Starting phenix.real_space_refine on Thu Mar 14 22:04:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxq_15014/03_2024/7zxq_15014.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxq_15014/03_2024/7zxq_15014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxq_15014/03_2024/7zxq_15014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxq_15014/03_2024/7zxq_15014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxq_15014/03_2024/7zxq_15014.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxq_15014/03_2024/7zxq_15014.pdb" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 6558 2.51 5 N 1656 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 47": "OE1" <-> "OE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 66": "OD1" <-> "OD2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 66": "OD1" <-> "OD2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 66": "OD1" <-> "OD2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9930 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1655 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain breaks: 1 Chain: "B" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1655 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain breaks: 1 Chain: "C" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1655 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain breaks: 1 Chain: "D" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1655 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain breaks: 1 Chain: "E" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1655 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain breaks: 1 Chain: "F" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1655 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain breaks: 1 Time building chain proxies: 5.70, per 1000 atoms: 0.57 Number of scatterers: 9930 At special positions: 0 Unit cell: (100.062, 100.062, 92.214, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 1626 8.00 N 1656 7.00 C 6558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.04 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.04 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.04 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.04 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 1.8 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 73.8% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.687A pdb=" N TYR A 7 " --> pdb=" O TRP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 42 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 107 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 123 through 157 Processing helix chain 'A' and resid 183 through 220 Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.687A pdb=" N TYR B 7 " --> pdb=" O TRP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 42 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 107 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 123 through 157 Processing helix chain 'B' and resid 183 through 220 Processing helix chain 'C' and resid 2 through 11 removed outlier: 3.687A pdb=" N TYR C 7 " --> pdb=" O TRP C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 42 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 107 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 123 through 157 Processing helix chain 'C' and resid 183 through 220 Processing helix chain 'D' and resid 2 through 11 removed outlier: 3.687A pdb=" N TYR D 7 " --> pdb=" O TRP D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 42 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 107 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 123 through 157 Processing helix chain 'D' and resid 183 through 220 Processing helix chain 'E' and resid 2 through 11 removed outlier: 3.687A pdb=" N TYR E 7 " --> pdb=" O TRP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 42 Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 107 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 123 through 157 Processing helix chain 'E' and resid 183 through 220 Processing helix chain 'F' and resid 2 through 11 removed outlier: 3.687A pdb=" N TYR F 7 " --> pdb=" O TRP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 42 Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 107 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 123 through 157 Processing helix chain 'F' and resid 183 through 220 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 4.123A pdb=" N ILE A 52 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 180 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 4.124A pdb=" N ILE B 52 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE B 180 " --> pdb=" O ILE B 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 4.124A pdb=" N ILE C 52 " --> pdb=" O PHE C 180 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE C 180 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 4.124A pdb=" N ILE D 52 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE D 180 " --> pdb=" O ILE D 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 4.124A pdb=" N ILE E 52 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE E 180 " --> pdb=" O ILE E 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 4.124A pdb=" N ILE F 52 " --> pdb=" O PHE F 180 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE F 180 " --> pdb=" O ILE F 52 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 2268 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: 2.67 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2994 1.35 - 1.47: 2716 1.47 - 1.59: 4358 1.59 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 10200 Sorted by residual: bond pdb=" CG PRO E 58 " pdb=" CD PRO E 58 " ideal model delta sigma weight residual 1.503 1.548 -0.045 3.40e-02 8.65e+02 1.77e+00 bond pdb=" CG PRO B 58 " pdb=" CD PRO B 58 " ideal model delta sigma weight residual 1.503 1.548 -0.045 3.40e-02 8.65e+02 1.75e+00 bond pdb=" CG PRO A 58 " pdb=" CD PRO A 58 " ideal model delta sigma weight residual 1.503 1.548 -0.045 3.40e-02 8.65e+02 1.74e+00 bond pdb=" CG PRO D 58 " pdb=" CD PRO D 58 " ideal model delta sigma weight residual 1.503 1.548 -0.045 3.40e-02 8.65e+02 1.74e+00 bond pdb=" CG PRO C 58 " pdb=" CD PRO C 58 " ideal model delta sigma weight residual 1.503 1.548 -0.045 3.40e-02 8.65e+02 1.74e+00 ... (remaining 10195 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.31: 265 106.31 - 113.25: 5746 113.25 - 120.18: 3345 120.18 - 127.12: 4383 127.12 - 134.06: 157 Bond angle restraints: 13896 Sorted by residual: angle pdb=" C ASN B 14 " pdb=" CA ASN B 14 " pdb=" CB ASN B 14 " ideal model delta sigma weight residual 116.34 109.74 6.60 1.40e+00 5.10e-01 2.22e+01 angle pdb=" C ASN E 14 " pdb=" CA ASN E 14 " pdb=" CB ASN E 14 " ideal model delta sigma weight residual 116.34 109.74 6.60 1.40e+00 5.10e-01 2.22e+01 angle pdb=" C ASN D 14 " pdb=" CA ASN D 14 " pdb=" CB ASN D 14 " ideal model delta sigma weight residual 116.34 109.74 6.60 1.40e+00 5.10e-01 2.22e+01 angle pdb=" C ASN A 14 " pdb=" CA ASN A 14 " pdb=" CB ASN A 14 " ideal model delta sigma weight residual 116.34 109.75 6.59 1.40e+00 5.10e-01 2.22e+01 angle pdb=" C ASN F 14 " pdb=" CA ASN F 14 " pdb=" CB ASN F 14 " ideal model delta sigma weight residual 116.34 109.75 6.59 1.40e+00 5.10e-01 2.21e+01 ... (remaining 13891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.52: 5179 13.52 - 27.03: 548 27.03 - 40.55: 171 40.55 - 54.07: 48 54.07 - 67.58: 12 Dihedral angle restraints: 5958 sinusoidal: 2316 harmonic: 3642 Sorted by residual: dihedral pdb=" CB CYS D 64 " pdb=" SG CYS D 64 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 143.33 -50.33 1 1.00e+01 1.00e-02 3.47e+01 dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 143.32 -50.32 1 1.00e+01 1.00e-02 3.47e+01 dihedral pdb=" CB CYS C 64 " pdb=" SG CYS C 64 " pdb=" SG CYS C 168 " pdb=" CB CYS C 168 " ideal model delta sinusoidal sigma weight residual 93.00 143.31 -50.31 1 1.00e+01 1.00e-02 3.47e+01 ... (remaining 5955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1051 0.033 - 0.066: 399 0.066 - 0.099: 127 0.099 - 0.133: 55 0.133 - 0.166: 6 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CA ILE F 20 " pdb=" N ILE F 20 " pdb=" C ILE F 20 " pdb=" CB ILE F 20 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CA ILE C 20 " pdb=" N ILE C 20 " pdb=" C ILE C 20 " pdb=" CB ILE C 20 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" CA ILE A 20 " pdb=" N ILE A 20 " pdb=" C ILE A 20 " pdb=" CB ILE A 20 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 1635 not shown) Planarity restraints: 1662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 57 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO B 58 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 58 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 58 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 57 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO A 58 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 57 " -0.050 5.00e-02 4.00e+02 7.54e-02 9.10e+00 pdb=" N PRO C 58 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 58 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 58 " -0.041 5.00e-02 4.00e+02 ... (remaining 1659 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 84 2.60 - 3.18: 8797 3.18 - 3.75: 16284 3.75 - 4.33: 18793 4.33 - 4.90: 33420 Nonbonded interactions: 77378 Sorted by model distance: nonbonded pdb=" O ILE D 71 " pdb=" OH TYR D 157 " model vdw 2.027 2.440 nonbonded pdb=" O ILE E 71 " pdb=" OH TYR E 157 " model vdw 2.027 2.440 nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 157 " model vdw 2.027 2.440 nonbonded pdb=" O ILE C 71 " pdb=" OH TYR C 157 " model vdw 2.027 2.440 nonbonded pdb=" O ILE F 71 " pdb=" OH TYR F 157 " model vdw 2.027 2.440 ... (remaining 77373 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 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: 2.390 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: 11.850 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 29.490 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10200 Z= 0.211 Angle : 0.662 9.385 13896 Z= 0.363 Chirality : 0.041 0.166 1638 Planarity : 0.006 0.076 1662 Dihedral : 12.725 67.582 3540 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.45 (0.24), residues: 1212 helix: 3.25 (0.16), residues: 852 sheet: -0.01 (0.73), residues: 60 loop : -3.28 (0.27), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 44 HIS 0.003 0.001 HIS C 73 PHE 0.007 0.001 PHE B 190 TYR 0.011 0.001 TYR A 151 ARG 0.003 0.000 ARG E 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.174 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2720 time to fit residues: 60.4551 Evaluate side-chains 106 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.0470 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- 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: 0.7259 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10200 Z= 0.286 Angle : 0.590 7.051 13896 Z= 0.303 Chirality : 0.042 0.173 1638 Planarity : 0.004 0.041 1662 Dihedral : 3.895 23.528 1344 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.99 % Allowed : 6.43 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.86 (0.24), residues: 1212 helix: 3.35 (0.16), residues: 864 sheet: 0.22 (0.79), residues: 60 loop : -2.70 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 77 HIS 0.003 0.001 HIS B 100 PHE 0.011 0.001 PHE C 180 TYR 0.012 0.002 TYR A 151 ARG 0.003 0.001 ARG F 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.781 Fit side-chains REVERT: A 89 LEU cc_start: 0.7968 (pp) cc_final: 0.7760 (pp) REVERT: D 89 LEU cc_start: 0.8008 (pp) cc_final: 0.7803 (pp) outliers start: 22 outliers final: 10 residues processed: 126 average time/residue: 0.2580 time to fit residues: 45.3492 Evaluate side-chains 107 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 41 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.0270 chunk 33 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 30 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 30.0000 overall best weight: 2.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10200 Z= 0.179 Angle : 0.513 6.872 13896 Z= 0.264 Chirality : 0.039 0.164 1638 Planarity : 0.003 0.030 1662 Dihedral : 3.691 21.660 1344 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.54 % Allowed : 9.06 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.11 (0.24), residues: 1212 helix: 3.55 (0.16), residues: 864 sheet: -0.08 (0.77), residues: 60 loop : -2.58 (0.30), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 77 HIS 0.002 0.001 HIS F 97 PHE 0.008 0.001 PHE B 180 TYR 0.013 0.001 TYR F 171 ARG 0.002 0.000 ARG C 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 1.212 Fit side-chains REVERT: B 162 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6548 (ttm) REVERT: C 169 ASP cc_start: 0.6699 (t0) cc_final: 0.6454 (t0) REVERT: E 162 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6531 (ttm) outliers start: 28 outliers final: 20 residues processed: 123 average time/residue: 0.2286 time to fit residues: 39.1834 Evaluate side-chains 127 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 3 TRP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 3 TRP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain E residue 3 TRP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 3 TRP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 41 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10200 Z= 0.230 Angle : 0.550 7.638 13896 Z= 0.281 Chirality : 0.040 0.169 1638 Planarity : 0.004 0.029 1662 Dihedral : 3.699 21.598 1344 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.26 % Allowed : 10.24 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.02 (0.24), residues: 1212 helix: 3.47 (0.16), residues: 864 sheet: -0.21 (0.80), residues: 60 loop : -2.53 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 77 HIS 0.003 0.001 HIS C 97 PHE 0.010 0.001 PHE F 68 TYR 0.012 0.001 TYR D 151 ARG 0.002 0.000 ARG E 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 107 time to evaluate : 1.184 Fit side-chains REVERT: A 105 MET cc_start: 0.1531 (OUTLIER) cc_final: 0.1040 (mtt) REVERT: B 162 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6554 (ttm) REVERT: D 105 MET cc_start: 0.1518 (OUTLIER) cc_final: 0.1032 (mtt) REVERT: E 162 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6551 (ttm) outliers start: 36 outliers final: 20 residues processed: 131 average time/residue: 0.2210 time to fit residues: 40.7422 Evaluate side-chains 119 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 3 TRP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 3 TRP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain E residue 3 TRP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 3 TRP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 41 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 59 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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: 0.7267 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10200 Z= 0.197 Angle : 0.504 7.194 13896 Z= 0.260 Chirality : 0.038 0.161 1638 Planarity : 0.003 0.027 1662 Dihedral : 3.624 19.898 1344 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.45 % Allowed : 12.86 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.15 (0.24), residues: 1212 helix: 3.61 (0.16), residues: 864 sheet: -0.30 (0.81), residues: 60 loop : -2.60 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 44 HIS 0.002 0.001 HIS D 73 PHE 0.008 0.001 PHE A 68 TYR 0.009 0.001 TYR A 151 ARG 0.001 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 1.225 Fit side-chains REVERT: A 105 MET cc_start: 0.1509 (OUTLIER) cc_final: 0.0994 (mtt) REVERT: B 162 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6541 (ttm) REVERT: D 105 MET cc_start: 0.1515 (OUTLIER) cc_final: 0.1021 (mtt) REVERT: E 162 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6535 (ttm) outliers start: 27 outliers final: 20 residues processed: 121 average time/residue: 0.2158 time to fit residues: 37.2030 Evaluate side-chains 125 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 3 TRP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 3 TRP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain E residue 3 TRP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 3 TRP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 41 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 116 optimal weight: 0.1980 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.7148 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10200 Z= 0.127 Angle : 0.472 7.947 13896 Z= 0.239 Chirality : 0.037 0.151 1638 Planarity : 0.003 0.029 1662 Dihedral : 3.280 16.054 1344 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.36 % Allowed : 13.41 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.46 (0.24), residues: 1212 helix: 3.84 (0.15), residues: 870 sheet: -0.17 (0.83), residues: 60 loop : -2.66 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 3 HIS 0.002 0.001 HIS E 94 PHE 0.006 0.001 PHE B 31 TYR 0.005 0.001 TYR C 7 ARG 0.002 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.322 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 137 average time/residue: 0.2052 time to fit residues: 40.4593 Evaluate side-chains 114 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 3 TRP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 3 TRP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 3 TRP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain F residue 3 TRP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 53 optimal weight: 0.3980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7164 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10200 Z= 0.136 Angle : 0.493 8.517 13896 Z= 0.244 Chirality : 0.037 0.151 1638 Planarity : 0.003 0.026 1662 Dihedral : 3.274 17.659 1344 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.81 % Allowed : 14.76 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.36 (0.24), residues: 1212 helix: 3.78 (0.15), residues: 876 sheet: -0.25 (0.84), residues: 60 loop : -2.88 (0.29), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 3 HIS 0.001 0.000 HIS E 100 PHE 0.012 0.001 PHE E 29 TYR 0.030 0.001 TYR C 171 ARG 0.001 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 1.247 Fit side-chains outliers start: 20 outliers final: 18 residues processed: 117 average time/residue: 0.2097 time to fit residues: 35.4046 Evaluate side-chains 114 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 3 TRP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 3 TRP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 3 TRP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain F residue 3 TRP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- 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: 0.7236 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10200 Z= 0.174 Angle : 0.516 8.394 13896 Z= 0.260 Chirality : 0.038 0.156 1638 Planarity : 0.003 0.027 1662 Dihedral : 3.407 19.247 1344 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.72 % Allowed : 15.13 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.37 (0.24), residues: 1212 helix: 3.76 (0.16), residues: 876 sheet: -0.09 (0.86), residues: 60 loop : -2.81 (0.30), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 44 HIS 0.002 0.001 HIS D 73 PHE 0.009 0.001 PHE C 29 TYR 0.009 0.001 TYR E 151 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 1.258 Fit side-chains REVERT: C 162 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6643 (ttm) outliers start: 19 outliers final: 18 residues processed: 113 average time/residue: 0.2106 time to fit residues: 34.3480 Evaluate side-chains 106 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 3 TRP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 162 MET Chi-restraints excluded: chain D residue 3 TRP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 3 TRP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain F residue 3 TRP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 30.0000 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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: 0.7271 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10200 Z= 0.197 Angle : 0.540 8.174 13896 Z= 0.272 Chirality : 0.039 0.159 1638 Planarity : 0.003 0.027 1662 Dihedral : 3.538 20.920 1344 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.08 % Allowed : 15.67 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.34 (0.24), residues: 1212 helix: 3.72 (0.16), residues: 876 sheet: -0.03 (0.86), residues: 60 loop : -2.77 (0.30), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 44 HIS 0.002 0.001 HIS B 73 PHE 0.009 0.001 PHE A 68 TYR 0.036 0.002 TYR D 171 ARG 0.001 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 1.067 Fit side-chains REVERT: B 162 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6580 (ttm) REVERT: E 162 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6579 (ttm) outliers start: 23 outliers final: 20 residues processed: 104 average time/residue: 0.1993 time to fit residues: 30.6297 Evaluate side-chains 105 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 3 TRP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 3 TRP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 3 TRP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 3 TRP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 10200 Z= 0.375 Angle : 0.647 8.000 13896 Z= 0.335 Chirality : 0.043 0.174 1638 Planarity : 0.004 0.027 1662 Dihedral : 4.025 22.953 1344 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.99 % Allowed : 15.94 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.83 (0.24), residues: 1212 helix: 3.30 (0.16), residues: 876 sheet: -0.41 (0.82), residues: 60 loop : -2.71 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 132 HIS 0.004 0.001 HIS D 73 PHE 0.015 0.002 PHE F 68 TYR 0.043 0.002 TYR E 171 ARG 0.003 0.001 ARG C 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 1.276 Fit side-chains REVERT: B 162 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6681 (ttm) REVERT: E 162 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6680 (ttm) outliers start: 22 outliers final: 20 residues processed: 105 average time/residue: 0.2154 time to fit residues: 32.7104 Evaluate side-chains 101 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 TRP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain B residue 3 TRP Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 3 TRP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 3 TRP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 3 TRP Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 3 TRP Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 0.0000 chunk 68 optimal weight: 0.8980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.067693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.052764 restraints weight = 48535.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.054127 restraints weight = 25658.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055028 restraints weight = 18260.508| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10200 Z= 0.141 Angle : 0.544 9.153 13896 Z= 0.272 Chirality : 0.038 0.151 1638 Planarity : 0.003 0.028 1662 Dihedral : 3.518 20.513 1344 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.99 % Allowed : 16.49 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.50 (0.25), residues: 1212 helix: 3.86 (0.16), residues: 876 sheet: -0.13 (0.86), residues: 60 loop : -2.74 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 3 HIS 0.002 0.001 HIS E 100 PHE 0.010 0.001 PHE B 29 TYR 0.008 0.001 TYR D 7 ARG 0.002 0.000 ARG B 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1799.45 seconds wall clock time: 33 minutes 18.88 seconds (1998.88 seconds total)