Starting phenix.real_space_refine on Tue Jun 25 20:12:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs5_38615/06_2024/8xs5_38615.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs5_38615/06_2024/8xs5_38615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs5_38615/06_2024/8xs5_38615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs5_38615/06_2024/8xs5_38615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs5_38615/06_2024/8xs5_38615.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs5_38615/06_2024/8xs5_38615.pdb" } resolution = 3.33 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= 0.006 sd= 0.068 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 5775 2.51 5 N 1425 2.21 5 O 1466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 695": "OE1" <-> "OE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A PHE 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 358": "OD1" <-> "OD2" Residue "B TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8705 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3630 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 23, 'TRANS': 430} Chain breaks: 4 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5075 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 34, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 5.26, per 1000 atoms: 0.60 Number of scatterers: 8705 At special positions: 0 Unit cell: (97.06, 127.655, 98.115, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1466 8.00 N 1425 7.00 C 5775 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.9 seconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 73.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 93 through 121 removed outlier: 3.986A pdb=" N ILE A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Proline residue: A 111 - end of helix removed outlier: 3.723A pdb=" N VAL A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 121 " --> pdb=" O TRP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 191 Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 241 through 269 removed outlier: 3.929A pdb=" N LEU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 313 removed outlier: 3.513A pdb=" N LYS A 303 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.593A pdb=" N THR A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.672A pdb=" N LEU A 364 " --> pdb=" O TRP A 361 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 400 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 428 through 437 removed outlier: 3.763A pdb=" N ILE A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 456 through 489 removed outlier: 3.911A pdb=" N PHE A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 583 removed outlier: 3.770A pdb=" N ARG A 572 " --> pdb=" O THR A 568 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 647 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 659 through 677 removed outlier: 4.279A pdb=" N VAL A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'B' and resid 4 through 30 removed outlier: 4.074A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.672A pdb=" N TYR B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 92 through 120 removed outlier: 3.545A pdb=" N VAL B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TRP B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 157 through 195 Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 242 through 269 Processing helix chain 'B' and resid 291 through 315 removed outlier: 3.626A pdb=" N VAL B 313 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 360 through 364 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 389 through 399 removed outlier: 3.772A pdb=" N ILE B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 438 removed outlier: 3.615A pdb=" N ILE B 425 " --> pdb=" O MET B 421 " (cutoff:3.500A) Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 440 through 452 removed outlier: 3.620A pdb=" N ILE B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 452 " --> pdb=" O MET B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 476 Processing helix chain 'B' and resid 477 through 489 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 512 through 532 removed outlier: 3.814A pdb=" N ALA B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 548 Processing helix chain 'B' and resid 554 through 559 removed outlier: 3.782A pdb=" N ALA B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 584 Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 590 through 612 removed outlier: 3.661A pdb=" N ILE B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 647 Processing helix chain 'B' and resid 654 through 659 Processing helix chain 'B' and resid 659 through 677 removed outlier: 3.810A pdb=" N VAL B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 703 through 709 Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 207 removed outlier: 5.725A pdb=" N ALA A 322 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240 removed outlier: 5.416A pdb=" N ALA B 322 " --> pdb=" O VAL B 239 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2457 1.33 - 1.45: 1626 1.45 - 1.57: 4799 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 8952 Sorted by residual: bond pdb=" C ARG A 198 " pdb=" N PRO A 199 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.28e-02 6.10e+03 5.26e+00 bond pdb=" CE1 TYR B 181 " pdb=" CZ TYR B 181 " ideal model delta sigma weight residual 1.378 1.323 0.055 2.40e-02 1.74e+03 5.17e+00 bond pdb=" CA GLY B 524 " pdb=" C GLY B 524 " ideal model delta sigma weight residual 1.515 1.501 0.014 6.20e-03 2.60e+04 4.98e+00 bond pdb=" CB ILE B 594 " pdb=" CG2 ILE B 594 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.39e+00 bond pdb=" CG1 ILE B 532 " pdb=" CD1 ILE B 532 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.09e+00 ... (remaining 8947 not shown) Histogram of bond angle deviations from ideal: 96.85 - 104.31: 178 104.31 - 111.76: 4267 111.76 - 119.21: 3034 119.21 - 126.67: 4543 126.67 - 134.12: 159 Bond angle restraints: 12181 Sorted by residual: angle pdb=" C ASN A 257 " pdb=" N TRP A 258 " pdb=" CA TRP A 258 " ideal model delta sigma weight residual 120.44 126.03 -5.59 1.30e+00 5.92e-01 1.85e+01 angle pdb=" N VAL A 119 " pdb=" CA VAL A 119 " pdb=" C VAL A 119 " ideal model delta sigma weight residual 113.47 109.59 3.88 1.01e+00 9.80e-01 1.48e+01 angle pdb=" C PHE B 109 " pdb=" N THR B 110 " pdb=" CA THR B 110 " ideal model delta sigma weight residual 121.80 112.52 9.28 2.44e+00 1.68e-01 1.45e+01 angle pdb=" CA TYR B 181 " pdb=" CB TYR B 181 " pdb=" CG TYR B 181 " ideal model delta sigma weight residual 113.90 120.38 -6.48 1.80e+00 3.09e-01 1.30e+01 angle pdb=" N ILE B 659 " pdb=" CA ILE B 659 " pdb=" C ILE B 659 " ideal model delta sigma weight residual 113.22 109.10 4.12 1.23e+00 6.61e-01 1.12e+01 ... (remaining 12176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 4728 16.87 - 33.74: 413 33.74 - 50.60: 93 50.60 - 67.47: 11 67.47 - 84.34: 5 Dihedral angle restraints: 5250 sinusoidal: 2035 harmonic: 3215 Sorted by residual: dihedral pdb=" CA GLU B 618 " pdb=" C GLU B 618 " pdb=" N SER B 619 " pdb=" CA SER B 619 " ideal model delta harmonic sigma weight residual 180.00 152.16 27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA GLU B 452 " pdb=" C GLU B 452 " pdb=" N GLY B 453 " pdb=" CA GLY B 453 " ideal model delta harmonic sigma weight residual -180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA VAL B 276 " pdb=" C VAL B 276 " pdb=" N LYS B 277 " pdb=" CA LYS B 277 " ideal model delta harmonic sigma weight residual 180.00 154.67 25.33 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 5247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 772 0.039 - 0.077: 417 0.077 - 0.116: 145 0.116 - 0.155: 35 0.155 - 0.194: 9 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CB THR B 587 " pdb=" CA THR B 587 " pdb=" OG1 THR B 587 " pdb=" CG2 THR B 587 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA LEU B 661 " pdb=" N LEU B 661 " pdb=" C LEU B 661 " pdb=" CB LEU B 661 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.20e-01 ... (remaining 1375 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 181 " 0.059 2.00e-02 2.50e+03 4.62e-02 4.26e+01 pdb=" CG TYR B 181 " -0.112 2.00e-02 2.50e+03 pdb=" CD1 TYR B 181 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 181 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 181 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 181 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 181 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 181 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 181 " 0.036 2.00e-02 2.50e+03 3.26e-02 2.12e+01 pdb=" CG TYR A 181 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TYR A 181 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 181 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 181 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 181 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 181 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 181 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 468 " -0.024 2.00e-02 2.50e+03 2.71e-02 1.47e+01 pdb=" CG TYR B 468 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR B 468 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR B 468 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 468 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 468 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 468 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 468 " 0.001 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 100 2.64 - 3.21: 8448 3.21 - 3.77: 13376 3.77 - 4.34: 17513 4.34 - 4.90: 29241 Nonbonded interactions: 68678 Sorted by model distance: nonbonded pdb=" NH1 ARG A 198 " pdb=" OE2 GLU A 355 " model vdw 2.081 2.520 nonbonded pdb=" ND2 ASN B 208 " pdb=" O THR B 346 " model vdw 2.181 2.520 nonbonded pdb=" O MET A 157 " pdb=" OG1 THR A 161 " model vdw 2.224 2.440 nonbonded pdb=" ND2 ASN A 208 " pdb=" O THR A 346 " model vdw 2.235 2.520 nonbonded pdb=" O GLU A 180 " pdb=" OG1 THR A 183 " model vdw 2.243 2.440 ... (remaining 68673 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.040 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.600 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.081 8952 Z= 0.712 Angle : 0.882 9.275 12181 Z= 0.493 Chirality : 0.053 0.194 1378 Planarity : 0.007 0.065 1513 Dihedral : 13.490 84.338 3158 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.74 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1068 helix: 0.85 (0.19), residues: 715 sheet: -2.25 (0.79), residues: 38 loop : -2.49 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 624 HIS 0.010 0.002 HIS A 379 PHE 0.023 0.002 PHE A 225 TYR 0.112 0.004 TYR B 181 ARG 0.012 0.001 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.895 Fit side-chains REVERT: A 200 ASP cc_start: 0.8281 (p0) cc_final: 0.7935 (p0) REVERT: A 212 ASP cc_start: 0.8651 (t0) cc_final: 0.7838 (t0) REVERT: A 214 ASP cc_start: 0.8847 (m-30) cc_final: 0.8461 (m-30) REVERT: A 215 GLU cc_start: 0.8058 (mp0) cc_final: 0.7466 (mp0) REVERT: B 159 PHE cc_start: 0.8241 (t80) cc_final: 0.7932 (t80) REVERT: B 387 PHE cc_start: 0.8032 (t80) cc_final: 0.7700 (t80) REVERT: B 556 GLU cc_start: 0.7738 (pm20) cc_final: 0.7128 (tm-30) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2149 time to fit residues: 39.9972 Evaluate side-chains 116 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.0050 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN B 14 ASN B 545 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8952 Z= 0.200 Angle : 0.604 8.458 12181 Z= 0.311 Chirality : 0.042 0.178 1378 Planarity : 0.006 0.059 1513 Dihedral : 4.819 24.765 1168 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.52 % Favored : 94.38 % Rotamer: Outliers : 1.00 % Allowed : 6.31 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.27), residues: 1068 helix: 1.54 (0.19), residues: 719 sheet: -2.35 (0.77), residues: 44 loop : -2.22 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 624 HIS 0.004 0.001 HIS A 714 PHE 0.023 0.001 PHE B 428 TYR 0.044 0.002 TYR B 181 ARG 0.003 0.000 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.029 Fit side-chains REVERT: A 200 ASP cc_start: 0.8108 (p0) cc_final: 0.7772 (p0) REVERT: A 212 ASP cc_start: 0.8620 (t0) cc_final: 0.8395 (t0) REVERT: A 214 ASP cc_start: 0.8778 (m-30) cc_final: 0.8536 (m-30) REVERT: A 683 TYR cc_start: 0.8568 (m-80) cc_final: 0.8219 (m-80) REVERT: A 709 GLN cc_start: 0.8138 (pp30) cc_final: 0.7787 (pp30) REVERT: B 159 PHE cc_start: 0.7973 (t80) cc_final: 0.7737 (t80) REVERT: B 395 PHE cc_start: 0.8809 (t80) cc_final: 0.8472 (t80) outliers start: 9 outliers final: 5 residues processed: 131 average time/residue: 0.2163 time to fit residues: 38.6709 Evaluate side-chains 116 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 545 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 98 optimal weight: 0.0770 chunk 106 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.0670 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN B 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8952 Z= 0.176 Angle : 0.563 7.436 12181 Z= 0.289 Chirality : 0.041 0.182 1378 Planarity : 0.005 0.056 1513 Dihedral : 4.511 21.480 1168 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 0.78 % Allowed : 8.86 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.27), residues: 1068 helix: 1.81 (0.19), residues: 719 sheet: -2.42 (0.75), residues: 44 loop : -2.23 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.020 0.001 PHE B 428 TYR 0.028 0.001 TYR B 181 ARG 0.004 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 0.734 Fit side-chains REVERT: A 200 ASP cc_start: 0.8110 (p0) cc_final: 0.7751 (p0) REVERT: A 212 ASP cc_start: 0.8787 (t0) cc_final: 0.8307 (t0) REVERT: A 340 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: A 709 GLN cc_start: 0.8014 (pp30) cc_final: 0.7740 (pp30) REVERT: B 159 PHE cc_start: 0.7851 (t80) cc_final: 0.7596 (t80) REVERT: B 395 PHE cc_start: 0.8801 (t80) cc_final: 0.8542 (t80) outliers start: 7 outliers final: 3 residues processed: 133 average time/residue: 0.2019 time to fit residues: 37.0907 Evaluate side-chains 117 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain B residue 567 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 50 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.3980 chunk 104 optimal weight: 0.9980 chunk 51 optimal weight: 0.0470 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8952 Z= 0.169 Angle : 0.548 6.650 12181 Z= 0.279 Chirality : 0.041 0.188 1378 Planarity : 0.005 0.061 1513 Dihedral : 4.372 20.380 1168 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.52 % Favored : 94.38 % Rotamer: Outliers : 1.55 % Allowed : 9.86 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 1068 helix: 1.99 (0.19), residues: 719 sheet: -2.45 (0.76), residues: 44 loop : -2.32 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 103 HIS 0.004 0.001 HIS A 628 PHE 0.018 0.001 PHE B 428 TYR 0.024 0.001 TYR B 181 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.953 Fit side-chains REVERT: A 190 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8038 (mt0) REVERT: A 200 ASP cc_start: 0.8105 (p0) cc_final: 0.7679 (p0) REVERT: A 212 ASP cc_start: 0.8705 (t0) cc_final: 0.8265 (t0) REVERT: A 320 MET cc_start: 0.7752 (ttp) cc_final: 0.7511 (ttm) REVERT: A 709 GLN cc_start: 0.8019 (pp30) cc_final: 0.7718 (pp30) REVERT: B 159 PHE cc_start: 0.7784 (t80) cc_final: 0.7567 (t80) REVERT: B 395 PHE cc_start: 0.8749 (t80) cc_final: 0.8517 (t80) REVERT: B 545 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8430 (m-40) REVERT: B 576 TYR cc_start: 0.8677 (m-10) cc_final: 0.8457 (m-10) outliers start: 14 outliers final: 7 residues processed: 127 average time/residue: 0.2124 time to fit residues: 37.1395 Evaluate side-chains 118 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain B residue 567 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8952 Z= 0.274 Angle : 0.577 6.645 12181 Z= 0.294 Chirality : 0.043 0.185 1378 Planarity : 0.005 0.062 1513 Dihedral : 4.361 20.437 1168 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.18 % Favored : 93.73 % Rotamer: Outliers : 1.55 % Allowed : 11.07 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 1068 helix: 2.02 (0.19), residues: 720 sheet: -2.55 (0.75), residues: 44 loop : -2.31 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 103 HIS 0.003 0.001 HIS A 628 PHE 0.024 0.001 PHE A 471 TYR 0.033 0.001 TYR B 181 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8095 (p0) cc_final: 0.7658 (p0) REVERT: A 212 ASP cc_start: 0.8758 (t0) cc_final: 0.8356 (t0) REVERT: A 709 GLN cc_start: 0.8034 (pp30) cc_final: 0.7773 (pp30) REVERT: B 159 PHE cc_start: 0.7857 (t80) cc_final: 0.7635 (t80) REVERT: B 378 MET cc_start: 0.7978 (mmt) cc_final: 0.7541 (mmt) REVERT: B 395 PHE cc_start: 0.8853 (t80) cc_final: 0.8588 (t80) REVERT: B 545 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8520 (m-40) outliers start: 14 outliers final: 9 residues processed: 129 average time/residue: 0.2115 time to fit residues: 37.5734 Evaluate side-chains 123 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain B residue 567 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 20.0000 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8952 Z= 0.243 Angle : 0.568 6.858 12181 Z= 0.289 Chirality : 0.042 0.188 1378 Planarity : 0.005 0.063 1513 Dihedral : 4.321 20.239 1168 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.62 % Favored : 94.19 % Rotamer: Outliers : 1.66 % Allowed : 13.18 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 1068 helix: 2.08 (0.19), residues: 720 sheet: -2.58 (0.74), residues: 44 loop : -2.28 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.015 0.001 PHE B 225 TYR 0.025 0.001 TYR B 181 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8085 (p0) cc_final: 0.7623 (p0) REVERT: A 212 ASP cc_start: 0.8754 (t0) cc_final: 0.8351 (t0) REVERT: A 320 MET cc_start: 0.7717 (ttm) cc_final: 0.7387 (ttm) REVERT: B 395 PHE cc_start: 0.8844 (t80) cc_final: 0.8594 (t80) outliers start: 15 outliers final: 10 residues processed: 131 average time/residue: 0.1926 time to fit residues: 35.3120 Evaluate side-chains 127 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 567 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8952 Z= 0.183 Angle : 0.557 7.501 12181 Z= 0.281 Chirality : 0.041 0.188 1378 Planarity : 0.005 0.063 1513 Dihedral : 4.224 19.792 1168 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.71 % Favored : 94.19 % Rotamer: Outliers : 1.11 % Allowed : 14.73 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 1068 helix: 2.17 (0.19), residues: 724 sheet: -2.58 (0.75), residues: 44 loop : -2.13 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 103 HIS 0.004 0.001 HIS A 628 PHE 0.024 0.001 PHE B 159 TYR 0.022 0.001 TYR A 368 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8174 (p0) cc_final: 0.7621 (p0) REVERT: A 212 ASP cc_start: 0.8736 (t0) cc_final: 0.8351 (t0) REVERT: A 320 MET cc_start: 0.7564 (ttm) cc_final: 0.7229 (tpp) REVERT: B 395 PHE cc_start: 0.8838 (t80) cc_final: 0.8636 (t80) outliers start: 10 outliers final: 7 residues processed: 127 average time/residue: 0.1885 time to fit residues: 33.5261 Evaluate side-chains 122 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 567 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8952 Z= 0.199 Angle : 0.562 7.793 12181 Z= 0.283 Chirality : 0.041 0.184 1378 Planarity : 0.005 0.063 1513 Dihedral : 4.176 19.559 1168 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.48 % Rotamer: Outliers : 1.00 % Allowed : 14.73 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.27), residues: 1068 helix: 2.20 (0.20), residues: 726 sheet: -2.51 (0.74), residues: 44 loop : -2.04 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 103 HIS 0.004 0.001 HIS A 628 PHE 0.024 0.001 PHE B 159 TYR 0.019 0.001 TYR A 181 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8052 (p0) cc_final: 0.7524 (p0) REVERT: A 212 ASP cc_start: 0.8752 (t0) cc_final: 0.8364 (t0) REVERT: B 395 PHE cc_start: 0.8889 (t80) cc_final: 0.8687 (t80) outliers start: 9 outliers final: 8 residues processed: 126 average time/residue: 0.2002 time to fit residues: 35.1832 Evaluate side-chains 125 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 567 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.3980 chunk 99 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8952 Z= 0.203 Angle : 0.574 9.147 12181 Z= 0.287 Chirality : 0.041 0.194 1378 Planarity : 0.005 0.062 1513 Dihedral : 4.168 19.386 1168 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.43 % Favored : 94.38 % Rotamer: Outliers : 1.11 % Allowed : 15.17 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.27), residues: 1068 helix: 2.22 (0.20), residues: 726 sheet: -2.44 (0.73), residues: 44 loop : -2.06 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 160 HIS 0.004 0.001 HIS A 628 PHE 0.025 0.001 PHE B 159 TYR 0.019 0.001 TYR A 181 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8039 (p0) cc_final: 0.7504 (p0) REVERT: A 212 ASP cc_start: 0.8746 (t0) cc_final: 0.8349 (t0) REVERT: B 395 PHE cc_start: 0.8890 (t80) cc_final: 0.8689 (t80) outliers start: 10 outliers final: 9 residues processed: 126 average time/residue: 0.2011 time to fit residues: 35.5152 Evaluate side-chains 126 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 567 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.0270 chunk 71 optimal weight: 0.0670 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 GLN B 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8952 Z= 0.167 Angle : 0.565 8.076 12181 Z= 0.282 Chirality : 0.041 0.189 1378 Planarity : 0.005 0.063 1513 Dihedral : 4.142 19.949 1168 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.66 % Rotamer: Outliers : 1.11 % Allowed : 15.28 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.27), residues: 1068 helix: 2.24 (0.20), residues: 727 sheet: -2.38 (0.74), residues: 44 loop : -2.03 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 103 HIS 0.004 0.000 HIS A 628 PHE 0.027 0.001 PHE B 159 TYR 0.024 0.001 TYR A 181 ARG 0.004 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 107 LYS cc_start: 0.5873 (mmmt) cc_final: 0.5557 (mmmt) REVERT: A 200 ASP cc_start: 0.8179 (p0) cc_final: 0.7584 (p0) REVERT: A 212 ASP cc_start: 0.8755 (t0) cc_final: 0.8334 (t0) REVERT: B 468 TYR cc_start: 0.8892 (t80) cc_final: 0.8582 (t80) outliers start: 10 outliers final: 7 residues processed: 126 average time/residue: 0.2086 time to fit residues: 36.3406 Evaluate side-chains 119 residues out of total 937 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 567 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 79 optimal weight: 0.0020 chunk 12 optimal weight: 20.0000 chunk 23 optimal weight: 0.0270 chunk 85 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 15 optimal weight: 0.0470 chunk 75 optimal weight: 0.3980 overall best weight: 0.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.179655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.112586 restraints weight = 10944.427| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.13 r_work: 0.3060 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8952 Z= 0.142 Angle : 0.560 9.271 12181 Z= 0.278 Chirality : 0.040 0.186 1378 Planarity : 0.005 0.064 1513 Dihedral : 4.035 18.998 1168 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 0.44 % Allowed : 16.28 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 1068 helix: 2.31 (0.20), residues: 727 sheet: -2.00 (0.80), residues: 39 loop : -1.96 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 103 HIS 0.004 0.000 HIS A 628 PHE 0.026 0.001 PHE A 471 TYR 0.018 0.001 TYR A 181 ARG 0.004 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2084.75 seconds wall clock time: 37 minutes 33.19 seconds (2253.19 seconds total)