Starting phenix.real_space_refine on Tue Feb 13 13:07:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwd_23545/02_2024/7lwd_23545_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwd_23545/02_2024/7lwd_23545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwd_23545/02_2024/7lwd_23545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwd_23545/02_2024/7lwd_23545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwd_23545/02_2024/7lwd_23545_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwd_23545/02_2024/7lwd_23545_updated.pdb" } resolution = 3.65 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= 0.002 sd= 0.041 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 129 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 34 5.16 5 C 4067 2.51 5 N 975 2.21 5 O 1087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 79": "NH1" <-> "NH2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A ASP 524": "OD1" <-> "OD2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 596": "NH1" <-> "NH2" Residue "A GLU 606": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6163 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4319 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 517} Chain: "H" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 101 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3, 68 Unusual residues: {'IXX': 1, 'NAG': 1, 'YG7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 3, 68 Unusual residues: {'IXX': 1, 'NAG': 1, 'YG7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 37 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C08AYG7 A 802 " occ=0.50 ... (64 atoms not shown) pdb=" O02BYG7 A 802 " occ=0.50 Time building chain proxies: 3.90, per 1000 atoms: 0.63 Number of scatterers: 6163 At special positions: 0 Unit cell: (84.888, 73.872, 116.64, 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 34 16.00 O 1087 8.00 N 975 7.00 C 4067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " 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: 2.36 Conformation dependent library (CDL) restraints added in 1.3 seconds 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 5 sheets defined 45.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 85 through 96 removed outlier: 3.711A pdb=" N SER A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 111 removed outlier: 5.212A pdb=" N PHE A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) Proline residue: A 106 - end of helix removed outlier: 3.737A pdb=" N GLN A 111 " --> pdb=" O TYR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.745A pdb=" N MET A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 151 through 154 No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 156 through 188 removed outlier: 4.179A pdb=" N GLY A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 173 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR A 176 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN A 177 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR A 178 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 253 through 269 removed outlier: 3.855A pdb=" N CYS A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 262 " --> pdb=" O CYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 No H-bonds generated for 'chain 'A' and resid 281 through 284' Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.762A pdb=" N VAL A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.174A pdb=" N PHE A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 320 No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 361 through 389 removed outlier: 4.303A pdb=" N SER A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 409 through 416 Processing helix chain 'A' and resid 425 through 453 removed outlier: 3.844A pdb=" N GLY A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 485 through 495 removed outlier: 4.831A pdb=" N LYS A 490 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR A 495 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 513 Processing helix chain 'A' and resid 518 through 529 removed outlier: 3.972A pdb=" N VAL A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 removed outlier: 4.483A pdb=" N VAL A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 556 removed outlier: 3.539A pdb=" N LEU A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A 556 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.810A pdb=" N ILE A 599 " --> pdb=" O TYR A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 removed outlier: 4.137A pdb=" N SER A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'H' and resid 83 through 86 No H-bonds generated for 'chain 'H' and resid 83 through 86' Processing helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing helix chain 'H' and resid 121 through 123 No H-bonds generated for 'chain 'H' and resid 121 through 123' Processing sheet with id= A, first strand: chain 'H' and resid 38 through 42 removed outlier: 3.648A pdb=" N ILE H 39 " --> pdb=" O MET H 100 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR H 88 " --> pdb=" O GLN H 101 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 56 through 58 removed outlier: 3.709A pdb=" N VAL H 112 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 24 through 27 removed outlier: 3.545A pdb=" N SER L 27 " --> pdb=" O SER L 42 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 112 through 114 removed outlier: 3.593A pdb=" N TRP L 59 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE L 72 " --> pdb=" O TRP L 59 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN L 61 " --> pdb=" O LEU L 70 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU L 70 " --> pdb=" O GLN L 61 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 89 through 91 removed outlier: 4.148A pdb=" N TYR L 94 " --> pdb=" O SER L 91 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 537 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: 1.54 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 926 1.25 - 1.39: 1706 1.39 - 1.53: 3326 1.53 - 1.67: 346 1.67 - 1.81: 49 Bond restraints: 6353 Sorted by residual: bond pdb=" C23AYG7 A 802 " pdb=" O01AYG7 A 802 " ideal model delta sigma weight residual 1.351 1.588 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C23BYG7 A 802 " pdb=" O01BYG7 A 802 " ideal model delta sigma weight residual 1.351 1.587 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C21BYG7 A 802 " pdb=" C26BYG7 A 802 " ideal model delta sigma weight residual 1.432 1.224 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C21AYG7 A 802 " pdb=" C26AYG7 A 802 " ideal model delta sigma weight residual 1.432 1.226 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C26BYG7 A 802 " pdb=" C29BYG7 A 802 " ideal model delta sigma weight residual 1.354 1.171 0.183 2.00e-02 2.50e+03 8.38e+01 ... (remaining 6348 not shown) Histogram of bond angle deviations from ideal: 88.85 - 107.07: 188 107.07 - 125.30: 8309 125.30 - 143.53: 154 143.53 - 161.75: 0 161.75 - 179.98: 2 Bond angle restraints: 8653 Sorted by residual: angle pdb=" C26BYG7 A 802 " pdb=" C29BYG7 A 802 " pdb=" O01BYG7 A 802 " ideal model delta sigma weight residual 111.69 131.58 -19.89 3.00e+00 1.11e-01 4.39e+01 angle pdb=" C26AYG7 A 802 " pdb=" C29AYG7 A 802 " pdb=" O01AYG7 A 802 " ideal model delta sigma weight residual 111.69 131.49 -19.80 3.00e+00 1.11e-01 4.36e+01 angle pdb=" C23BYG7 A 802 " pdb=" O01BYG7 A 802 " pdb=" C29BYG7 A 802 " ideal model delta sigma weight residual 106.53 88.85 17.68 3.00e+00 1.11e-01 3.47e+01 angle pdb=" C23AYG7 A 802 " pdb=" O01AYG7 A 802 " pdb=" C29AYG7 A 802 " ideal model delta sigma weight residual 106.53 88.98 17.55 3.00e+00 1.11e-01 3.42e+01 angle pdb=" C GLU L 47 " pdb=" N SER L 48 " pdb=" CA SER L 48 " ideal model delta sigma weight residual 121.70 131.48 -9.78 1.80e+00 3.09e-01 2.95e+01 ... (remaining 8648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.23: 3530 33.23 - 66.46: 74 66.46 - 99.69: 10 99.69 - 132.92: 6 132.92 - 166.15: 2 Dihedral angle restraints: 3622 sinusoidal: 1412 harmonic: 2210 Sorted by residual: dihedral pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " pdb=" SG CYS A 209 " pdb=" CB CYS A 209 " ideal model delta sinusoidal sigma weight residual 93.00 142.29 -49.29 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" C13BYG7 A 802 " pdb=" C14BYG7 A 802 " pdb=" C16BYG7 A 802 " pdb=" C17BYG7 A 802 " ideal model delta sinusoidal sigma weight residual -62.61 103.54 -166.15 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA GLU L 47 " pdb=" C GLU L 47 " pdb=" N SER L 48 " pdb=" CA SER L 48 " ideal model delta harmonic sigma weight residual 0.00 22.50 -22.50 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 3619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 546 0.031 - 0.061: 283 0.061 - 0.092: 78 0.092 - 0.122: 30 0.122 - 0.153: 1 Chirality restraints: 938 Sorted by residual: chirality pdb=" CA PHE A 380 " pdb=" N PHE A 380 " pdb=" C PHE A 380 " pdb=" CB PHE A 380 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" CA ILE L 41 " pdb=" N ILE L 41 " pdb=" C ILE L 41 " pdb=" CB ILE L 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA TRP A 103 " pdb=" N TRP A 103 " pdb=" C TRP A 103 " pdb=" CB TRP A 103 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 935 not shown) Planarity restraints: 1060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 465 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" C PHE A 465 " -0.048 2.00e-02 2.50e+03 pdb=" O PHE A 465 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 466 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 103 " 0.014 2.00e-02 2.50e+03 1.14e-02 3.25e+00 pdb=" CG TRP A 103 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 103 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 103 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 103 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 103 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 287 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 288 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " 0.020 5.00e-02 4.00e+02 ... (remaining 1057 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 52 2.60 - 3.17: 5570 3.17 - 3.75: 9646 3.75 - 4.32: 13542 4.32 - 4.90: 22119 Nonbonded interactions: 50929 Sorted by model distance: nonbonded pdb=" ND2 ASN A 208 " pdb=" C1 NAG A 803 " model vdw 2.024 3.550 nonbonded pdb=" OG SER A 199 " pdb=" OD2 ASP H 74 " model vdw 2.209 2.440 nonbonded pdb=" ND2 ASN A 208 " pdb=" C2 NAG A 803 " model vdw 2.225 3.550 nonbonded pdb=" OH TYR A 185 " pdb=" OE1 GLN A 254 " model vdw 2.319 2.440 nonbonded pdb=" NE2 GLN H 25 " pdb=" OG1 THR H 134 " model vdw 2.326 2.520 ... (remaining 50924 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 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: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 13.190 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.740 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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: 40.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 0.237 6353 Z= 0.672 Angle : 0.972 19.885 8653 Z= 0.406 Chirality : 0.039 0.153 938 Planarity : 0.004 0.036 1060 Dihedral : 16.267 166.146 2211 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.25), residues: 763 helix: -1.97 (0.23), residues: 353 sheet: -4.04 (0.39), residues: 93 loop : -3.15 (0.30), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 103 HIS 0.001 0.000 HIS A 456 PHE 0.024 0.001 PHE A 287 TYR 0.014 0.001 TYR A 186 ARG 0.002 0.000 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7891 (tpp) cc_final: 0.7537 (tpp) REVERT: A 201 LYS cc_start: 0.6290 (mmtt) cc_final: 0.5828 (tttm) REVERT: A 595 TYR cc_start: 0.7996 (t80) cc_final: 0.7562 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1827 time to fit residues: 31.4592 Evaluate side-chains 105 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 177 ASN A 208 ASN A 368 ASN A 416 ASN H 25 GLN L 62 GLN L 78 GLN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6353 Z= 0.232 Angle : 0.576 9.585 8653 Z= 0.295 Chirality : 0.041 0.158 938 Planarity : 0.005 0.047 1060 Dihedral : 11.372 174.255 894 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 1.40 % Allowed : 13.33 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.28), residues: 763 helix: -1.19 (0.26), residues: 352 sheet: -3.55 (0.44), residues: 90 loop : -2.57 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 103 HIS 0.002 0.000 HIS A 143 PHE 0.017 0.002 PHE A 586 TYR 0.018 0.001 TYR A 312 ARG 0.003 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8267 (t80) cc_final: 0.8000 (t80) REVERT: A 201 LYS cc_start: 0.6677 (mmtt) cc_final: 0.6043 (tttm) REVERT: A 386 MET cc_start: 0.7705 (mtp) cc_final: 0.7394 (mtp) REVERT: A 392 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6703 (tm-30) REVERT: A 399 LYS cc_start: 0.5831 (mmtt) cc_final: 0.4970 (mptt) REVERT: A 595 TYR cc_start: 0.8033 (t80) cc_final: 0.7680 (t80) REVERT: L 66 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7430 (mt0) outliers start: 9 outliers final: 7 residues processed: 115 average time/residue: 0.1663 time to fit residues: 25.8512 Evaluate side-chains 111 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.0570 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 55 optimal weight: 9.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6353 Z= 0.171 Angle : 0.517 9.463 8653 Z= 0.269 Chirality : 0.039 0.155 938 Planarity : 0.004 0.040 1060 Dihedral : 10.510 175.174 894 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.17 % Allowed : 16.28 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -2.70 (0.29), residues: 763 helix: -0.84 (0.27), residues: 353 sheet: -3.23 (0.46), residues: 90 loop : -2.35 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 103 HIS 0.001 0.000 HIS L 100 PHE 0.016 0.001 PHE A 380 TYR 0.018 0.001 TYR A 312 ARG 0.001 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8280 (t80) cc_final: 0.8044 (t80) REVERT: A 145 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7427 (t0) REVERT: A 201 LYS cc_start: 0.6725 (mmtt) cc_final: 0.6041 (tttm) REVERT: A 392 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6878 (tm-30) REVERT: A 399 LYS cc_start: 0.5692 (mmtt) cc_final: 0.4934 (mptt) REVERT: A 595 TYR cc_start: 0.7903 (t80) cc_final: 0.7583 (t80) outliers start: 14 outliers final: 7 residues processed: 112 average time/residue: 0.1572 time to fit residues: 24.1452 Evaluate side-chains 107 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 0.0000 chunk 73 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6353 Z= 0.199 Angle : 0.526 9.454 8653 Z= 0.273 Chirality : 0.040 0.159 938 Planarity : 0.004 0.038 1060 Dihedral : 10.418 173.720 894 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.48 % Allowed : 17.36 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -2.51 (0.29), residues: 763 helix: -0.73 (0.27), residues: 359 sheet: -3.14 (0.48), residues: 84 loop : -2.25 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 103 HIS 0.008 0.001 HIS A 456 PHE 0.018 0.001 PHE A 380 TYR 0.019 0.001 TYR H 50 ARG 0.003 0.000 ARG H 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 134 TYR cc_start: 0.8295 (t80) cc_final: 0.8057 (t80) REVERT: A 145 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7449 (t0) REVERT: A 201 LYS cc_start: 0.6827 (mmtt) cc_final: 0.6226 (mmtp) REVERT: A 399 LYS cc_start: 0.5681 (mmtt) cc_final: 0.5123 (mptt) REVERT: A 595 TYR cc_start: 0.7919 (t80) cc_final: 0.7589 (t80) REVERT: L 66 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7312 (mt0) outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 0.1685 time to fit residues: 24.4906 Evaluate side-chains 106 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 50 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 456 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6353 Z= 0.311 Angle : 0.581 10.252 8653 Z= 0.303 Chirality : 0.042 0.173 938 Planarity : 0.004 0.038 1060 Dihedral : 10.431 167.185 894 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.10 % Allowed : 18.76 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -2.57 (0.29), residues: 763 helix: -0.89 (0.26), residues: 362 sheet: -3.35 (0.49), residues: 72 loop : -2.15 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 103 HIS 0.008 0.001 HIS A 456 PHE 0.019 0.002 PHE A 380 TYR 0.020 0.002 TYR A 312 ARG 0.004 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 176 TYR cc_start: 0.8610 (t80) cc_final: 0.8347 (t80) REVERT: A 201 LYS cc_start: 0.7112 (mmtt) cc_final: 0.6536 (mmtp) REVERT: A 399 LYS cc_start: 0.5930 (mmtt) cc_final: 0.5225 (mptt) REVERT: A 595 TYR cc_start: 0.7986 (t80) cc_final: 0.7650 (t80) REVERT: A 605 LYS cc_start: 0.8454 (tppt) cc_final: 0.8193 (tppt) REVERT: L 66 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7442 (mt0) outliers start: 20 outliers final: 13 residues processed: 122 average time/residue: 0.1643 time to fit residues: 27.6066 Evaluate side-chains 120 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.2980 chunk 66 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 0.0050 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6353 Z= 0.189 Angle : 0.532 9.601 8653 Z= 0.278 Chirality : 0.040 0.163 938 Planarity : 0.004 0.039 1060 Dihedral : 10.293 169.468 894 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.48 % Allowed : 20.93 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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: -2.36 (0.30), residues: 763 helix: -0.71 (0.27), residues: 364 sheet: -2.78 (0.50), residues: 84 loop : -2.14 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 103 HIS 0.007 0.001 HIS A 456 PHE 0.019 0.001 PHE A 380 TYR 0.024 0.002 TYR H 79 ARG 0.001 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7045 (mmtt) cc_final: 0.6561 (mmtp) REVERT: A 392 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6850 (tm-30) REVERT: A 528 MET cc_start: 0.7825 (ttp) cc_final: 0.7586 (ttm) REVERT: A 595 TYR cc_start: 0.7907 (t80) cc_final: 0.7574 (t80) REVERT: H 37 VAL cc_start: 0.8976 (p) cc_final: 0.8704 (m) REVERT: L 66 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7344 (mt0) outliers start: 16 outliers final: 12 residues processed: 110 average time/residue: 0.1456 time to fit residues: 22.6571 Evaluate side-chains 112 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6353 Z= 0.226 Angle : 0.545 9.705 8653 Z= 0.285 Chirality : 0.040 0.175 938 Planarity : 0.004 0.040 1060 Dihedral : 10.285 168.206 894 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.10 % Allowed : 21.40 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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 (0.30), residues: 763 helix: -0.63 (0.28), residues: 351 sheet: -2.93 (0.53), residues: 72 loop : -1.87 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 103 HIS 0.007 0.001 HIS A 456 PHE 0.020 0.001 PHE A 380 TYR 0.018 0.002 TYR H 79 ARG 0.002 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7133 (mmtt) cc_final: 0.6527 (mmtp) REVERT: A 392 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6770 (tm-30) REVERT: A 595 TYR cc_start: 0.7895 (t80) cc_final: 0.7571 (t80) REVERT: H 37 VAL cc_start: 0.8966 (p) cc_final: 0.8692 (m) REVERT: L 66 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7388 (mt0) outliers start: 20 outliers final: 17 residues processed: 108 average time/residue: 0.1466 time to fit residues: 22.1958 Evaluate side-chains 111 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 456 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6353 Z= 0.183 Angle : 0.535 9.620 8653 Z= 0.279 Chirality : 0.040 0.183 938 Planarity : 0.004 0.039 1060 Dihedral : 10.228 169.548 894 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.95 % Allowed : 21.86 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % 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 (0.30), residues: 763 helix: -0.55 (0.28), residues: 353 sheet: -2.85 (0.53), residues: 73 loop : -1.82 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 103 HIS 0.007 0.001 HIS A 456 PHE 0.020 0.001 PHE A 380 TYR 0.017 0.001 TYR A 312 ARG 0.001 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7031 (mmtt) cc_final: 0.6522 (mmtp) REVERT: A 392 GLU cc_start: 0.6989 (tm-30) cc_final: 0.6772 (tm-30) REVERT: A 595 TYR cc_start: 0.7818 (t80) cc_final: 0.7483 (t80) REVERT: H 37 VAL cc_start: 0.8963 (p) cc_final: 0.8695 (m) REVERT: L 66 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7347 (mt0) outliers start: 19 outliers final: 18 residues processed: 105 average time/residue: 0.1446 time to fit residues: 22.0350 Evaluate side-chains 110 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 20 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN A 456 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6353 Z= 0.179 Angle : 0.529 9.638 8653 Z= 0.275 Chirality : 0.040 0.171 938 Planarity : 0.004 0.040 1060 Dihedral : 10.197 170.393 894 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.95 % Allowed : 22.02 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.30), residues: 763 helix: -0.52 (0.27), residues: 355 sheet: -2.62 (0.54), residues: 72 loop : -1.73 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 103 HIS 0.008 0.001 HIS A 456 PHE 0.018 0.001 PHE A 380 TYR 0.017 0.001 TYR A 312 ARG 0.001 0.000 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7016 (mmtt) cc_final: 0.6712 (mmtp) REVERT: A 536 PHE cc_start: 0.8366 (t80) cc_final: 0.8162 (t80) REVERT: H 37 VAL cc_start: 0.8933 (p) cc_final: 0.8679 (m) REVERT: L 66 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7332 (mt0) outliers start: 19 outliers final: 17 residues processed: 104 average time/residue: 0.1396 time to fit residues: 20.9106 Evaluate side-chains 107 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 0.2980 chunk 64 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6353 Z= 0.162 Angle : 0.539 11.660 8653 Z= 0.277 Chirality : 0.039 0.166 938 Planarity : 0.004 0.038 1060 Dihedral : 10.216 172.306 894 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.48 % Allowed : 22.33 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.30), residues: 763 helix: -0.46 (0.27), residues: 359 sheet: -2.23 (0.53), residues: 83 loop : -1.70 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 103 HIS 0.002 0.000 HIS L 100 PHE 0.018 0.001 PHE A 380 TYR 0.017 0.001 TYR A 312 ARG 0.001 0.000 ARG H 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: H 37 VAL cc_start: 0.8917 (p) cc_final: 0.8649 (m) REVERT: H 50 TYR cc_start: 0.7704 (m-80) cc_final: 0.7284 (m-80) REVERT: L 66 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7282 (mt0) outliers start: 16 outliers final: 14 residues processed: 101 average time/residue: 0.1646 time to fit residues: 23.3984 Evaluate side-chains 104 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 7 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.171029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148188 restraints weight = 8197.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.151876 restraints weight = 5298.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.154308 restraints weight = 3920.702| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6353 Z= 0.181 Angle : 0.549 10.401 8653 Z= 0.281 Chirality : 0.039 0.171 938 Planarity : 0.004 0.040 1060 Dihedral : 10.214 172.505 894 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.48 % Allowed : 22.48 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.30), residues: 763 helix: -0.48 (0.27), residues: 359 sheet: -2.32 (0.55), residues: 72 loop : -1.62 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 103 HIS 0.001 0.000 HIS L 100 PHE 0.017 0.001 PHE A 380 TYR 0.018 0.001 TYR A 312 ARG 0.001 0.000 ARG H 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1752.82 seconds wall clock time: 32 minutes 43.39 seconds (1963.39 seconds total)