Starting phenix.real_space_refine on Thu Feb 15 15:18:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1b_16377/02_2024/8c1b_16377.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1b_16377/02_2024/8c1b_16377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1b_16377/02_2024/8c1b_16377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1b_16377/02_2024/8c1b_16377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1b_16377/02_2024/8c1b_16377.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1b_16377/02_2024/8c1b_16377.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.057 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 27 5.16 5 C 4105 2.51 5 N 1119 2.21 5 O 1318 1.98 5 H 6106 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 387": "OE1" <-> "OE2" Residue "R GLU 47": "OE1" <-> "OE2" Residue "R ASP 114": "OD1" <-> "OD2" Residue "X TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12675 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 4913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 4913 Classifications: {'peptide': 319} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 296} Chain: "R" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 2646 Classifications: {'peptide': 169} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 162} Chain: "X" Number of atoms: 4913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 4913 Classifications: {'peptide': 319} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 296} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLY H 315 " occ=0.00 ... (5 atoms not shown) pdb=" HA3 GLY H 315 " occ=0.00 residue: pdb=" N HIS H 316 " occ=0.00 ... (15 atoms not shown) pdb=" HE2 HIS H 316 " occ=0.00 residue: pdb=" N GLY X 315 " occ=0.00 ... (5 atoms not shown) pdb=" HA3 GLY X 315 " occ=0.00 residue: pdb=" N HIS X 316 " occ=0.00 ... (15 atoms not shown) pdb=" HE2 HIS X 316 " occ=0.00 Time building chain proxies: 6.01, per 1000 atoms: 0.47 Number of scatterers: 12675 At special positions: 0 Unit cell: (96.3713, 122.278, 103.625, 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 27 16.00 O 1318 8.00 N 1119 7.00 C 4105 6.00 H 6106 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS H 237 " - pdb=" SG CYS X 325 " distance=2.06 Simple disulfide: pdb=" SG CYS H 251 " - pdb=" SG CYS H 309 " distance=2.04 Simple disulfide: pdb=" SG CYS H 325 " - pdb=" SG CYS X 237 " distance=2.05 Simple disulfide: pdb=" SG CYS H 355 " - pdb=" SG CYS H 415 " distance=2.04 Simple disulfide: pdb=" SG CYS H 461 " - pdb=" SG CYS H 521 " distance=2.04 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 68 " distance=2.04 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 151 " distance=2.04 Simple disulfide: pdb=" SG CYS X 251 " - pdb=" SG CYS X 309 " distance=2.04 Simple disulfide: pdb=" SG CYS X 355 " - pdb=" SG CYS X 415 " distance=2.03 Simple disulfide: pdb=" SG CYS X 461 " - pdb=" SG CYS X 521 " 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 Atom "HETATM12645 O5 NAG R 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA A 3 " - " MAN A 4 " " BMA C 3 " - " MAN C 4 " ALPHA1-4 " NAG B 2 " - " MAN B 3 " ALPHA1-6 " BMA A 3 " - " MAN A 5 " " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 1 " - " ASN H 391 " " NAG B 1 " - " ASN R 42 " " NAG C 1 " - " ASN X 391 " " NAG R 501 " - " ASN R 166 " " NAG R 502 " - " ASN R 21 " " NAG R 503 " - " ASN R 135 " Time building additional restraints: 9.55 Conformation dependent library (CDL) restraints added in 1.3 seconds 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1524 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 19 sheets defined 9.9% alpha, 48.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'H' and resid 273 through 275 No H-bonds generated for 'chain 'H' and resid 273 through 275' Processing helix chain 'H' and resid 298 through 303 Processing helix chain 'H' and resid 341 through 347 Processing helix chain 'H' and resid 403 through 409 Processing helix chain 'H' and resid 483 through 485 No H-bonds generated for 'chain 'H' and resid 483 through 485' Processing helix chain 'H' and resid 509 through 516 Processing helix chain 'R' and resid 59 through 63 Processing helix chain 'R' and resid 111 through 113 No H-bonds generated for 'chain 'R' and resid 111 through 113' Processing helix chain 'R' and resid 142 through 146 removed outlier: 3.698A pdb=" N SER R 146 " --> pdb=" O VAL R 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 275 No H-bonds generated for 'chain 'X' and resid 273 through 275' Processing helix chain 'X' and resid 298 through 303 Processing helix chain 'X' and resid 341 through 347 Processing helix chain 'X' and resid 403 through 409 Processing helix chain 'X' and resid 483 through 485 No H-bonds generated for 'chain 'X' and resid 483 through 485' Processing helix chain 'X' and resid 510 through 516 Processing sheet with id=AA1, first strand: chain 'H' and resid 277 through 284 removed outlier: 6.381A pdb=" N ALA H 288 " --> pdb=" O GLY H 255 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY H 255 " --> pdb=" O ALA H 288 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN H 248 " --> pdb=" O SER H 235 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA X 288 " --> pdb=" O GLY X 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 270 through 271 Processing sheet with id=AA3, first strand: chain 'H' and resid 334 through 337 removed outlier: 4.712A pdb=" N ASP H 359 " --> pdb=" O LEU H 394 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU H 394 " --> pdb=" O ASP H 359 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 368 through 373 Processing sheet with id=AA5, first strand: chain 'H' and resid 441 through 446 removed outlier: 5.532A pdb=" N PHE H 500 " --> pdb=" O ASN H 465 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 441 through 446 removed outlier: 5.532A pdb=" N PHE H 500 " --> pdb=" O ASN H 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 480 through 481 Processing sheet with id=AA8, first strand: chain 'R' and resid 6 through 10 Processing sheet with id=AA9, first strand: chain 'R' and resid 15 through 17 removed outlier: 6.568A pdb=" N ILE R 16 " --> pdb=" O PHE R 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 44 through 46 removed outlier: 4.480A pdb=" N TRP R 39 " --> pdb=" O SER R 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 88 through 92 Processing sheet with id=AB3, first strand: chain 'R' and resid 96 through 98 removed outlier: 6.709A pdb=" N VAL R 97 " --> pdb=" O ILE R 170 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR R 148 " --> pdb=" O LYS R 122 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS R 122 " --> pdb=" O THR R 148 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TYR R 150 " --> pdb=" O TYR R 120 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TYR R 120 " --> pdb=" O TYR R 150 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR R 152 " --> pdb=" O VAL R 118 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL R 118 " --> pdb=" O THR R 152 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS R 128 " --> pdb=" O TYR R 120 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS R 122 " --> pdb=" O ALA R 126 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ALA R 126 " --> pdb=" O LYS R 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 96 through 98 removed outlier: 6.709A pdb=" N VAL R 97 " --> pdb=" O ILE R 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'X' and resid 270 through 271 Processing sheet with id=AB6, first strand: chain 'X' and resid 334 through 337 removed outlier: 3.774A pdb=" N ASP X 359 " --> pdb=" O LEU X 394 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU X 394 " --> pdb=" O ASP X 359 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 368 through 373 Processing sheet with id=AB8, first strand: chain 'X' and resid 441 through 446 removed outlier: 5.418A pdb=" N PHE X 500 " --> pdb=" O ASN X 465 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 441 through 446 removed outlier: 5.418A pdb=" N PHE X 500 " --> pdb=" O ASN X 465 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'X' and resid 480 through 481 292 hydrogen bonds defined for protein. 747 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: 4.39 Time building geometry restraints manager: 10.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 6106 1.04 - 1.24: 798 1.24 - 1.44: 2168 1.44 - 1.64: 3731 1.64 - 1.84: 34 Bond restraints: 12837 Sorted by residual: bond pdb=" N ASP X 224 " pdb=" H1 ASP X 224 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ASP H 224 " pdb=" H1 ASP H 224 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C1 NAG R 501 " pdb=" O5 NAG R 501 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" CA VAL R 22 " pdb=" CB VAL R 22 " ideal model delta sigma weight residual 1.540 1.590 -0.050 1.36e-02 5.41e+03 1.35e+01 bond pdb=" C1 NAG R 502 " pdb=" O5 NAG R 502 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.25e+00 ... (remaining 12832 not shown) Histogram of bond angle deviations from ideal: 97.81 - 105.05: 208 105.05 - 112.29: 14283 112.29 - 119.54: 3503 119.54 - 126.78: 4907 126.78 - 134.02: 150 Bond angle restraints: 23051 Sorted by residual: angle pdb=" C ASN R 166 " pdb=" CA ASN R 166 " pdb=" CB ASN R 166 " ideal model delta sigma weight residual 109.84 121.81 -11.97 1.63e+00 3.76e-01 5.39e+01 angle pdb=" CA GLN R 157 " pdb=" CB GLN R 157 " pdb=" CG GLN R 157 " ideal model delta sigma weight residual 114.10 126.53 -12.43 2.00e+00 2.50e-01 3.87e+01 angle pdb=" N VAL R 22 " pdb=" CA VAL R 22 " pdb=" CB VAL R 22 " ideal model delta sigma weight residual 111.23 119.92 -8.69 1.65e+00 3.67e-01 2.77e+01 angle pdb=" C GLU H 319 " pdb=" CA GLU H 319 " pdb=" CB GLU H 319 " ideal model delta sigma weight residual 110.62 101.26 9.36 1.86e+00 2.89e-01 2.53e+01 angle pdb=" C GLY R 64 " pdb=" N GLU R 65 " pdb=" CA GLU R 65 " ideal model delta sigma weight residual 120.82 127.56 -6.74 1.41e+00 5.03e-01 2.29e+01 ... (remaining 23046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.05: 5853 22.05 - 44.10: 402 44.10 - 66.15: 84 66.15 - 88.20: 27 88.20 - 110.26: 10 Dihedral angle restraints: 6376 sinusoidal: 3601 harmonic: 2775 Sorted by residual: dihedral pdb=" CB CYS H 325 " pdb=" SG CYS H 325 " pdb=" SG CYS X 237 " pdb=" CB CYS X 237 " ideal model delta sinusoidal sigma weight residual -86.00 -167.92 81.92 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CB CYS H 237 " pdb=" SG CYS H 237 " pdb=" SG CYS X 325 " pdb=" CB CYS X 325 " ideal model delta sinusoidal sigma weight residual 93.00 166.28 -73.28 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" C ASN R 166 " pdb=" N ASN R 166 " pdb=" CA ASN R 166 " pdb=" CB ASN R 166 " ideal model delta harmonic sigma weight residual -122.60 -139.35 16.75 0 2.50e+00 1.60e-01 4.49e+01 ... (remaining 6373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 980 0.115 - 0.229: 85 0.229 - 0.344: 6 0.344 - 0.458: 1 0.458 - 0.572: 1 Chirality restraints: 1073 Sorted by residual: chirality pdb=" CA ASN R 166 " pdb=" N ASN R 166 " pdb=" C ASN R 166 " pdb=" CB ASN R 166 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.19e+00 chirality pdb=" CG LEU R 90 " pdb=" CB LEU R 90 " pdb=" CD1 LEU R 90 " pdb=" CD2 LEU R 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA GLN R 157 " pdb=" N GLN R 157 " pdb=" C GLN R 157 " pdb=" CB GLN R 157 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 1070 not shown) Planarity restraints: 1911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 166 " -0.005 2.00e-02 2.50e+03 9.57e-02 1.15e+02 pdb=" CG ASN R 166 " -0.119 2.00e-02 2.50e+03 pdb=" OD1 ASN R 166 " 0.117 2.00e-02 2.50e+03 pdb=" ND2 ASN R 166 " -0.091 2.00e-02 2.50e+03 pdb=" C1 NAG R 501 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 166 " 0.029 2.00e-02 2.50e+03 5.82e-02 3.39e+01 pdb=" CG ASN R 166 " -0.101 2.00e-02 2.50e+03 pdb=" OD1 ASN R 166 " 0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN R 166 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR X 257 " 0.084 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO X 258 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO X 258 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO X 258 " 0.067 5.00e-02 4.00e+02 ... (remaining 1908 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 2448 2.29 - 2.87: 26597 2.87 - 3.45: 30408 3.45 - 4.02: 43005 4.02 - 4.60: 63202 Nonbonded interactions: 165660 Sorted by model distance: nonbonded pdb=" HE2 HIS H 477 " pdb=" O LYS H 516 " model vdw 1.713 1.850 nonbonded pdb="HE22 GLN H 234 " pdb=" O SER X 235 " model vdw 1.733 1.850 nonbonded pdb=" O GLY R 124 " pdb="HH22 ARG X 390 " model vdw 1.737 1.850 nonbonded pdb=" HE2 HIS X 477 " pdb=" O LYS X 516 " model vdw 1.746 1.850 nonbonded pdb=" HE ARG X 522 " pdb=" OE1 GLN X 535 " model vdw 1.751 1.850 ... (remaining 165655 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 'C' } ncs_group { reference = chain 'H' selection = chain 'X' } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.190 Extract box with map and model: 13.550 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 41.450 Find NCS groups from input model: 0.390 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 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 : 0.007 0.077 6731 Z= 0.482 Angle : 1.307 12.434 9174 Z= 0.710 Chirality : 0.068 0.572 1073 Planarity : 0.009 0.124 1160 Dihedral : 16.551 110.256 2703 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.24 % Favored : 95.51 % Rotamer: Outliers : 0.28 % Allowed : 9.33 % Favored : 90.39 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.29), residues: 801 helix: -1.61 (0.63), residues: 56 sheet: 1.02 (0.27), residues: 357 loop : -0.81 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP R 13 HIS 0.013 0.003 HIS H 381 PHE 0.021 0.003 PHE X 318 TYR 0.021 0.003 TYR R 80 ARG 0.015 0.001 ARG R 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 25 average time/residue: 0.3340 time to fit residues: 12.9221 Evaluate side-chains 20 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 389 GLN X 419 HIS X 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6731 Z= 0.201 Angle : 0.600 5.604 9174 Z= 0.311 Chirality : 0.043 0.175 1073 Planarity : 0.005 0.064 1160 Dihedral : 10.475 68.602 1193 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.25 % Allowed : 8.91 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.29), residues: 801 helix: -1.51 (0.60), residues: 58 sheet: 1.35 (0.26), residues: 371 loop : 0.06 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 513 HIS 0.004 0.001 HIS R 134 PHE 0.008 0.001 PHE X 500 TYR 0.006 0.001 TYR H 256 ARG 0.003 0.000 ARG X 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 20 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 474 GLN cc_start: 0.6351 (OUTLIER) cc_final: 0.6150 (mm-40) outliers start: 9 outliers final: 4 residues processed: 28 average time/residue: 0.2482 time to fit residues: 11.6475 Evaluate side-chains 25 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 263 ILE Chi-restraints excluded: chain R residue 72 GLN Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 474 GLN Chi-restraints excluded: chain X residue 520 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.0470 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 381 HIS X 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6731 Z= 0.241 Angle : 0.575 5.038 9174 Z= 0.296 Chirality : 0.042 0.228 1073 Planarity : 0.004 0.048 1160 Dihedral : 8.113 49.994 1193 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.11 % Allowed : 8.36 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.29), residues: 801 helix: -1.56 (0.61), residues: 58 sheet: 1.67 (0.26), residues: 341 loop : 0.35 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 513 HIS 0.004 0.001 HIS X 316 PHE 0.008 0.001 PHE H 445 TYR 0.008 0.001 TYR R 149 ARG 0.006 0.000 ARG X 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 22 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 29 average time/residue: 0.3112 time to fit residues: 14.0614 Evaluate side-chains 26 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 72 GLN Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.0770 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 37 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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: 0.7158 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6731 Z= 0.139 Angle : 0.511 5.892 9174 Z= 0.260 Chirality : 0.041 0.156 1073 Planarity : 0.004 0.040 1160 Dihedral : 6.839 48.916 1193 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.84 % Allowed : 9.05 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.30), residues: 801 helix: -1.32 (0.63), residues: 58 sheet: 1.73 (0.26), residues: 347 loop : 0.59 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 513 HIS 0.002 0.001 HIS X 316 PHE 0.007 0.001 PHE X 501 TYR 0.005 0.001 TYR X 307 ARG 0.003 0.000 ARG X 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 24 average time/residue: 0.2486 time to fit residues: 10.4469 Evaluate side-chains 24 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 72 GLN Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6731 Z= 0.245 Angle : 0.553 4.194 9174 Z= 0.283 Chirality : 0.040 0.142 1073 Planarity : 0.004 0.039 1160 Dihedral : 6.433 55.806 1193 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.11 % Allowed : 9.89 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.29), residues: 801 helix: -1.45 (0.62), residues: 58 sheet: 1.48 (0.26), residues: 340 loop : 0.53 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 513 HIS 0.006 0.001 HIS H 477 PHE 0.009 0.001 PHE X 346 TYR 0.007 0.001 TYR R 131 ARG 0.007 0.000 ARG X 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 20 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 427 MET cc_start: 0.7928 (mpp) cc_final: 0.7588 (mpp) outliers start: 8 outliers final: 5 residues processed: 27 average time/residue: 0.3059 time to fit residues: 13.1539 Evaluate side-chains 23 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 72 GLN Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6731 Z= 0.276 Angle : 0.572 4.350 9174 Z= 0.297 Chirality : 0.040 0.137 1073 Planarity : 0.004 0.039 1160 Dihedral : 6.274 55.839 1193 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.11 % Allowed : 10.58 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.29), residues: 801 helix: -1.68 (0.62), residues: 57 sheet: 1.21 (0.25), residues: 345 loop : 0.29 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 110 HIS 0.009 0.001 HIS H 477 PHE 0.013 0.002 PHE R 84 TYR 0.012 0.002 TYR X 307 ARG 0.011 0.001 ARG H 348 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 21 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 28 average time/residue: 0.2325 time to fit residues: 11.2778 Evaluate side-chains 25 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 72 GLN Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Chi-restraints excluded: chain X residue 529 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7300 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6731 Z= 0.154 Angle : 0.499 4.444 9174 Z= 0.255 Chirality : 0.040 0.148 1073 Planarity : 0.004 0.040 1160 Dihedral : 5.777 53.550 1193 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.97 % Allowed : 10.72 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.30), residues: 801 helix: -1.33 (0.65), residues: 57 sheet: 1.37 (0.26), residues: 341 loop : 0.58 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 513 HIS 0.003 0.001 HIS H 421 PHE 0.006 0.001 PHE X 501 TYR 0.020 0.001 TYR X 307 ARG 0.004 0.000 ARG X 390 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 21 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 27 average time/residue: 0.2384 time to fit residues: 11.1316 Evaluate side-chains 25 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 72 GLN Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Chi-restraints excluded: chain X residue 529 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 0.1980 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6731 Z= 0.231 Angle : 0.531 4.963 9174 Z= 0.272 Chirality : 0.040 0.131 1073 Planarity : 0.004 0.037 1160 Dihedral : 5.712 49.139 1193 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.11 % Allowed : 11.00 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.30), residues: 801 helix: -1.30 (0.67), residues: 57 sheet: 1.24 (0.26), residues: 347 loop : 0.50 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 110 HIS 0.005 0.001 HIS R 70 PHE 0.009 0.001 PHE H 445 TYR 0.020 0.001 TYR X 307 ARG 0.006 0.000 ARG X 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 17 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 24 average time/residue: 0.2494 time to fit residues: 10.5960 Evaluate side-chains 25 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 17 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 ASN Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 72 GLN Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 520 ILE Chi-restraints excluded: chain X residue 529 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7381 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6731 Z= 0.233 Angle : 0.545 4.802 9174 Z= 0.281 Chirality : 0.040 0.167 1073 Planarity : 0.004 0.039 1160 Dihedral : 5.657 49.868 1193 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.11 % Allowed : 11.42 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.30), residues: 801 helix: -1.68 (0.61), residues: 63 sheet: 1.14 (0.26), residues: 336 loop : 0.32 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 110 HIS 0.007 0.001 HIS H 477 PHE 0.010 0.001 PHE X 318 TYR 0.011 0.001 TYR X 307 ARG 0.005 0.001 ARG X 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 19 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 98 MET cc_start: 0.8016 (ppp) cc_final: 0.7629 (ppp) outliers start: 8 outliers final: 7 residues processed: 25 average time/residue: 0.3008 time to fit residues: 12.1528 Evaluate side-chains 25 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 18 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 344 ASP Chi-restraints excluded: chain X residue 404 THR Chi-restraints excluded: chain X residue 520 ILE Chi-restraints excluded: chain X residue 529 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7351 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6731 Z= 0.172 Angle : 0.505 4.689 9174 Z= 0.259 Chirality : 0.040 0.146 1073 Planarity : 0.004 0.038 1160 Dihedral : 5.405 47.799 1193 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.84 % Allowed : 11.56 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.30), residues: 801 helix: -1.46 (0.64), residues: 63 sheet: 1.25 (0.26), residues: 336 loop : 0.43 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 513 HIS 0.002 0.001 HIS H 242 PHE 0.006 0.001 PHE X 318 TYR 0.016 0.001 TYR X 307 ARG 0.003 0.000 ARG X 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 98 MET cc_start: 0.7998 (ppp) cc_final: 0.7599 (ppp) outliers start: 6 outliers final: 6 residues processed: 24 average time/residue: 0.3182 time to fit residues: 11.9914 Evaluate side-chains 25 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 68 CYS Chi-restraints excluded: chain R residue 72 GLN Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain X residue 520 ILE Chi-restraints excluded: chain X residue 529 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 69 GLN ** 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 = 0.3988 r_free = 0.3988 target = 0.073112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.059450 restraints weight = 95488.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.061655 restraints weight = 40640.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.062213 restraints weight = 23767.058| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6731 Z= 0.171 Angle : 0.498 4.558 9174 Z= 0.254 Chirality : 0.040 0.145 1073 Planarity : 0.004 0.039 1160 Dihedral : 5.247 46.631 1193 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.70 % Allowed : 11.84 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.30), residues: 801 helix: -1.43 (0.64), residues: 63 sheet: 1.30 (0.26), residues: 336 loop : 0.41 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 513 HIS 0.002 0.001 HIS H 242 PHE 0.007 0.001 PHE X 318 TYR 0.008 0.001 TYR X 307 ARG 0.003 0.000 ARG X 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3102.63 seconds wall clock time: 56 minutes 0.94 seconds (3360.94 seconds total)