Starting phenix.real_space_refine on Mon Mar 11 04:25:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fht_29103/03_2024/8fht_29103.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fht_29103/03_2024/8fht_29103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fht_29103/03_2024/8fht_29103.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fht_29103/03_2024/8fht_29103.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fht_29103/03_2024/8fht_29103.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fht_29103/03_2024/8fht_29103.pdb" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 42 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 4618 2.51 5 N 1106 2.21 5 O 1236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 400": "OD1" <-> "OD2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 400": "OD1" <-> "OD2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7006 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3501 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 18, 'TRANS': 449} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3501 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 18, 'TRANS': 449} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.22, per 1000 atoms: 0.60 Number of scatterers: 7006 At special positions: 0 Unit cell: (105.78, 81.7, 94.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 42 16.00 Na 2 11.00 O 1236 8.00 N 1106 7.00 C 4618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 421 " distance=2.06 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 436 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 421 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 436 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.3 seconds 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 80.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 152 through 158 removed outlier: 4.145A pdb=" N TYR A 156 " --> pdb=" O GLY A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 195 removed outlier: 6.748A pdb=" N ILE A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N VAL A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 removed outlier: 4.175A pdb=" N PHE A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 250 removed outlier: 4.418A pdb=" N SER A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 278 Processing helix chain 'A' and resid 279 through 306 removed outlier: 4.734A pdb=" N VAL A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 321 through 329 Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 349 through 352 removed outlier: 3.573A pdb=" N THR A 352 " --> pdb=" O PRO A 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 352' Processing helix chain 'A' and resid 355 through 360 removed outlier: 4.345A pdb=" N ILE A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.547A pdb=" N LEU A 364 " --> pdb=" O SER A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 364' Processing helix chain 'A' and resid 366 through 395 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 427 through 434 Processing helix chain 'A' and resid 445 through 451 removed outlier: 3.509A pdb=" N MET A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 486 removed outlier: 3.872A pdb=" N ILE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 486 " --> pdb=" O CYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 496 removed outlier: 3.504A pdb=" N PHE A 494 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 521 Processing helix chain 'A' and resid 524 through 554 Proline residue: A 530 - end of helix Processing helix chain 'A' and resid 566 through 585 Processing helix chain 'A' and resid 585 through 606 Processing helix chain 'B' and resid 142 through 151 Processing helix chain 'B' and resid 152 through 158 removed outlier: 4.132A pdb=" N TYR B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 195 removed outlier: 6.942A pdb=" N ILE B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N VAL B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 212 removed outlier: 4.164A pdb=" N PHE B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 250 removed outlier: 4.430A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 278 Processing helix chain 'B' and resid 279 through 306 removed outlier: 4.740A pdb=" N VAL B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'B' and resid 321 through 329 Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 349 through 352 removed outlier: 3.559A pdb=" N THR B 352 " --> pdb=" O PRO B 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 352' Processing helix chain 'B' and resid 355 through 360 removed outlier: 4.315A pdb=" N ILE B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 364 removed outlier: 3.536A pdb=" N LEU B 364 " --> pdb=" O SER B 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 361 through 364' Processing helix chain 'B' and resid 366 through 395 Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 427 through 434 removed outlier: 3.600A pdb=" N THR B 431 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 451 removed outlier: 3.608A pdb=" N MET B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 486 removed outlier: 3.858A pdb=" N ILE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 486 " --> pdb=" O CYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 removed outlier: 3.510A pdb=" N PHE B 494 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 521 Processing helix chain 'B' and resid 524 through 554 Proline residue: B 530 - end of helix Processing helix chain 'B' and resid 566 through 585 Processing helix chain 'B' and resid 585 through 606 535 hydrogen bonds defined for protein. 1584 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: 2.50 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1078 1.31 - 1.44: 2024 1.44 - 1.57: 4014 1.57 - 1.71: 0 1.71 - 1.84: 62 Bond restraints: 7178 Sorted by residual: bond pdb=" C LEU A 601 " pdb=" O LEU A 601 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.18e-02 7.18e+03 2.10e+01 bond pdb=" CA TYR A 602 " pdb=" C TYR A 602 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.27e-02 6.20e+03 1.49e+01 bond pdb=" CA TYR B 602 " pdb=" C TYR B 602 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.32e-02 5.74e+03 1.36e+01 bond pdb=" N LEU A 601 " pdb=" CA LEU A 601 " ideal model delta sigma weight residual 1.459 1.419 0.040 1.23e-02 6.61e+03 1.05e+01 bond pdb=" CA TYR A 602 " pdb=" CB TYR A 602 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.55e-02 4.16e+03 9.81e+00 ... (remaining 7173 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.35: 134 105.35 - 112.51: 3746 112.51 - 119.68: 2313 119.68 - 126.85: 3502 126.85 - 134.02: 111 Bond angle restraints: 9806 Sorted by residual: angle pdb=" N CYS B 416 " pdb=" CA CYS B 416 " pdb=" C CYS B 416 " ideal model delta sigma weight residual 108.90 121.19 -12.29 1.63e+00 3.76e-01 5.69e+01 angle pdb=" N LEU A 419 " pdb=" CA LEU A 419 " pdb=" C LEU A 419 " ideal model delta sigma weight residual 111.36 115.92 -4.56 1.09e+00 8.42e-01 1.75e+01 angle pdb=" N CYS A 416 " pdb=" CA CYS A 416 " pdb=" C CYS A 416 " ideal model delta sigma weight residual 108.52 115.27 -6.75 1.63e+00 3.76e-01 1.72e+01 angle pdb=" N ALA A 420 " pdb=" CA ALA A 420 " pdb=" C ALA A 420 " ideal model delta sigma weight residual 111.37 117.81 -6.44 1.65e+00 3.67e-01 1.52e+01 angle pdb=" CA GLY A 414 " pdb=" C GLY A 414 " pdb=" N ALA A 415 " ideal model delta sigma weight residual 114.67 118.78 -4.11 1.11e+00 8.12e-01 1.37e+01 ... (remaining 9801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 3734 16.26 - 32.51: 278 32.51 - 48.77: 73 48.77 - 65.02: 17 65.02 - 81.28: 6 Dihedral angle restraints: 4108 sinusoidal: 1440 harmonic: 2668 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 436 " pdb=" CB CYS A 436 " ideal model delta sinusoidal sigma weight residual 93.00 172.85 -79.85 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS A 416 " pdb=" SG CYS A 416 " pdb=" SG CYS A 421 " pdb=" CB CYS A 421 " ideal model delta sinusoidal sigma weight residual -86.00 -32.42 -53.58 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" C VAL B 603 " pdb=" N VAL B 603 " pdb=" CA VAL B 603 " pdb=" CB VAL B 603 " ideal model delta harmonic sigma weight residual -122.00 -131.87 9.87 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 4105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1017 0.063 - 0.126: 131 0.126 - 0.188: 12 0.188 - 0.251: 4 0.251 - 0.314: 4 Chirality restraints: 1168 Sorted by residual: chirality pdb=" CA VAL B 603 " pdb=" N VAL B 603 " pdb=" C VAL B 603 " pdb=" CB VAL B 603 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA CYS B 416 " pdb=" N CYS B 416 " pdb=" C CYS B 416 " pdb=" CB CYS B 416 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA VAL A 603 " pdb=" N VAL A 603 " pdb=" C VAL A 603 " pdb=" CB VAL A 603 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1165 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 602 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C TYR B 602 " 0.065 2.00e-02 2.50e+03 pdb=" O TYR B 602 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL B 603 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 602 " 0.019 2.00e-02 2.50e+03 3.65e-02 1.34e+01 pdb=" C TYR A 602 " -0.063 2.00e-02 2.50e+03 pdb=" O TYR A 602 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL A 603 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 601 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C LEU A 601 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU A 601 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR A 602 " 0.013 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1166 2.76 - 3.29: 7025 3.29 - 3.83: 12038 3.83 - 4.36: 12922 4.36 - 4.90: 23686 Nonbonded interactions: 56837 Sorted by model distance: nonbonded pdb=" O TRP B 151 " pdb="NA NA B1101 " model vdw 2.220 2.470 nonbonded pdb=" O TRP A 151 " pdb="NA NA A1101 " model vdw 2.228 2.470 nonbonded pdb=" O SER B 345 " pdb=" OG SER B 533 " model vdw 2.297 2.440 nonbonded pdb=" OG SER A 468 " pdb="NA NA A1101 " model vdw 2.299 2.470 nonbonded pdb=" O SER A 345 " pdb=" OG SER A 533 " model vdw 2.309 2.440 ... (remaining 56832 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' } 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.000 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.370 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:2.740 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 0.054 7178 Z= 0.237 Angle : 0.633 12.293 9806 Z= 0.365 Chirality : 0.047 0.314 1168 Planarity : 0.004 0.037 1206 Dihedral : 12.982 81.279 2396 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.96 % Allowed : 0.96 % Favored : 98.07 % Cbeta Deviations : 0.35 % 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: 2.06 (0.28), residues: 932 helix: 2.22 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -0.94 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 586 HIS 0.002 0.001 HIS B 234 PHE 0.025 0.002 PHE B 238 TYR 0.018 0.001 TYR A 602 ARG 0.002 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 0.724 Fit side-chains REVERT: B 417 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7170 (mt-10) outliers start: 7 outliers final: 0 residues processed: 117 average time/residue: 0.1805 time to fit residues: 28.5463 Evaluate side-chains 101 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 27 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7178 Z= 0.212 Angle : 0.499 4.701 9806 Z= 0.272 Chirality : 0.039 0.170 1168 Planarity : 0.004 0.036 1206 Dihedral : 4.187 50.539 991 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.38 % Allowed : 7.30 % Favored : 91.32 % 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: 2.11 (0.28), residues: 932 helix: 2.29 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.89 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 586 HIS 0.003 0.001 HIS A 549 PHE 0.018 0.002 PHE A 598 TYR 0.011 0.001 TYR B 602 ARG 0.001 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7894 (t) cc_final: 0.7622 (p) REVERT: B 309 SER cc_start: 0.7983 (t) cc_final: 0.7763 (p) outliers start: 10 outliers final: 7 residues processed: 108 average time/residue: 0.1914 time to fit residues: 27.8602 Evaluate side-chains 101 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 0.0670 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7178 Z= 0.146 Angle : 0.457 4.583 9806 Z= 0.248 Chirality : 0.038 0.168 1168 Planarity : 0.004 0.035 1206 Dihedral : 3.392 13.477 988 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.52 % Allowed : 9.50 % Favored : 88.98 % 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: 2.38 (0.28), residues: 932 helix: 2.49 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.80 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 586 HIS 0.001 0.000 HIS A 549 PHE 0.009 0.001 PHE A 453 TYR 0.009 0.001 TYR B 605 ARG 0.001 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7961 (t) cc_final: 0.7677 (p) REVERT: B 309 SER cc_start: 0.8029 (t) cc_final: 0.7815 (p) outliers start: 11 outliers final: 7 residues processed: 106 average time/residue: 0.1883 time to fit residues: 26.9834 Evaluate side-chains 103 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN B 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7178 Z= 0.217 Angle : 0.485 4.747 9806 Z= 0.265 Chirality : 0.039 0.182 1168 Planarity : 0.004 0.036 1206 Dihedral : 3.458 13.340 988 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.34 % Allowed : 10.06 % Favored : 87.60 % 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: 2.25 (0.28), residues: 932 helix: 2.35 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.74 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 586 HIS 0.003 0.001 HIS A 549 PHE 0.027 0.002 PHE A 238 TYR 0.016 0.001 TYR B 602 ARG 0.001 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7911 (t) cc_final: 0.7623 (p) REVERT: B 309 SER cc_start: 0.7955 (t) cc_final: 0.7690 (p) outliers start: 17 outliers final: 13 residues processed: 105 average time/residue: 0.1907 time to fit residues: 26.8173 Evaluate side-chains 106 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 546 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7178 Z= 0.198 Angle : 0.468 4.555 9806 Z= 0.257 Chirality : 0.038 0.180 1168 Planarity : 0.004 0.036 1206 Dihedral : 3.430 13.569 988 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.20 % Allowed : 11.29 % Favored : 86.50 % 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: 2.29 (0.28), residues: 932 helix: 2.40 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.74 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 586 HIS 0.002 0.001 HIS B 549 PHE 0.020 0.001 PHE A 238 TYR 0.015 0.001 TYR B 602 ARG 0.001 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7912 (t) cc_final: 0.7598 (p) REVERT: A 343 MET cc_start: 0.7720 (mmt) cc_final: 0.7221 (mmt) REVERT: B 309 SER cc_start: 0.7946 (t) cc_final: 0.7670 (p) outliers start: 16 outliers final: 15 residues processed: 100 average time/residue: 0.2026 time to fit residues: 27.3745 Evaluate side-chains 105 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 546 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.7700 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7178 Z= 0.192 Angle : 0.470 4.528 9806 Z= 0.258 Chirality : 0.038 0.190 1168 Planarity : 0.004 0.036 1206 Dihedral : 3.412 13.815 988 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.89 % Allowed : 11.57 % Favored : 85.54 % 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: 2.36 (0.28), residues: 932 helix: 2.45 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.73 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 586 HIS 0.002 0.000 HIS A 549 PHE 0.019 0.001 PHE A 238 TYR 0.015 0.001 TYR B 602 ARG 0.001 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7891 (t) cc_final: 0.7564 (p) REVERT: A 343 MET cc_start: 0.7731 (mmt) cc_final: 0.7288 (mmt) REVERT: B 309 SER cc_start: 0.7955 (t) cc_final: 0.7684 (p) outliers start: 21 outliers final: 14 residues processed: 103 average time/residue: 0.1916 time to fit residues: 26.7452 Evaluate side-chains 102 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 546 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 74 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7725 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7178 Z= 0.213 Angle : 0.483 4.625 9806 Z= 0.265 Chirality : 0.039 0.189 1168 Planarity : 0.004 0.036 1206 Dihedral : 3.452 13.531 988 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.20 % Allowed : 12.53 % Favored : 85.26 % 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: 2.31 (0.27), residues: 932 helix: 2.40 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.73 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 586 HIS 0.003 0.001 HIS A 549 PHE 0.017 0.002 PHE A 238 TYR 0.006 0.001 TYR A 249 ARG 0.001 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7808 (t) cc_final: 0.7577 (p) REVERT: A 343 MET cc_start: 0.7812 (mmt) cc_final: 0.7430 (mmt) REVERT: B 309 SER cc_start: 0.7941 (t) cc_final: 0.7668 (p) REVERT: B 343 MET cc_start: 0.7712 (mmt) cc_final: 0.7194 (mmt) outliers start: 16 outliers final: 15 residues processed: 101 average time/residue: 0.1960 time to fit residues: 26.7138 Evaluate side-chains 105 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 567 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 0.0050 chunk 84 optimal weight: 0.0010 chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.4200 ------------------------------------------------------------------------------- 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: 0.7668 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7178 Z= 0.149 Angle : 0.447 4.428 9806 Z= 0.247 Chirality : 0.037 0.180 1168 Planarity : 0.004 0.036 1206 Dihedral : 3.286 14.700 988 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.20 % Allowed : 13.09 % Favored : 84.71 % 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: 2.56 (0.28), residues: 932 helix: 2.58 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -0.77 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 586 HIS 0.001 0.000 HIS A 549 PHE 0.017 0.001 PHE A 238 TYR 0.007 0.001 TYR A 602 ARG 0.001 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7769 (t) cc_final: 0.7529 (p) REVERT: A 343 MET cc_start: 0.7729 (mmt) cc_final: 0.7333 (mmt) REVERT: B 309 SER cc_start: 0.7865 (t) cc_final: 0.7548 (p) outliers start: 16 outliers final: 13 residues processed: 103 average time/residue: 0.1896 time to fit residues: 26.5100 Evaluate side-chains 106 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 546 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7702 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7178 Z= 0.186 Angle : 0.468 4.969 9806 Z= 0.258 Chirality : 0.038 0.188 1168 Planarity : 0.004 0.036 1206 Dihedral : 3.332 13.746 988 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.20 % Allowed : 13.22 % Favored : 84.57 % 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: 2.53 (0.28), residues: 932 helix: 2.59 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.69 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 586 HIS 0.002 0.001 HIS A 549 PHE 0.016 0.001 PHE A 238 TYR 0.004 0.001 TYR A 249 ARG 0.001 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7707 (t) cc_final: 0.7437 (p) REVERT: A 343 MET cc_start: 0.7800 (mmt) cc_final: 0.7418 (mmt) REVERT: B 309 SER cc_start: 0.7714 (t) cc_final: 0.7432 (p) REVERT: B 343 MET cc_start: 0.7709 (mmt) cc_final: 0.7194 (mmt) outliers start: 16 outliers final: 13 residues processed: 100 average time/residue: 0.1887 time to fit residues: 25.2477 Evaluate side-chains 103 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 546 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.7747 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7178 Z= 0.246 Angle : 0.509 5.278 9806 Z= 0.280 Chirality : 0.040 0.199 1168 Planarity : 0.004 0.035 1206 Dihedral : 3.510 13.130 988 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.07 % Allowed : 13.36 % Favored : 84.57 % 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: 2.19 (0.28), residues: 932 helix: 2.29 (0.19), residues: 670 sheet: None (None), residues: 0 loop : -0.82 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 568 HIS 0.004 0.001 HIS A 549 PHE 0.016 0.002 PHE A 238 TYR 0.007 0.001 TYR A 249 ARG 0.001 0.000 ARG B 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7659 (t) cc_final: 0.7364 (p) REVERT: A 343 MET cc_start: 0.7820 (mmt) cc_final: 0.7378 (mmt) REVERT: B 309 SER cc_start: 0.7708 (t) cc_final: 0.7411 (p) outliers start: 15 outliers final: 14 residues processed: 102 average time/residue: 0.1948 time to fit residues: 26.6444 Evaluate side-chains 107 residues out of total 756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 546 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.188784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140433 restraints weight = 7211.393| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.29 r_work: 0.3476 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7178 Z= 0.227 Angle : 0.500 5.258 9806 Z= 0.274 Chirality : 0.039 0.196 1168 Planarity : 0.004 0.035 1206 Dihedral : 3.518 13.451 988 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.07 % Allowed : 13.22 % Favored : 84.71 % 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: 2.23 (0.28), residues: 932 helix: 2.32 (0.19), residues: 670 sheet: None (None), residues: 0 loop : -0.82 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 586 HIS 0.003 0.001 HIS A 549 PHE 0.016 0.002 PHE A 238 TYR 0.012 0.001 TYR B 602 ARG 0.001 0.000 ARG A 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1605.56 seconds wall clock time: 29 minutes 45.68 seconds (1785.68 seconds total)