Starting phenix.real_space_refine on Fri May 10 16:42:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmq_37658/05_2024/8wmq_37658_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmq_37658/05_2024/8wmq_37658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmq_37658/05_2024/8wmq_37658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmq_37658/05_2024/8wmq_37658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmq_37658/05_2024/8wmq_37658_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wmq_37658/05_2024/8wmq_37658_trim_updated.pdb" } resolution = 3.3 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 5300 2.51 5 N 1316 2.21 5 O 1472 1.98 5 H 8208 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 41": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ASP 284": "OD1" <-> "OD2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B GLU 444": "OE1" <-> "OE2" Residue "B PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 501": "OE1" <-> "OE2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 16348 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.84, per 1000 atoms: 0.48 Number of scatterers: 16348 At special positions: 0 Unit cell: (96.163, 114.885, 101.269, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1472 8.00 N 1316 7.00 C 5300 6.00 H 8208 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.04 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 13.74 Conformation dependent library (CDL) restraints added in 1.7 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 2 sheets defined 60.6% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'B' and resid 20 through 29 Processing helix chain 'B' and resid 32 through 36 Processing helix chain 'B' and resid 39 through 42 No H-bonds generated for 'chain 'B' and resid 39 through 42' Processing helix chain 'B' and resid 47 through 74 removed outlier: 5.530A pdb=" N TYR B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 109 through 112 Processing helix chain 'B' and resid 118 through 149 Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.760A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 201 removed outlier: 3.542A pdb=" N ILE B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 213 through 232 removed outlier: 4.510A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'B' and resid 295 through 312 Processing helix chain 'B' and resid 318 through 330 Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 377 through 404 Processing helix chain 'B' and resid 417 through 434 Processing helix chain 'B' and resid 443 through 450 Processing helix chain 'B' and resid 457 through 469 Processing helix chain 'B' and resid 473 through 476 No H-bonds generated for 'chain 'B' and resid 473 through 476' Processing helix chain 'B' and resid 481 through 501 Proline residue: B 486 - end of helix removed outlier: 4.177A pdb=" N LYS B 497 " --> pdb=" O VAL B 493 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER B 498 " --> pdb=" O MET B 494 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL B 499 " --> pdb=" O MET B 495 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N THR B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 523 Proline residue: B 512 - end of helix removed outlier: 3.637A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 526 through 540 Processing helix chain 'B' and resid 542 through 553 Processing helix chain 'A' and resid 20 through 29 Processing helix chain 'A' and resid 32 through 36 Processing helix chain 'A' and resid 39 through 42 No H-bonds generated for 'chain 'A' and resid 39 through 42' Processing helix chain 'A' and resid 47 through 60 Processing helix chain 'A' and resid 62 through 74 removed outlier: 4.891A pdb=" N ASN A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 109 through 112 Processing helix chain 'A' and resid 118 through 149 Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.862A pdb=" N ALA A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 201 Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 213 through 232 removed outlier: 4.510A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 295 through 312 Processing helix chain 'A' and resid 318 through 331 Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 377 through 405 Processing helix chain 'A' and resid 417 through 434 Processing helix chain 'A' and resid 443 through 451 Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'A' and resid 473 through 476 No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 481 through 501 Proline residue: A 486 - end of helix removed outlier: 4.171A pdb=" N LYS A 497 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N SER A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR A 500 " --> pdb=" O MET A 496 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLU A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 523 Proline residue: A 512 - end of helix removed outlier: 3.634A pdb=" N MET A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 526 through 553 removed outlier: 4.891A pdb=" N TRP A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 156 through 158 Processing sheet with id= B, first strand: chain 'A' and resid 156 through 158 422 hydrogen bonds defined for protein. 1200 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: 7.15 Time building geometry restraints manager: 14.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8204 1.03 - 1.23: 14 1.23 - 1.42: 3414 1.42 - 1.62: 4820 1.62 - 1.81: 84 Bond restraints: 16536 Sorted by residual: bond pdb=" C6 ZEA A 701 " pdb=" N10 ZEA A 701 " ideal model delta sigma weight residual 1.336 1.466 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C6 ZEA B 701 " pdb=" N10 ZEA B 701 " ideal model delta sigma weight residual 1.336 1.466 -0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 1.502 1.596 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 1.502 1.596 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 1.500 1.557 -0.057 2.00e-02 2.50e+03 8.08e+00 ... (remaining 16531 not shown) Histogram of bond angle deviations from ideal: 79.62 - 97.20: 4 97.20 - 114.79: 20971 114.79 - 132.38: 8927 132.38 - 149.96: 18 149.96 - 167.55: 2 Bond angle restraints: 29922 Sorted by residual: angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C15 ZEA B 701 " ideal model delta sigma weight residual 125.58 167.55 -41.97 3.00e+00 1.11e-01 1.96e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 125.58 167.55 -41.97 3.00e+00 1.11e-01 1.96e+02 angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 121.92 87.91 34.01 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 121.92 87.94 33.98 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C14 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 112.50 79.62 32.88 3.00e+00 1.11e-01 1.20e+02 ... (remaining 29917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.94: 7404 24.94 - 49.87: 339 49.87 - 74.80: 132 74.80 - 99.74: 4 99.74 - 124.67: 3 Dihedral angle restraints: 7882 sinusoidal: 4248 harmonic: 3634 Sorted by residual: dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sinusoidal sigma weight residual -86.00 -145.94 59.94 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B 78 " pdb=" SG CYS B 78 " pdb=" SG CYS B 123 " pdb=" CB CYS B 123 " ideal model delta sinusoidal sigma weight residual -86.00 -144.84 58.84 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CA VAL A 484 " pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta harmonic sigma weight residual 180.00 150.51 29.49 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 7879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1137 0.053 - 0.105: 191 0.105 - 0.158: 27 0.158 - 0.210: 0 0.210 - 0.263: 1 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 270 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ILE A 362 " pdb=" N ILE A 362 " pdb=" C ILE A 362 " pdb=" CB ILE A 362 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CB THR B 250 " pdb=" CA THR B 250 " pdb=" OG1 THR B 250 " pdb=" CG2 THR B 250 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1353 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO A 487 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO B 487 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 340 " 0.043 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO A 341 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " 0.035 5.00e-02 4.00e+02 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 797 2.19 - 2.79: 32181 2.79 - 3.39: 45346 3.39 - 4.00: 56911 4.00 - 4.60: 90116 Nonbonded interactions: 225351 Sorted by model distance: nonbonded pdb=" O LEU A 519 " pdb=" HG1 THR A 523 " model vdw 1.583 1.850 nonbonded pdb=" O LEU B 519 " pdb=" HG1 THR B 523 " model vdw 1.584 1.850 nonbonded pdb=" HG SER A 268 " pdb=" OD1 ASN A 270 " model vdw 1.608 1.850 nonbonded pdb=" O SER B 88 " pdb="HD21 ASN A 270 " model vdw 1.630 1.850 nonbonded pdb=" O PHE B 332 " pdb=" HG1 THR B 338 " model vdw 1.633 1.850 ... (remaining 225346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.600 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: 0.240 Extract box with map and model: 3.930 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 56.090 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.004 0.130 8328 Z= 0.281 Angle : 1.070 41.971 11334 Z= 0.456 Chirality : 0.040 0.263 1356 Planarity : 0.005 0.065 1400 Dihedral : 14.040 124.675 2938 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.89 (0.26), residues: 1076 helix: 1.65 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.07 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 482 HIS 0.003 0.001 HIS A 360 PHE 0.010 0.001 PHE A 189 TYR 0.013 0.001 TYR B 309 ARG 0.017 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.332 Fit side-chains REVERT: B 390 ASP cc_start: 0.7078 (m-30) cc_final: 0.6821 (m-30) REVERT: B 444 GLU cc_start: 0.6848 (mp0) cc_final: 0.6634 (mp0) REVERT: A 390 ASP cc_start: 0.7144 (m-30) cc_final: 0.6882 (m-30) REVERT: A 444 GLU cc_start: 0.6869 (mp0) cc_final: 0.6630 (mp0) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.3017 time to fit residues: 62.3527 Evaluate side-chains 108 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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: 0.8980 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8328 Z= 0.295 Angle : 1.009 37.414 11334 Z= 0.415 Chirality : 0.041 0.190 1356 Planarity : 0.005 0.069 1400 Dihedral : 8.556 111.351 1236 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.47 % Allowed : 6.41 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.58 (0.26), residues: 1076 helix: 1.46 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -1.29 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.003 0.001 HIS B 350 PHE 0.016 0.002 PHE A 189 TYR 0.008 0.001 TYR A 181 ARG 0.003 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 1.265 Fit side-chains REVERT: B 390 ASP cc_start: 0.7197 (m-30) cc_final: 0.6924 (m-30) REVERT: B 444 GLU cc_start: 0.7030 (mp0) cc_final: 0.6765 (mp0) REVERT: A 390 ASP cc_start: 0.7141 (m-30) cc_final: 0.6871 (m-30) outliers start: 4 outliers final: 4 residues processed: 108 average time/residue: 0.3049 time to fit residues: 52.1930 Evaluate side-chains 109 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 335 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8328 Z= 0.173 Angle : 0.977 36.807 11334 Z= 0.388 Chirality : 0.039 0.166 1356 Planarity : 0.005 0.067 1400 Dihedral : 8.103 105.662 1236 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.70 % Allowed : 7.23 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.85 (0.26), residues: 1076 helix: 1.64 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.11 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 482 HIS 0.001 0.001 HIS A 350 PHE 0.013 0.001 PHE A 189 TYR 0.008 0.001 TYR A 181 ARG 0.002 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 1.415 Fit side-chains REVERT: B 390 ASP cc_start: 0.7163 (m-30) cc_final: 0.6895 (m-30) REVERT: B 444 GLU cc_start: 0.6970 (mp0) cc_final: 0.6697 (mp0) REVERT: A 390 ASP cc_start: 0.7144 (m-30) cc_final: 0.6885 (m-30) REVERT: A 444 GLU cc_start: 0.6973 (mp0) cc_final: 0.6658 (mp0) outliers start: 6 outliers final: 6 residues processed: 110 average time/residue: 0.3091 time to fit residues: 52.9496 Evaluate side-chains 111 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8328 Z= 0.157 Angle : 0.969 37.233 11334 Z= 0.380 Chirality : 0.038 0.162 1356 Planarity : 0.005 0.066 1400 Dihedral : 7.605 98.177 1236 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.70 % Allowed : 8.28 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.10 (0.27), residues: 1076 helix: 1.79 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -0.94 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.001 0.001 HIS A 541 PHE 0.012 0.001 PHE B 555 TYR 0.007 0.001 TYR A 181 ARG 0.002 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 1.229 Fit side-chains REVERT: B 390 ASP cc_start: 0.7178 (m-30) cc_final: 0.6913 (m-30) REVERT: A 203 PHE cc_start: 0.7947 (m-80) cc_final: 0.7661 (m-10) REVERT: A 390 ASP cc_start: 0.7105 (m-30) cc_final: 0.6834 (m-30) outliers start: 6 outliers final: 5 residues processed: 115 average time/residue: 0.3436 time to fit residues: 59.7458 Evaluate side-chains 112 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8328 Z= 0.302 Angle : 1.010 37.243 11334 Z= 0.414 Chirality : 0.041 0.166 1356 Planarity : 0.005 0.069 1400 Dihedral : 7.597 93.534 1236 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.52 % Allowed : 8.86 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.60 (0.26), residues: 1076 helix: 1.51 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -1.34 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 543 HIS 0.003 0.001 HIS A 350 PHE 0.019 0.002 PHE B 555 TYR 0.008 0.001 TYR A 27 ARG 0.002 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.553 Fit side-chains REVERT: B 390 ASP cc_start: 0.7194 (m-30) cc_final: 0.6963 (m-30) REVERT: A 203 PHE cc_start: 0.8026 (m-80) cc_final: 0.7737 (m-80) REVERT: A 390 ASP cc_start: 0.7184 (m-30) cc_final: 0.6929 (m-30) outliers start: 13 outliers final: 11 residues processed: 104 average time/residue: 0.3187 time to fit residues: 50.4980 Evaluate side-chains 109 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 551 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 0.0570 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 0.0060 chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 0.0030 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 overall best weight: 1.8128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8328 Z= 0.188 Angle : 0.981 36.544 11334 Z= 0.389 Chirality : 0.039 0.160 1356 Planarity : 0.005 0.067 1400 Dihedral : 7.226 88.348 1236 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.28 % Allowed : 10.14 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.88 (0.26), residues: 1076 helix: 1.72 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.20 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.001 HIS B 289 PHE 0.021 0.001 PHE A 555 TYR 0.008 0.001 TYR A 181 ARG 0.002 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 106 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.7996 (m-80) cc_final: 0.7651 (m-10) outliers start: 11 outliers final: 11 residues processed: 112 average time/residue: 0.3256 time to fit residues: 56.0208 Evaluate side-chains 115 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8328 Z= 0.145 Angle : 0.972 36.435 11334 Z= 0.380 Chirality : 0.038 0.157 1356 Planarity : 0.005 0.066 1400 Dihedral : 6.804 79.767 1236 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.17 % Allowed : 10.61 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.13 (0.27), residues: 1076 helix: 1.83 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -0.97 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.001 HIS A 289 PHE 0.011 0.001 PHE A 189 TYR 0.008 0.001 TYR A 181 ARG 0.002 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.7942 (m-80) cc_final: 0.7581 (m-10) outliers start: 10 outliers final: 9 residues processed: 111 average time/residue: 0.3283 time to fit residues: 55.7624 Evaluate side-chains 111 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 466 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 551 VAL 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: 5.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8328 Z= 0.205 Angle : 0.984 36.530 11334 Z= 0.389 Chirality : 0.039 0.160 1356 Planarity : 0.005 0.067 1400 Dihedral : 6.444 70.693 1236 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.28 % Allowed : 11.66 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.03 (0.26), residues: 1076 helix: 1.82 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.11 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS A 350 PHE 0.021 0.001 PHE A 555 TYR 0.008 0.001 TYR A 181 ARG 0.002 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.7983 (m-80) cc_final: 0.7625 (m-80) outliers start: 11 outliers final: 11 residues processed: 109 average time/residue: 0.3473 time to fit residues: 56.5213 Evaluate side-chains 112 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 466 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8328 Z= 0.185 Angle : 0.980 36.511 11334 Z= 0.386 Chirality : 0.039 0.161 1356 Planarity : 0.005 0.067 1400 Dihedral : 5.798 54.378 1236 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.40 % Allowed : 12.24 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.08 (0.26), residues: 1076 helix: 1.86 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.09 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 482 HIS 0.002 0.001 HIS B 289 PHE 0.012 0.001 PHE A 189 TYR 0.008 0.001 TYR A 181 ARG 0.006 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.7994 (m-80) cc_final: 0.7677 (m-80) outliers start: 12 outliers final: 12 residues processed: 111 average time/residue: 0.3618 time to fit residues: 60.2210 Evaluate side-chains 114 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 466 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 0.2980 chunk 85 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8328 Z= 0.182 Angle : 0.974 36.534 11334 Z= 0.384 Chirality : 0.038 0.172 1356 Planarity : 0.005 0.066 1400 Dihedral : 5.304 54.404 1236 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.52 % Allowed : 12.12 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.16 (0.26), residues: 1076 helix: 1.92 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.01 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.002 0.001 HIS A 289 PHE 0.012 0.001 PHE A 466 TYR 0.008 0.001 TYR A 181 ARG 0.005 0.000 ARG A 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.8010 (m-80) cc_final: 0.7690 (m-80) outliers start: 13 outliers final: 12 residues processed: 107 average time/residue: 0.3622 time to fit residues: 57.4988 Evaluate side-chains 111 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 TYR Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 466 PHE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.092445 restraints weight = 41605.982| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.51 r_work: 0.3142 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8328 Z= 0.272 Angle : 0.995 36.555 11334 Z= 0.404 Chirality : 0.040 0.178 1356 Planarity : 0.005 0.067 1400 Dihedral : 5.546 55.226 1236 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.52 % Allowed : 12.35 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.82 (0.26), residues: 1076 helix: 1.68 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.23 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 380 HIS 0.003 0.001 HIS A 289 PHE 0.017 0.002 PHE A 189 TYR 0.008 0.001 TYR A 181 ARG 0.006 0.000 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3608.96 seconds wall clock time: 65 minutes 11.42 seconds (3911.42 seconds total)