Starting phenix.real_space_refine on Wed Feb 14 01:55:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjv_22899/02_2024/7kjv_22899_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjv_22899/02_2024/7kjv_22899.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjv_22899/02_2024/7kjv_22899_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjv_22899/02_2024/7kjv_22899_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjv_22899/02_2024/7kjv_22899_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjv_22899/02_2024/7kjv_22899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjv_22899/02_2024/7kjv_22899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjv_22899/02_2024/7kjv_22899_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjv_22899/02_2024/7kjv_22899_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.086 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 P 44 5.49 5 Mg 1 5.21 5 S 12 5.16 5 C 5250 2.51 5 N 1410 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 72": "NH1" <-> "NH2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B GLU 399": "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: 8361 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4186 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 18, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3214 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 30, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 474 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 9} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 466 Classifications: {'DNA': 1, 'RNA': 21} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 13} Link IDs: {'rna3p': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {' MG': 1, 'BOG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.24, per 1000 atoms: 0.63 Number of scatterers: 8361 At special positions: 0 Unit cell: (77.08, 101.68, 117.26, 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) S 12 16.00 P 44 15.00 Mg 1 11.99 O 1644 8.00 N 1410 7.00 C 5250 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.4 seconds 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1772 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 9 sheets defined 36.0% alpha, 14.0% beta 21 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 4.24 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.786A pdb=" N LYS A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 154 through 174 removed outlier: 4.873A pdb=" N ALA A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.676A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 254 through 269 removed outlier: 4.053A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.649A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 364 through 383 Processing helix chain 'A' and resid 395 through 404 Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 516 through 527 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.941A pdb=" N GLN A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 Processing helix chain 'B' and resid 78 through 90 removed outlier: 5.107A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.568A pdb=" N PHE B 116 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 154 through 174 removed outlier: 3.869A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 195 through 211 Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 254 through 269 removed outlier: 3.967A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 395 through 404 removed outlier: 5.812A pdb=" N THR B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing sheet with id= A, first strand: chain 'A' and resid 47 through 49 Processing sheet with id= B, first strand: chain 'A' and resid 105 through 110 Processing sheet with id= C, first strand: chain 'A' and resid 227 through 229 Processing sheet with id= D, first strand: chain 'A' and resid 414 through 416 removed outlier: 6.423A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 464 through 468 removed outlier: 4.031A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS A 530 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 495 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR A 532 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR A 497 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA A 534 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 47 through 49 Processing sheet with id= G, first strand: chain 'B' and resid 60 through 64 Processing sheet with id= H, first strand: chain 'B' and resid 105 through 110 Processing sheet with id= I, first strand: chain 'B' and resid 414 through 416 removed outlier: 5.828A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2425 1.34 - 1.46: 1736 1.46 - 1.58: 4403 1.58 - 1.69: 86 1.69 - 1.81: 21 Bond restraints: 8671 Sorted by residual: bond pdb=" C4' G47 D 71 " pdb=" C3' G47 D 71 " ideal model delta sigma weight residual 1.303 1.514 -0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C4' G47 D 71 " pdb=" O4' G47 D 71 " ideal model delta sigma weight residual 1.623 1.446 0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" C2 G47 D 71 " pdb=" N3 G47 D 71 " ideal model delta sigma weight residual 1.462 1.311 0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N3 G47 D 71 " pdb=" C4 G47 D 71 " ideal model delta sigma weight residual 1.492 1.342 0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C2 G47 D 71 " pdb=" N2 G47 D 71 " ideal model delta sigma weight residual 1.454 1.334 0.120 2.00e-02 2.50e+03 3.59e+01 ... (remaining 8666 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.13: 560 107.13 - 113.87: 5016 113.87 - 120.60: 3282 120.60 - 127.34: 2953 127.34 - 134.07: 213 Bond angle restraints: 12024 Sorted by residual: angle pdb=" C1' G47 D 71 " pdb=" N9 G47 D 71 " pdb=" C8 G47 D 71 " ideal model delta sigma weight residual 104.99 129.27 -24.28 3.00e+00 1.11e-01 6.55e+01 angle pdb=" N LYS B 395 " pdb=" CA LYS B 395 " pdb=" C LYS B 395 " ideal model delta sigma weight residual 111.28 115.38 -4.10 1.09e+00 8.42e-01 1.42e+01 angle pdb=" O ILE B 393 " pdb=" C ILE B 393 " pdb=" N GLN B 394 " ideal model delta sigma weight residual 123.00 119.00 4.00 1.14e+00 7.69e-01 1.23e+01 angle pdb=" C THR B 107 " pdb=" CA THR B 107 " pdb=" CB THR B 107 " ideal model delta sigma weight residual 109.50 115.41 -5.91 1.69e+00 3.50e-01 1.22e+01 angle pdb=" O1P G47 D 71 " pdb=" P G47 D 71 " pdb=" O2P G47 D 71 " ideal model delta sigma weight residual 109.47 119.21 -9.74 3.00e+00 1.11e-01 1.05e+01 ... (remaining 12019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.85: 4728 19.85 - 39.69: 359 39.69 - 59.54: 100 59.54 - 79.38: 61 79.38 - 99.23: 4 Dihedral angle restraints: 5252 sinusoidal: 2506 harmonic: 2746 Sorted by residual: dihedral pdb=" CA VAL A 552 " pdb=" C VAL A 552 " pdb=" N SER A 553 " pdb=" CA SER A 553 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA VAL B 90 " pdb=" C VAL B 90 " pdb=" N GLN B 91 " pdb=" CA GLN B 91 " ideal model delta harmonic sigma weight residual 180.00 -162.45 -17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA LEU A 264 " pdb=" C LEU A 264 " pdb=" N ASN A 265 " pdb=" CA ASN A 265 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1057 0.038 - 0.075: 198 0.075 - 0.113: 96 0.113 - 0.150: 21 0.150 - 0.188: 3 Chirality restraints: 1375 Sorted by residual: chirality pdb=" C3' G D 69 " pdb=" C4' G D 69 " pdb=" O3' G D 69 " pdb=" C2' G D 69 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CA GLN B 394 " pdb=" N GLN B 394 " pdb=" C GLN B 394 " pdb=" CB GLN B 394 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" C2' G D 69 " pdb=" C3' G D 69 " pdb=" O2' G D 69 " pdb=" C1' G D 69 " both_signs ideal model delta sigma weight residual False -2.75 -2.60 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 1372 not shown) Planarity restraints: 1351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G47 D 71 " -0.074 2.00e-02 2.50e+03 1.40e-01 6.38e+02 pdb=" N9 G47 D 71 " -0.014 2.00e-02 2.50e+03 pdb=" C8 G47 D 71 " 0.069 2.00e-02 2.50e+03 pdb=" N7 G47 D 71 " 0.094 2.00e-02 2.50e+03 pdb=" C5 G47 D 71 " 0.027 2.00e-02 2.50e+03 pdb=" C6 G47 D 71 " 0.016 2.00e-02 2.50e+03 pdb=" O6 G47 D 71 " 0.063 2.00e-02 2.50e+03 pdb=" N1 G47 D 71 " -0.070 2.00e-02 2.50e+03 pdb=" C2 G47 D 71 " -0.131 2.00e-02 2.50e+03 pdb=" N2 G47 D 71 " -0.206 2.00e-02 2.50e+03 pdb=" N3 G47 D 71 " -0.121 2.00e-02 2.50e+03 pdb=" C4 G47 D 71 " -0.042 2.00e-02 2.50e+03 pdb=" C6A G47 D 71 " 0.388 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 393 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C ILE B 393 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE B 393 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN B 394 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 271 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO B 272 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " -0.035 5.00e-02 4.00e+02 ... (remaining 1348 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1292 2.76 - 3.30: 8118 3.30 - 3.83: 15180 3.83 - 4.37: 18090 4.37 - 4.90: 29495 Nonbonded interactions: 72175 Sorted by model distance: nonbonded pdb=" NE ARG A 557 " pdb=" OP1 U C 201 " model vdw 2.227 2.520 nonbonded pdb=" OE1 GLU A 122 " pdb=" NH1 ARG A 125 " model vdw 2.228 2.520 nonbonded pdb=" O GLY A 444 " pdb=" NE2 GLN A 478 " model vdw 2.231 2.520 nonbonded pdb=" NZ LYS B 82 " pdb=" OE2 GLU B 413 " model vdw 2.249 2.520 nonbonded pdb=" OH TYR A 354 " pdb=" OE1 GLU A 370 " model vdw 2.262 2.440 ... (remaining 72170 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 12.410 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 29.690 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 0.211 8671 Z= 0.311 Angle : 0.585 24.278 12024 Z= 0.278 Chirality : 0.040 0.188 1375 Planarity : 0.005 0.140 1351 Dihedral : 16.915 99.228 3480 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.26 % Allowed : 0.13 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.29), residues: 929 helix: 1.95 (0.30), residues: 335 sheet: -0.04 (0.43), residues: 156 loop : -0.53 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 410 HIS 0.008 0.001 HIS B 208 PHE 0.013 0.001 PHE A 346 TYR 0.016 0.001 TYR A 483 ARG 0.011 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.981 Fit side-chains REVERT: A 323 LYS cc_start: 0.7832 (mtmm) cc_final: 0.7594 (mtmm) REVERT: A 431 LYS cc_start: 0.8536 (mttp) cc_final: 0.8085 (mptt) REVERT: A 511 ASP cc_start: 0.7021 (m-30) cc_final: 0.6795 (m-30) REVERT: B 28 GLU cc_start: 0.7582 (tp30) cc_final: 0.7188 (tm-30) REVERT: B 40 GLU cc_start: 0.7361 (tp30) cc_final: 0.6732 (pt0) REVERT: B 234 LEU cc_start: 0.7995 (mt) cc_final: 0.7784 (mt) REVERT: B 294 PRO cc_start: 0.8789 (Cg_endo) cc_final: 0.8392 (Cg_exo) REVERT: B 394 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7243 (tt0) REVERT: B 395 LYS cc_start: 0.8471 (tttt) cc_final: 0.8248 (tttp) outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 1.3101 time to fit residues: 148.9501 Evaluate side-chains 67 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 242 GLN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN A 520 GLN B 175 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8671 Z= 0.304 Angle : 0.574 9.250 12024 Z= 0.286 Chirality : 0.043 0.179 1375 Planarity : 0.004 0.055 1351 Dihedral : 15.856 92.598 1719 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.97 % Allowed : 8.41 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 929 helix: 1.70 (0.29), residues: 333 sheet: -0.16 (0.43), residues: 157 loop : -0.47 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 88 HIS 0.002 0.001 HIS B 235 PHE 0.014 0.002 PHE B 416 TYR 0.014 0.002 TYR A 188 ARG 0.007 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 1.065 Fit side-chains REVERT: A 41 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.5635 (mtt) REVERT: A 323 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7667 (mtmm) REVERT: A 356 ARG cc_start: 0.8009 (ttt-90) cc_final: 0.6966 (mpt180) REVERT: A 431 LYS cc_start: 0.8630 (mttp) cc_final: 0.8082 (mptt) REVERT: A 451 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7482 (mptt) REVERT: A 511 ASP cc_start: 0.7046 (m-30) cc_final: 0.6821 (m-30) REVERT: B 28 GLU cc_start: 0.7607 (tp30) cc_final: 0.7255 (tm-30) REVERT: B 40 GLU cc_start: 0.7466 (tp30) cc_final: 0.6723 (pt0) REVERT: B 294 PRO cc_start: 0.8853 (Cg_endo) cc_final: 0.8409 (Cg_exo) REVERT: B 328 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: B 395 LYS cc_start: 0.8556 (tttt) cc_final: 0.8313 (tttt) outliers start: 15 outliers final: 6 residues processed: 81 average time/residue: 1.1506 time to fit residues: 100.6563 Evaluate side-chains 67 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 70 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN A 269 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8671 Z= 0.363 Angle : 0.578 9.554 12024 Z= 0.287 Chirality : 0.043 0.177 1375 Planarity : 0.004 0.051 1351 Dihedral : 15.899 91.120 1719 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.02 % Allowed : 10.51 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.28), residues: 929 helix: 1.48 (0.29), residues: 332 sheet: -0.37 (0.42), residues: 157 loop : -0.50 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 88 HIS 0.002 0.001 HIS A 235 PHE 0.014 0.002 PHE B 416 TYR 0.016 0.002 TYR A 183 ARG 0.006 0.001 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 1.002 Fit side-chains REVERT: A 41 MET cc_start: 0.6096 (OUTLIER) cc_final: 0.5594 (mtt) REVERT: A 264 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7413 (pp) REVERT: A 323 LYS cc_start: 0.7821 (mtmm) cc_final: 0.7526 (mtmm) REVERT: A 356 ARG cc_start: 0.7977 (ttt-90) cc_final: 0.6923 (mpp-170) REVERT: A 358 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7716 (ttm170) REVERT: A 388 LYS cc_start: 0.7565 (mttm) cc_final: 0.7144 (tptt) REVERT: A 431 LYS cc_start: 0.8667 (mttp) cc_final: 0.8190 (mptt) REVERT: A 474 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7183 (m-40) REVERT: A 511 ASP cc_start: 0.6896 (m-30) cc_final: 0.6666 (m-30) REVERT: B 28 GLU cc_start: 0.7649 (tp30) cc_final: 0.7291 (tm-30) REVERT: B 40 GLU cc_start: 0.7500 (tp30) cc_final: 0.6745 (pt0) REVERT: B 294 PRO cc_start: 0.8889 (Cg_endo) cc_final: 0.8426 (Cg_exo) REVERT: B 328 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: B 395 LYS cc_start: 0.8575 (tttt) cc_final: 0.8238 (tttt) outliers start: 23 outliers final: 7 residues processed: 81 average time/residue: 1.0797 time to fit residues: 94.5148 Evaluate side-chains 67 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8671 Z= 0.195 Angle : 0.507 8.465 12024 Z= 0.250 Chirality : 0.040 0.142 1375 Planarity : 0.004 0.046 1351 Dihedral : 15.809 91.837 1719 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.10 % Allowed : 12.61 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.28), residues: 929 helix: 1.74 (0.29), residues: 334 sheet: -0.58 (0.40), residues: 169 loop : -0.37 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 88 HIS 0.002 0.001 HIS A 361 PHE 0.020 0.001 PHE A 130 TYR 0.011 0.001 TYR A 188 ARG 0.005 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 0.775 Fit side-chains REVERT: A 41 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5592 (mtt) REVERT: A 323 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7633 (mtmm) REVERT: A 356 ARG cc_start: 0.7881 (ttt-90) cc_final: 0.6860 (mpt180) REVERT: A 358 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7687 (ttm170) REVERT: A 388 LYS cc_start: 0.7530 (mttm) cc_final: 0.7179 (tptt) REVERT: A 431 LYS cc_start: 0.8673 (mttp) cc_final: 0.8209 (mptt) REVERT: A 474 ASN cc_start: 0.7368 (OUTLIER) cc_final: 0.7048 (m-40) REVERT: A 511 ASP cc_start: 0.6804 (m-30) cc_final: 0.6561 (m-30) REVERT: B 40 GLU cc_start: 0.7511 (tp30) cc_final: 0.6827 (pt0) REVERT: B 294 PRO cc_start: 0.8890 (Cg_endo) cc_final: 0.8441 (Cg_exo) REVERT: B 328 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: B 395 LYS cc_start: 0.8562 (tttt) cc_final: 0.8261 (tttt) outliers start: 16 outliers final: 6 residues processed: 79 average time/residue: 1.1084 time to fit residues: 94.3499 Evaluate side-chains 72 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8671 Z= 0.358 Angle : 0.571 9.038 12024 Z= 0.282 Chirality : 0.042 0.174 1375 Planarity : 0.004 0.043 1351 Dihedral : 15.945 90.970 1719 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.37 % Allowed : 14.19 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.28), residues: 929 helix: 1.53 (0.29), residues: 331 sheet: -0.67 (0.40), residues: 168 loop : -0.43 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 88 HIS 0.002 0.001 HIS A 235 PHE 0.014 0.002 PHE B 416 TYR 0.017 0.002 TYR A 183 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 60 time to evaluate : 0.892 Fit side-chains REVERT: A 41 MET cc_start: 0.6039 (OUTLIER) cc_final: 0.5512 (mtt) REVERT: A 323 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7682 (mtmm) REVERT: A 356 ARG cc_start: 0.7919 (ttt-90) cc_final: 0.6947 (mpp-170) REVERT: A 358 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7707 (ttm170) REVERT: A 388 LYS cc_start: 0.7542 (mttm) cc_final: 0.7134 (tptm) REVERT: A 431 LYS cc_start: 0.8664 (mttp) cc_final: 0.8158 (mptt) REVERT: A 474 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.7119 (m-40) REVERT: A 511 ASP cc_start: 0.6908 (m-30) cc_final: 0.6674 (m-30) REVERT: B 40 GLU cc_start: 0.7519 (tp30) cc_final: 0.6843 (pt0) REVERT: B 294 PRO cc_start: 0.8915 (Cg_endo) cc_final: 0.8443 (Cg_exo) REVERT: B 328 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: B 395 LYS cc_start: 0.8548 (tttt) cc_final: 0.8244 (tttt) outliers start: 18 outliers final: 8 residues processed: 71 average time/residue: 1.1619 time to fit residues: 88.8027 Evaluate side-chains 69 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 358 ARG Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8671 Z= 0.402 Angle : 0.588 9.965 12024 Z= 0.291 Chirality : 0.043 0.191 1375 Planarity : 0.004 0.043 1351 Dihedral : 16.028 90.822 1719 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.63 % Allowed : 14.32 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.28), residues: 929 helix: 1.36 (0.28), residues: 331 sheet: -0.64 (0.41), residues: 159 loop : -0.57 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 88 HIS 0.002 0.001 HIS A 361 PHE 0.015 0.002 PHE B 416 TYR 0.017 0.002 TYR A 183 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.978 Fit side-chains REVERT: A 41 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5506 (mtt) REVERT: A 85 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7019 (pp30) REVERT: A 356 ARG cc_start: 0.7929 (ttt-90) cc_final: 0.6888 (mpp-170) REVERT: A 388 LYS cc_start: 0.7519 (mttm) cc_final: 0.7134 (tptm) REVERT: A 431 LYS cc_start: 0.8722 (mttp) cc_final: 0.8158 (mptt) REVERT: A 474 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.7192 (m-40) REVERT: A 511 ASP cc_start: 0.6933 (m-30) cc_final: 0.6703 (m-30) REVERT: B 40 GLU cc_start: 0.7536 (tp30) cc_final: 0.6767 (pt0) REVERT: B 328 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: B 395 LYS cc_start: 0.8548 (tttt) cc_final: 0.8245 (tttt) outliers start: 20 outliers final: 9 residues processed: 71 average time/residue: 1.1527 time to fit residues: 88.2979 Evaluate side-chains 69 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 378 GLU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.0980 chunk 53 optimal weight: 0.0050 chunk 68 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8671 Z= 0.151 Angle : 0.494 8.683 12024 Z= 0.244 Chirality : 0.039 0.137 1375 Planarity : 0.004 0.044 1351 Dihedral : 15.849 91.203 1719 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.84 % Allowed : 15.37 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 929 helix: 1.76 (0.29), residues: 334 sheet: -0.70 (0.40), residues: 169 loop : -0.41 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 402 HIS 0.002 0.000 HIS A 361 PHE 0.010 0.001 PHE B 416 TYR 0.010 0.001 TYR A 188 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.762 Fit side-chains REVERT: A 85 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.6956 (pp30) REVERT: A 223 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.6286 (mtmt) REVERT: A 323 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7702 (mtmm) REVERT: A 356 ARG cc_start: 0.7833 (ttt-90) cc_final: 0.6870 (mpt180) REVERT: A 388 LYS cc_start: 0.7542 (mttm) cc_final: 0.7218 (tptm) REVERT: A 431 LYS cc_start: 0.8700 (mttp) cc_final: 0.8178 (mptt) REVERT: A 474 ASN cc_start: 0.7412 (OUTLIER) cc_final: 0.7109 (m-40) REVERT: A 511 ASP cc_start: 0.6784 (m-30) cc_final: 0.6533 (m-30) REVERT: B 294 PRO cc_start: 0.8834 (Cg_endo) cc_final: 0.8376 (Cg_exo) REVERT: B 328 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: B 395 LYS cc_start: 0.8538 (tttt) cc_final: 0.8261 (tttt) outliers start: 14 outliers final: 6 residues processed: 71 average time/residue: 0.9626 time to fit residues: 74.4942 Evaluate side-chains 69 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 0.0060 chunk 81 optimal weight: 1.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8671 Z= 0.394 Angle : 0.581 9.420 12024 Z= 0.286 Chirality : 0.043 0.181 1375 Planarity : 0.004 0.046 1351 Dihedral : 15.915 90.363 1719 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.50 % Allowed : 15.24 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.28), residues: 929 helix: 1.44 (0.29), residues: 333 sheet: -0.75 (0.40), residues: 168 loop : -0.47 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 406 HIS 0.003 0.001 HIS A 361 PHE 0.014 0.002 PHE B 416 TYR 0.018 0.002 TYR A 183 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 59 time to evaluate : 0.892 Fit side-chains REVERT: A 85 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7024 (pp30) REVERT: A 223 LYS cc_start: 0.6610 (OUTLIER) cc_final: 0.6338 (mtmt) REVERT: A 356 ARG cc_start: 0.7917 (ttt-90) cc_final: 0.6925 (mpp-170) REVERT: A 388 LYS cc_start: 0.7576 (mttm) cc_final: 0.7160 (tptm) REVERT: A 431 LYS cc_start: 0.8710 (mttp) cc_final: 0.8167 (mptt) REVERT: A 474 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.7174 (m-40) REVERT: A 511 ASP cc_start: 0.6900 (m-30) cc_final: 0.6667 (m-30) REVERT: B 40 GLU cc_start: 0.7535 (tp30) cc_final: 0.6861 (pt0) REVERT: B 328 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: B 395 LYS cc_start: 0.8546 (tttt) cc_final: 0.8250 (tttt) outliers start: 19 outliers final: 8 residues processed: 71 average time/residue: 1.0485 time to fit residues: 81.0328 Evaluate side-chains 72 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 52 optimal weight: 0.1980 chunk 37 optimal weight: 0.0970 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8671 Z= 0.156 Angle : 0.490 7.926 12024 Z= 0.241 Chirality : 0.039 0.142 1375 Planarity : 0.004 0.044 1351 Dihedral : 15.783 90.690 1719 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.10 % Allowed : 15.77 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.28), residues: 929 helix: 1.83 (0.29), residues: 333 sheet: -0.67 (0.40), residues: 169 loop : -0.41 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 402 HIS 0.002 0.000 HIS A 361 PHE 0.011 0.001 PHE B 416 TYR 0.010 0.001 TYR A 188 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.874 Fit side-chains REVERT: A 223 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.6208 (mtmt) REVERT: A 323 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7707 (mtmm) REVERT: A 356 ARG cc_start: 0.7799 (ttt-90) cc_final: 0.6863 (mpt180) REVERT: A 388 LYS cc_start: 0.7519 (mttm) cc_final: 0.7211 (tptm) REVERT: A 431 LYS cc_start: 0.8668 (mttp) cc_final: 0.8170 (mptt) REVERT: A 474 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.7064 (m-40) REVERT: A 511 ASP cc_start: 0.6761 (m-30) cc_final: 0.6504 (m-30) REVERT: B 40 GLU cc_start: 0.7529 (tp30) cc_final: 0.6838 (pt0) REVERT: B 328 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: B 395 LYS cc_start: 0.8527 (tttt) cc_final: 0.8256 (tttt) outliers start: 16 outliers final: 9 residues processed: 75 average time/residue: 1.0240 time to fit residues: 83.5318 Evaluate side-chains 76 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 81 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8671 Z= 0.186 Angle : 0.497 7.855 12024 Z= 0.243 Chirality : 0.039 0.143 1375 Planarity : 0.004 0.044 1351 Dihedral : 15.750 90.060 1719 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.84 % Allowed : 15.90 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.28), residues: 929 helix: 1.82 (0.29), residues: 334 sheet: -0.64 (0.40), residues: 169 loop : -0.34 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 406 HIS 0.003 0.001 HIS A 361 PHE 0.011 0.001 PHE B 416 TYR 0.012 0.001 TYR A 483 ARG 0.004 0.000 ARG B 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.900 Fit side-chains REVERT: A 223 LYS cc_start: 0.6534 (OUTLIER) cc_final: 0.6215 (mtmt) REVERT: A 323 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7683 (mtmm) REVERT: A 356 ARG cc_start: 0.7796 (ttt-90) cc_final: 0.6897 (mpp-170) REVERT: A 388 LYS cc_start: 0.7551 (mttm) cc_final: 0.7220 (tptm) REVERT: A 431 LYS cc_start: 0.8668 (mttp) cc_final: 0.8177 (mptt) REVERT: A 474 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.7061 (m-40) REVERT: A 511 ASP cc_start: 0.6822 (m-30) cc_final: 0.6587 (m-30) REVERT: B 40 GLU cc_start: 0.7536 (tp30) cc_final: 0.6859 (pt0) REVERT: B 328 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: B 395 LYS cc_start: 0.8537 (tttt) cc_final: 0.8263 (tttt) outliers start: 14 outliers final: 10 residues processed: 73 average time/residue: 1.0013 time to fit residues: 79.4305 Evaluate side-chains 76 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 130 PHE Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 79 optimal weight: 0.0170 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.155319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.115952 restraints weight = 9395.892| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.62 r_work: 0.3244 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8671 Z= 0.166 Angle : 0.488 7.580 12024 Z= 0.238 Chirality : 0.039 0.143 1375 Planarity : 0.004 0.043 1351 Dihedral : 15.714 89.842 1719 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.58 % Allowed : 16.29 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.28), residues: 929 helix: 1.88 (0.29), residues: 334 sheet: -0.70 (0.38), residues: 179 loop : -0.27 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 402 HIS 0.002 0.000 HIS A 361 PHE 0.010 0.001 PHE B 416 TYR 0.010 0.001 TYR A 183 ARG 0.004 0.000 ARG B 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2736.53 seconds wall clock time: 49 minutes 59.02 seconds (2999.02 seconds total)