Starting phenix.real_space_refine on Sat Apr 6 23:26:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvv_12614/04_2024/7nvv_12614_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvv_12614/04_2024/7nvv_12614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvv_12614/04_2024/7nvv_12614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvv_12614/04_2024/7nvv_12614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvv_12614/04_2024/7nvv_12614_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvv_12614/04_2024/7nvv_12614_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.953 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: 8 Type Number sf(0) Gaussians P 52 5.49 5 Mg 1 5.21 5 S 42 5.16 5 Be 1 3.05 5 C 5635 2.51 5 N 1579 2.21 5 O 1758 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "7 PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9071 Number of models: 1 Model: "" Number of chains: 9 Chain: "2" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2357 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Chain: "5" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "7" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4890 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Chain: "N" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 505 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "T" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 520 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "W" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 124 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "Y" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "7" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.30, per 1000 atoms: 0.58 Number of scatterers: 9071 At special positions: 0 Unit cell: (142.8, 90.3, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 42 16.00 P 52 15.00 Mg 1 11.99 F 3 9.00 O 1758 8.00 N 1579 7.00 C 5635 6.00 Be 1 4.00 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: 4.19 Conformation dependent library (CDL) restraints added in 1.5 seconds 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 7 sheets defined 44.8% alpha, 10.7% beta 25 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain '2' and resid 146 through 163 removed outlier: 3.756A pdb=" N LYS 2 150 " --> pdb=" O PRO 2 146 " (cutoff:3.500A) Processing helix chain '2' and resid 173 through 182 Processing helix chain '2' and resid 198 through 205 removed outlier: 3.705A pdb=" N GLN 2 202 " --> pdb=" O SER 2 198 " (cutoff:3.500A) Processing helix chain '2' and resid 208 through 226 removed outlier: 3.801A pdb=" N GLN 2 224 " --> pdb=" O LEU 2 220 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER 2 225 " --> pdb=" O GLN 2 221 " (cutoff:3.500A) Processing helix chain '2' and resid 230 through 241 Processing helix chain '2' and resid 256 through 267 Processing helix chain '2' and resid 285 through 288 No H-bonds generated for 'chain '2' and resid 285 through 288' Processing helix chain '2' and resid 322 through 330 Processing helix chain '2' and resid 348 through 357 Processing helix chain '2' and resid 361 through 370 Processing helix chain '2' and resid 374 through 378 removed outlier: 4.021A pdb=" N LYS 2 378 " --> pdb=" O PRO 2 374 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 374 through 378' Processing helix chain '2' and resid 385 through 398 removed outlier: 3.694A pdb=" N ARG 2 398 " --> pdb=" O TRP 2 394 " (cutoff:3.500A) Processing helix chain '2' and resid 415 through 428 removed outlier: 3.705A pdb=" N GLU 2 419 " --> pdb=" O GLN 2 415 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU 2 420 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing helix chain '2' and resid 445 through 457 removed outlier: 4.228A pdb=" N SER 2 449 " --> pdb=" O PRO 2 445 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASP 2 450 " --> pdb=" O ALA 2 446 " (cutoff:3.500A) Processing helix chain '5' and resid 14 through 26 Processing helix chain '5' and resid 47 through 63 removed outlier: 5.047A pdb=" N ASN 5 51 " --> pdb=" O GLU 5 48 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL 5 52 " --> pdb=" O LEU 5 49 " (cutoff:3.500A) Processing helix chain '7' and resid 93 through 103 removed outlier: 3.512A pdb=" N ALA 7 102 " --> pdb=" O ASP 7 98 " (cutoff:3.500A) Processing helix chain '7' and resid 120 through 129 Processing helix chain '7' and resid 133 through 143 Processing helix chain '7' and resid 150 through 158 Processing helix chain '7' and resid 182 through 190 Processing helix chain '7' and resid 192 through 196 Processing helix chain '7' and resid 274 through 286 removed outlier: 4.941A pdb=" N GLU 7 278 " --> pdb=" O GLU 7 275 " (cutoff:3.500A) Processing helix chain '7' and resid 297 through 299 No H-bonds generated for 'chain '7' and resid 297 through 299' Processing helix chain '7' and resid 318 through 327 Processing helix chain '7' and resid 346 through 357 Processing helix chain '7' and resid 368 through 381 Processing helix chain '7' and resid 410 through 414 Processing helix chain '7' and resid 421 through 431 removed outlier: 3.653A pdb=" N VAL 7 426 " --> pdb=" O GLU 7 422 " (cutoff:3.500A) Processing helix chain '7' and resid 443 through 445 No H-bonds generated for 'chain '7' and resid 443 through 445' Processing helix chain '7' and resid 452 through 457 Processing helix chain '7' and resid 477 through 483 Processing helix chain '7' and resid 493 through 499 Processing helix chain '7' and resid 516 through 524 removed outlier: 3.542A pdb=" N GLU 7 521 " --> pdb=" O GLU 7 517 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA 7 524 " --> pdb=" O ARG 7 520 " (cutoff:3.500A) Processing helix chain '7' and resid 530 through 535 Processing helix chain '7' and resid 538 through 554 removed outlier: 3.529A pdb=" N ARG 7 554 " --> pdb=" O PHE 7 550 " (cutoff:3.500A) Processing helix chain '7' and resid 565 through 575 Processing helix chain '7' and resid 586 through 598 Processing helix chain '7' and resid 609 through 611 No H-bonds generated for 'chain '7' and resid 609 through 611' Processing helix chain '7' and resid 633 through 643 removed outlier: 3.870A pdb=" N ARG 7 642 " --> pdb=" O GLN 7 638 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL 7 643 " --> pdb=" O ARG 7 639 " (cutoff:3.500A) Processing helix chain '7' and resid 668 through 676 Processing helix chain '7' and resid 678 through 683 Processing helix chain '7' and resid 706 through 719 Processing helix chain 'W' and resid 279 through 282 No H-bonds generated for 'chain 'W' and resid 279 through 282' Processing sheet with id= A, first strand: chain '2' and resid 307 through 309 removed outlier: 6.559A pdb=" N GLN 2 345 " --> pdb=" O MET 2 334 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N MET 2 334 " --> pdb=" O GLN 2 345 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 407 through 409 removed outlier: 3.686A pdb=" N MET 2 441 " --> pdb=" O TYR 2 409 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE 2 433 " --> pdb=" O VAL 2 442 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '5' and resid 8 through 11 removed outlier: 3.563A pdb=" N PHE 5 44 " --> pdb=" O GLN 5 36 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN 5 36 " --> pdb=" O PHE 5 44 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '7' and resid 76 through 78 removed outlier: 5.786A pdb=" N LYS 7 117 " --> pdb=" O PRO 7 106 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '7' and resid 167 through 171 removed outlier: 4.167A pdb=" N TYR 7 175 " --> pdb=" O VAL 7 272 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '7' and resid 389 through 392 removed outlier: 6.422A pdb=" N VAL 7 405 " --> pdb=" O CYS 7 390 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N PHE 7 392 " --> pdb=" O VAL 7 405 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE 7 407 " --> pdb=" O PHE 7 392 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS 7 361 " --> pdb=" O ALA 7 406 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N SER 7 408 " --> pdb=" O CYS 7 361 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL 7 363 " --> pdb=" O SER 7 408 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU 7 437 " --> pdb=" O LEU 7 362 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU 7 364 " --> pdb=" O LEU 7 437 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE 7 439 " --> pdb=" O LEU 7 364 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY 7 336 " --> pdb=" O GLY 7 465 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N THR 7 467 " --> pdb=" O GLY 7 336 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE 7 338 " --> pdb=" O THR 7 467 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL 7 339 " --> pdb=" O LEU 7 488 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU 7 490 " --> pdb=" O VAL 7 339 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '7' and resid 688 through 690 removed outlier: 7.665A pdb=" N ALA 7 657 " --> pdb=" O GLN 7 506 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA 7 508 " --> pdb=" O ALA 7 657 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE 7 659 " --> pdb=" O ALA 7 508 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL 7 510 " --> pdb=" O PHE 7 659 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N SER 7 661 " --> pdb=" O VAL 7 510 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 4.33 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: 2696 1.34 - 1.45: 1554 1.45 - 1.57: 4939 1.57 - 1.69: 101 1.69 - 1.81: 68 Bond restraints: 9358 Sorted by residual: bond pdb=" C4 ADP 7 901 " pdb=" C5 ADP 7 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" BE BEF 7 903 " pdb=" F2 BEF 7 903 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C5 ADP 7 901 " pdb=" C6 ADP 7 901 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" BE BEF 7 903 " pdb=" F3 BEF 7 903 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" BE BEF 7 903 " pdb=" F1 BEF 7 903 " ideal model delta sigma weight residual 1.476 1.532 -0.056 2.00e-02 2.50e+03 7.97e+00 ... (remaining 9353 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.96: 549 106.96 - 113.70: 5145 113.70 - 120.45: 3630 120.45 - 127.19: 3373 127.19 - 133.94: 175 Bond angle restraints: 12872 Sorted by residual: angle pdb=" PA ADP 7 901 " pdb=" O3A ADP 7 901 " pdb=" PB ADP 7 901 " ideal model delta sigma weight residual 120.50 131.47 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C2' ADP 7 901 " pdb=" C3' ADP 7 901 " pdb=" C4' ADP 7 901 " ideal model delta sigma weight residual 111.00 100.21 10.79 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C1' ADP 7 901 " pdb=" C2' ADP 7 901 " pdb=" C3' ADP 7 901 " ideal model delta sigma weight residual 111.00 100.53 10.47 3.00e+00 1.11e-01 1.22e+01 angle pdb=" F2 BEF 7 903 " pdb=" BE BEF 7 903 " pdb=" F3 BEF 7 903 " ideal model delta sigma weight residual 119.96 109.73 10.23 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N1 ADP 7 901 " pdb=" C2 ADP 7 901 " pdb=" N3 ADP 7 901 " ideal model delta sigma weight residual 120.00 129.29 -9.29 3.00e+00 1.11e-01 9.59e+00 ... (remaining 12867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.52: 4965 23.52 - 47.03: 433 47.03 - 70.55: 97 70.55 - 94.06: 9 94.06 - 117.58: 1 Dihedral angle restraints: 5505 sinusoidal: 2566 harmonic: 2939 Sorted by residual: dihedral pdb=" C5' ADP 7 901 " pdb=" O5' ADP 7 901 " pdb=" PA ADP 7 901 " pdb=" O2A ADP 7 901 " ideal model delta sinusoidal sigma weight residual -60.00 -177.57 117.58 1 2.00e+01 2.50e-03 3.51e+01 dihedral pdb=" O1B ADP 7 901 " pdb=" O3A ADP 7 901 " pdb=" PB ADP 7 901 " pdb=" PA ADP 7 901 " ideal model delta sinusoidal sigma weight residual -60.00 -128.87 68.87 1 2.00e+01 2.50e-03 1.53e+01 dihedral pdb=" CA ASP 7 563 " pdb=" CB ASP 7 563 " pdb=" CG ASP 7 563 " pdb=" OD1 ASP 7 563 " ideal model delta sinusoidal sigma weight residual -30.00 -87.40 57.40 1 2.00e+01 2.50e-03 1.11e+01 ... (remaining 5502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1047 0.033 - 0.066: 246 0.066 - 0.099: 101 0.099 - 0.132: 52 0.132 - 0.165: 2 Chirality restraints: 1448 Sorted by residual: chirality pdb=" C3' ADP 7 901 " pdb=" C2' ADP 7 901 " pdb=" C4' ADP 7 901 " pdb=" O3' ADP 7 901 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA ILE 7 580 " pdb=" N ILE 7 580 " pdb=" C ILE 7 580 " pdb=" CB ILE 7 580 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE 7 559 " pdb=" N ILE 7 559 " pdb=" C ILE 7 559 " pdb=" CB ILE 7 559 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 1445 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 7 62 " 0.172 9.50e-02 1.11e+02 7.70e-02 3.83e+00 pdb=" NE ARG 7 62 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG 7 62 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG 7 62 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG 7 62 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE 2 338 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO 2 339 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO 2 339 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO 2 339 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR 7 581 " 0.009 2.00e-02 2.50e+03 9.58e-03 1.84e+00 pdb=" CG TYR 7 581 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR 7 581 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR 7 581 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR 7 581 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR 7 581 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR 7 581 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR 7 581 " 0.000 2.00e-02 2.50e+03 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 70 2.57 - 3.15: 7431 3.15 - 3.73: 15164 3.73 - 4.32: 21166 4.32 - 4.90: 33987 Nonbonded interactions: 77818 Sorted by model distance: nonbonded pdb=" O LYS 7 165 " pdb=" OG SER 7 179 " model vdw 1.984 2.440 nonbonded pdb=" OG SER 2 172 " pdb=" OD1 ASP 2 174 " model vdw 2.000 2.440 nonbonded pdb="MG MG 7 902 " pdb=" F1 BEF 7 903 " model vdw 2.009 2.120 nonbonded pdb=" OH TYR 7 319 " pdb=" O ALA 7 344 " model vdw 2.014 2.440 nonbonded pdb=" O PHE 7 378 " pdb=" OG SER 7 382 " model vdw 2.018 2.440 ... (remaining 77813 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: 6.000 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: 18.530 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.480 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.003 0.109 9358 Z= 0.178 Angle : 0.519 10.969 12872 Z= 0.261 Chirality : 0.038 0.165 1448 Planarity : 0.003 0.077 1459 Dihedral : 17.438 117.575 3593 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.28), residues: 961 helix: 1.96 (0.25), residues: 468 sheet: -0.30 (0.45), residues: 144 loop : -0.04 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 280 HIS 0.002 0.000 HIS 7 114 PHE 0.009 0.001 PHE 7 482 TYR 0.023 0.001 TYR 7 581 ARG 0.008 0.000 ARG 7 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7789 (t-100) cc_final: 0.7486 (t-100) REVERT: 2 336 TYR cc_start: 0.8502 (m-80) cc_final: 0.8175 (m-80) REVERT: 7 495 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7080 (mm-30) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 1.3979 time to fit residues: 283.2492 Evaluate side-chains 117 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.0570 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.4700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 173 GLN 2 224 GLN ** 2 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 190 GLN 7 366 ASN 7 388 GLN ** 7 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 668 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9358 Z= 0.275 Angle : 0.568 6.441 12872 Z= 0.299 Chirality : 0.041 0.199 1448 Planarity : 0.004 0.033 1459 Dihedral : 18.359 88.299 1632 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.77 % Allowed : 13.06 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.71 (0.27), residues: 961 helix: 1.43 (0.25), residues: 472 sheet: -0.56 (0.44), residues: 139 loop : -0.29 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 213 HIS 0.011 0.001 HIS 7 286 PHE 0.029 0.001 PHE 2 261 TYR 0.021 0.001 TYR 7 581 ARG 0.006 0.001 ARG 2 426 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7678 (t-100) cc_final: 0.7352 (t-100) REVERT: 2 258 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7378 (tm) REVERT: 2 336 TYR cc_start: 0.8497 (m-80) cc_final: 0.7977 (m-80) REVERT: 7 141 ARG cc_start: 0.7075 (mtm110) cc_final: 0.6842 (mtt-85) REVERT: 7 428 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7277 (tp30) REVERT: 7 612 ASP cc_start: 0.7749 (p0) cc_final: 0.7529 (p0) outliers start: 24 outliers final: 9 residues processed: 133 average time/residue: 1.2231 time to fit residues: 174.5583 Evaluate side-chains 120 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 260 ASN Chi-restraints excluded: chain 2 residue 265 LEU Chi-restraints excluded: chain 2 residue 410 ASN Chi-restraints excluded: chain 5 residue 51 ASN Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 0.0040 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 353 GLN ** 2 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 366 ASN 7 564 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9358 Z= 0.235 Angle : 0.553 7.764 12872 Z= 0.285 Chirality : 0.041 0.346 1448 Planarity : 0.004 0.038 1459 Dihedral : 18.540 82.474 1632 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.12 % Allowed : 15.38 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.40 (0.26), residues: 961 helix: 1.18 (0.24), residues: 468 sheet: -0.65 (0.44), residues: 139 loop : -0.46 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 213 HIS 0.007 0.001 HIS 7 286 PHE 0.029 0.002 PHE 2 261 TYR 0.019 0.001 TYR 7 534 ARG 0.004 0.000 ARG 7 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7670 (t-100) cc_final: 0.7371 (t-100) REVERT: 2 336 TYR cc_start: 0.8527 (m-80) cc_final: 0.7982 (m-80) REVERT: 5 11 GLU cc_start: 0.7295 (tt0) cc_final: 0.7063 (tt0) REVERT: 5 61 MET cc_start: 0.8776 (mmt) cc_final: 0.8572 (mmp) REVERT: 7 428 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7275 (tp30) outliers start: 27 outliers final: 13 residues processed: 129 average time/residue: 1.0434 time to fit residues: 145.6688 Evaluate side-chains 117 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 438 LYS Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 49 LEU Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 366 ASN Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 26 optimal weight: 0.0670 chunk 80 optimal weight: 0.0980 chunk 54 optimal weight: 0.1980 overall best weight: 0.1918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 366 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9358 Z= 0.176 Angle : 0.533 8.509 12872 Z= 0.273 Chirality : 0.039 0.317 1448 Planarity : 0.003 0.040 1459 Dihedral : 18.488 76.954 1632 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.31 % Allowed : 17.69 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 961 helix: 1.10 (0.24), residues: 470 sheet: -0.62 (0.44), residues: 139 loop : -0.48 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 7 77 HIS 0.005 0.001 HIS 2 424 PHE 0.017 0.001 PHE 2 268 TYR 0.018 0.001 TYR 7 534 ARG 0.003 0.000 ARG 7 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7507 (t-100) cc_final: 0.7141 (t-100) REVERT: 2 261 PHE cc_start: 0.7745 (t80) cc_final: 0.7508 (t80) REVERT: 2 336 TYR cc_start: 0.8518 (m-80) cc_final: 0.8007 (m-80) REVERT: 7 428 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7226 (tp30) outliers start: 20 outliers final: 10 residues processed: 125 average time/residue: 1.0866 time to fit residues: 146.4569 Evaluate side-chains 112 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 410 ASN Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 371 VAL Chi-restraints excluded: chain 7 residue 604 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 86 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN 2 211 GLN ** 2 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 424 HIS ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 366 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9358 Z= 0.227 Angle : 0.546 8.330 12872 Z= 0.280 Chirality : 0.040 0.308 1448 Planarity : 0.004 0.045 1459 Dihedral : 18.645 77.899 1632 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.24 % Allowed : 17.69 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.23 (0.26), residues: 961 helix: 1.03 (0.24), residues: 470 sheet: -0.69 (0.43), residues: 139 loop : -0.55 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 7 77 HIS 0.005 0.001 HIS 7 114 PHE 0.022 0.001 PHE 2 236 TYR 0.019 0.001 TYR 7 534 ARG 0.003 0.000 ARG 7 676 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7576 (t-100) cc_final: 0.7165 (t-100) REVERT: 2 336 TYR cc_start: 0.8513 (m-80) cc_final: 0.8034 (m-80) REVERT: 7 428 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7240 (tp30) outliers start: 28 outliers final: 15 residues processed: 122 average time/residue: 1.0766 time to fit residues: 142.2107 Evaluate side-chains 114 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 207 ASP Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 2 residue 410 ASN Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 371 VAL Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN ** 7 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9358 Z= 0.293 Angle : 0.582 11.082 12872 Z= 0.295 Chirality : 0.041 0.317 1448 Planarity : 0.004 0.049 1459 Dihedral : 18.888 80.636 1632 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.58 % Allowed : 18.96 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.01 (0.26), residues: 961 helix: 0.80 (0.24), residues: 473 sheet: -0.87 (0.42), residues: 139 loop : -0.60 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 2 455 HIS 0.008 0.001 HIS 7 114 PHE 0.025 0.002 PHE 2 236 TYR 0.021 0.001 TYR 7 534 ARG 0.004 0.000 ARG 7 676 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7642 (t-100) cc_final: 0.7229 (t-100) REVERT: 2 336 TYR cc_start: 0.8515 (m-80) cc_final: 0.8029 (m-80) REVERT: 7 428 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7201 (tp30) outliers start: 31 outliers final: 18 residues processed: 124 average time/residue: 1.1175 time to fit residues: 149.9259 Evaluate side-chains 121 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 207 ASP Chi-restraints excluded: chain 2 residue 262 LEU Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 2 residue 410 ASN Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 24 ASP Chi-restraints excluded: chain 5 residue 43 VAL Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 371 VAL Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 38 optimal weight: 0.0980 chunk 57 optimal weight: 0.2980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 3 ASN 5 64 ASN 7 711 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9358 Z= 0.223 Angle : 0.588 15.979 12872 Z= 0.291 Chirality : 0.040 0.348 1448 Planarity : 0.004 0.052 1459 Dihedral : 18.867 80.576 1632 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.58 % Allowed : 19.31 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.02 (0.26), residues: 961 helix: 0.82 (0.24), residues: 472 sheet: -0.82 (0.42), residues: 139 loop : -0.67 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 7 77 HIS 0.005 0.001 HIS 7 114 PHE 0.018 0.001 PHE 2 236 TYR 0.020 0.001 TYR 7 534 ARG 0.003 0.000 ARG 7 676 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7622 (t-100) cc_final: 0.7154 (t-100) REVERT: 7 428 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7166 (tp30) REVERT: 7 588 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7219 (tm-30) outliers start: 31 outliers final: 16 residues processed: 126 average time/residue: 1.0838 time to fit residues: 147.9077 Evaluate side-chains 116 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 207 ASP Chi-restraints excluded: chain 2 residue 262 LEU Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 43 VAL Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 371 VAL Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 588 GLU Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.2980 chunk 18 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 75 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.0970 chunk 84 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN 2 224 GLN ** 2 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 3 ASN 5 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9358 Z= 0.223 Angle : 0.612 16.589 12872 Z= 0.298 Chirality : 0.042 0.451 1448 Planarity : 0.004 0.053 1459 Dihedral : 18.867 81.088 1632 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.35 % Allowed : 20.23 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.02 (0.26), residues: 961 helix: 0.80 (0.24), residues: 472 sheet: -0.73 (0.43), residues: 137 loop : -0.69 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 7 77 HIS 0.005 0.001 HIS 7 114 PHE 0.027 0.002 PHE 2 433 TYR 0.019 0.001 TYR 7 534 ARG 0.005 0.000 ARG 2 285 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7638 (t-100) cc_final: 0.7189 (t-100) REVERT: 2 336 TYR cc_start: 0.8528 (m-80) cc_final: 0.8000 (m-80) REVERT: 7 428 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7157 (tp30) REVERT: 7 588 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7209 (tm-30) outliers start: 29 outliers final: 17 residues processed: 123 average time/residue: 1.0635 time to fit residues: 141.4499 Evaluate side-chains 117 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 207 ASP Chi-restraints excluded: chain 2 residue 262 LEU Chi-restraints excluded: chain 2 residue 360 THR Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 43 VAL Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 371 VAL Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 588 GLU Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.4980 chunk 54 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 461 HIS ** 7 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9358 Z= 0.259 Angle : 0.629 15.403 12872 Z= 0.306 Chirality : 0.043 0.447 1448 Planarity : 0.004 0.054 1459 Dihedral : 18.976 79.443 1632 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.89 % Allowed : 20.81 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.09 (0.26), residues: 961 helix: 0.74 (0.24), residues: 473 sheet: -0.80 (0.42), residues: 139 loop : -0.71 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 7 77 HIS 0.006 0.001 HIS 7 114 PHE 0.018 0.002 PHE 2 418 TYR 0.020 0.001 TYR 7 534 ARG 0.003 0.000 ARG 2 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7653 (t-100) cc_final: 0.7201 (t-100) REVERT: 5 31 LYS cc_start: 0.7857 (tppt) cc_final: 0.7155 (ptpt) REVERT: 7 428 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7138 (tp30) REVERT: 7 588 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7211 (tm-30) outliers start: 25 outliers final: 18 residues processed: 118 average time/residue: 1.1134 time to fit residues: 141.8142 Evaluate side-chains 117 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 207 ASP Chi-restraints excluded: chain 2 residue 262 LEU Chi-restraints excluded: chain 2 residue 360 THR Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 43 VAL Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 371 VAL Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 588 GLU Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 99 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.0020 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 3 ASN 5 64 ASN 7 64 GLN ** 7 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 711 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9358 Z= 0.253 Angle : 0.638 14.919 12872 Z= 0.308 Chirality : 0.043 0.444 1448 Planarity : 0.004 0.055 1459 Dihedral : 18.999 78.724 1632 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.89 % Allowed : 21.04 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.08 (0.26), residues: 961 helix: 0.80 (0.24), residues: 466 sheet: -0.77 (0.42), residues: 144 loop : -0.76 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 455 HIS 0.006 0.001 HIS 7 114 PHE 0.021 0.002 PHE 2 418 TYR 0.021 0.001 TYR 7 534 ARG 0.003 0.000 ARG 2 285 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: 2 213 TRP cc_start: 0.7666 (t-100) cc_final: 0.7238 (t-100) REVERT: 5 31 LYS cc_start: 0.7818 (tppt) cc_final: 0.7073 (ptpt) REVERT: 7 428 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7174 (tp30) REVERT: 7 588 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7198 (tm-30) outliers start: 25 outliers final: 19 residues processed: 124 average time/residue: 1.1455 time to fit residues: 153.0021 Evaluate side-chains 123 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 207 ASP Chi-restraints excluded: chain 2 residue 262 LEU Chi-restraints excluded: chain 2 residue 360 THR Chi-restraints excluded: chain 2 residue 407 VAL Chi-restraints excluded: chain 5 residue 3 ASN Chi-restraints excluded: chain 5 residue 16 MET Chi-restraints excluded: chain 5 residue 43 VAL Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 7 residue 76 LEU Chi-restraints excluded: chain 7 residue 101 VAL Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 169 VAL Chi-restraints excluded: chain 7 residue 267 THR Chi-restraints excluded: chain 7 residue 308 ILE Chi-restraints excluded: chain 7 residue 371 VAL Chi-restraints excluded: chain 7 residue 385 ASP Chi-restraints excluded: chain 7 residue 417 THR Chi-restraints excluded: chain 7 residue 588 GLU Chi-restraints excluded: chain 7 residue 604 THR Chi-restraints excluded: chain 7 residue 686 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 81 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 0.0870 chunk 57 optimal weight: 0.3980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 161 HIS 2 173 GLN ** 2 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN 7 64 GLN ** 7 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 711 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.163114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.116504 restraints weight = 12117.246| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.03 r_work: 0.3364 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9358 Z= 0.221 Angle : 0.657 14.686 12872 Z= 0.315 Chirality : 0.043 0.439 1448 Planarity : 0.004 0.054 1459 Dihedral : 18.987 78.541 1632 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.66 % Allowed : 21.39 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.08 (0.26), residues: 961 helix: 0.81 (0.24), residues: 466 sheet: -0.76 (0.42), residues: 144 loop : -0.79 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 2 455 HIS 0.005 0.001 HIS 7 114 PHE 0.016 0.001 PHE 2 418 TYR 0.020 0.001 TYR 7 534 ARG 0.002 0.000 ARG 7 676 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3700.45 seconds wall clock time: 67 minutes 8.48 seconds (4028.48 seconds total)