttp80) REVERT: B 119 GLN cc_start: 0.7224 (mm110) cc_final: 0.6987 (mm-40) outliers start: 21 outliers final: 17 residues processed: 193 average time/residue: 0.2284 time to fit residues: 56.4282 Evaluate side-chains 199 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 324 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 50.0000 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 30.0000 chunk 105 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.7040 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7464 Z= 0.165 Angle : 0.574 10.391 10206 Z= 0.291 Chirality : 0.043 0.161 1284 Planarity : 0.004 0.052 1326 Dihedral : 5.097 78.010 1200 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.48 % Allowed : 27.29 % Favored : 70.23 % 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: 2.23 (0.25), residues: 1140 helix: 2.01 (0.19), residues: 768 sheet: 1.22 (0.64), residues: 60 loop : 0.28 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 66 HIS 0.002 0.001 HIS B 107 PHE 0.018 0.001 PHE B 43 TYR 0.017 0.001 TYR A 162 ARG 0.007 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 181 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7608 (ttp80) cc_final: 0.7406 (ttt-90) REVERT: A 149 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8041 (mm-30) REVERT: A 319 PHE cc_start: 0.6438 (m-10) cc_final: 0.6108 (m-10) REVERT: B 41 ASP cc_start: 0.7970 (t0) cc_final: 0.7719 (t0) REVERT: B 67 MET cc_start: 0.8650 (tpp) cc_final: 0.8388 (mmp) REVERT: B 83 TYR cc_start: 0.9195 (t80) cc_final: 0.8790 (t80) REVERT: B 98 MET cc_start: 0.6862 (tpt) cc_final: 0.4716 (tpt) REVERT: B 119 GLN cc_start: 0.7069 (mm110) cc_final: 0.6853 (mm-40) outliers start: 13 outliers final: 12 residues processed: 188 average time/residue: 0.2290 time to fit residues: 55.4234 Evaluate side-chains 189 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 177 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0040 chunk 102 optimal weight: 40.0000 chunk 105 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 92 optimal weight: 50.0000 chunk 67 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- 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: 0.7114 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7464 Z= 0.240 Angle : 0.626 12.033 10206 Z= 0.318 Chirality : 0.045 0.169 1284 Planarity : 0.004 0.050 1326 Dihedral : 5.204 74.952 1200 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.05 % Allowed : 26.91 % Favored : 70.04 % 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: 2.13 (0.26), residues: 1140 helix: 1.91 (0.19), residues: 768 sheet: 1.17 (0.63), residues: 60 loop : 0.35 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 66 HIS 0.002 0.001 HIS A 107 PHE 0.017 0.001 PHE B 43 TYR 0.011 0.001 TYR A 162 ARG 0.007 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8067 (mm-30) REVERT: A 319 PHE cc_start: 0.6361 (m-10) cc_final: 0.5956 (m-10) REVERT: B 41 ASP cc_start: 0.8067 (t0) cc_final: 0.7634 (t0) REVERT: B 78 ARG cc_start: 0.7543 (ttp80) cc_final: 0.7312 (ttp80) REVERT: B 83 TYR cc_start: 0.9208 (t80) cc_final: 0.8822 (t80) outliers start: 16 outliers final: 14 residues processed: 182 average time/residue: 0.2252 time to fit residues: 52.6935 Evaluate side-chains 188 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 174 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 66 TRP Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 40.0000 chunk 104 optimal weight: 0.0770 chunk 90 optimal weight: 50.0000 chunk 9 optimal weight: 0.0570 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7464 Z= 0.166 Angle : 0.588 11.750 10206 Z= 0.295 Chirality : 0.043 0.148 1284 Planarity : 0.004 0.050 1326 Dihedral : 5.082 78.618 1200 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.67 % Allowed : 27.67 % Favored : 69.66 % 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: 2.28 (0.26), residues: 1140 helix: 2.04 (0.19), residues: 768 sheet: 1.34 (0.63), residues: 60 loop : 0.31 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 66 HIS 0.001 0.001 HIS B 107 PHE 0.017 0.001 PHE B 43 TYR 0.015 0.001 TYR A 162 ARG 0.008 0.001 ARG A 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8050 (mm-30) REVERT: A 228 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8341 (mttm) REVERT: A 319 PHE cc_start: 0.6392 (m-10) cc_final: 0.5927 (m-10) REVERT: B 41 ASP cc_start: 0.8128 (t0) cc_final: 0.7738 (t0) REVERT: B 67 MET cc_start: 0.8639 (tpp) cc_final: 0.8288 (mmp) outliers start: 14 outliers final: 13 residues processed: 186 average time/residue: 0.2263 time to fit residues: 54.3243 Evaluate side-chains 192 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 179 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 66 TRP Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 196 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 50.0000 chunk 37 optimal weight: 50.0000 chunk 93 optimal weight: 0.4980 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.217449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.168256 restraints weight = 9733.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.172316 restraints weight = 5837.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.174958 restraints weight = 4124.248| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7464 Z= 0.170 Angle : 0.590 11.565 10206 Z= 0.296 Chirality : 0.043 0.161 1284 Planarity : 0.004 0.050 1326 Dihedral : 5.080 79.519 1200 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.29 % Allowed : 28.05 % Favored : 69.66 % 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: 2.34 (0.25), residues: 1140 helix: 2.08 (0.19), residues: 768 sheet: 1.45 (0.62), residues: 60 loop : 0.33 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 66 HIS 0.001 0.001 HIS B 107 PHE 0.018 0.001 PHE B 116 TYR 0.013 0.001 TYR A 162 ARG 0.008 0.001 ARG A 229 =============================================================================== Job complete usr+sys time: 1666.01 seconds wall clock time: 31 minutes 36.84 seconds (1896.84 seconds total)