Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 15:34:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/08_2023/7efd_31084.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/08_2023/7efd_31084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/08_2023/7efd_31084.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/08_2023/7efd_31084.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/08_2023/7efd_31084.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efd_31084/08_2023/7efd_31084.pdb" } resolution = 1.77 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= 0.007 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 4 5.16 5 C 2392 2.51 5 N 668 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "C TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "D TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D GLU 116": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 4004 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1001 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 160, 951 Unusual residues: {'BTN': 1} Classifications: {'peptide': 120, 'undetermined': 1, 'water': 39} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 40} Not linked: pdbres="LYS A 134 " pdbres="BTN A5100 " Not linked: pdbres="BTN A5100 " pdbres="HOH A5201 " Not linked: pdbres="HOH A5201 " pdbres="HOH A5202 " Not linked: pdbres="HOH A5202 " pdbres="HOH A5203 " Not linked: pdbres="HOH A5203 " pdbres="HOH A5204 " ... (remaining 35 not shown) Conformer: "B" Number of residues, atoms: 155, 931 Classifications: {'peptide': 120, 'water': 35} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 35} Not linked: pdbres="LYS A 134 " pdbres="HOH A5201 " Not linked: pdbres="HOH A5201 " pdbres="HOH A5202 " Not linked: pdbres="HOH A5202 " pdbres="HOH A5203 " Not linked: pdbres="HOH A5203 " pdbres="HOH A5204 " Not linked: pdbres="HOH A5204 " pdbres="HOH A5205 " ... (remaining 30 not shown) bond proxies already assigned to first conformer: 867 Chain: "B" Number of atoms: 1001 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 160, 951 Unusual residues: {'BTN': 1} Classifications: {'peptide': 120, 'undetermined': 1, 'water': 39} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 40} Not linked: pdbres="LYS B 134 " pdbres="BTN B5100 " Not linked: pdbres="BTN B5100 " pdbres="HOH B5201 " Not linked: pdbres="HOH B5201 " pdbres="HOH B5202 " Not linked: pdbres="HOH B5202 " pdbres="HOH B5203 " Not linked: pdbres="HOH B5203 " pdbres="HOH B5204 " ... (remaining 35 not shown) Conformer: "B" Number of residues, atoms: 155, 931 Classifications: {'peptide': 120, 'water': 35} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 35} Not linked: pdbres="LYS B 134 " pdbres="HOH B5201 " Not linked: pdbres="HOH B5201 " pdbres="HOH B5202 " Not linked: pdbres="HOH B5202 " pdbres="HOH B5203 " Not linked: pdbres="HOH B5203 " pdbres="HOH B5204 " Not linked: pdbres="HOH B5204 " pdbres="HOH B5205 " ... (remaining 30 not shown) bond proxies already assigned to first conformer: 867 Chain: "C" Number of atoms: 1001 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 160, 951 Unusual residues: {'BTN': 1} Classifications: {'peptide': 120, 'undetermined': 1, 'water': 39} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 40} Not linked: pdbres="LYS C 134 " pdbres="BTN C5100 " Not linked: pdbres="BTN C5100 " pdbres="HOH C5201 " Not linked: pdbres="HOH C5201 " pdbres="HOH C5202 " Not linked: pdbres="HOH C5202 " pdbres="HOH C5203 " Not linked: pdbres="HOH C5203 " pdbres="HOH C5204 " ... (remaining 35 not shown) Conformer: "B" Number of residues, atoms: 155, 931 Classifications: {'peptide': 120, 'water': 35} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 35} Not linked: pdbres="LYS C 134 " pdbres="HOH C5201 " Not linked: pdbres="HOH C5201 " pdbres="HOH C5202 " Not linked: pdbres="HOH C5202 " pdbres="HOH C5203 " Not linked: pdbres="HOH C5203 " pdbres="HOH C5204 " Not linked: pdbres="HOH C5204 " pdbres="HOH C5205 " ... (remaining 30 not shown) bond proxies already assigned to first conformer: 867 Chain: "D" Number of atoms: 1001 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 160, 951 Unusual residues: {'BTN': 1} Classifications: {'peptide': 120, 'undetermined': 1, 'water': 39} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 40} Not linked: pdbres="LYS D 134 " pdbres="BTN D5100 " Not linked: pdbres="BTN D5100 " pdbres="HOH D5201 " Not linked: pdbres="HOH D5201 " pdbres="HOH D5202 " Not linked: pdbres="HOH D5202 " pdbres="HOH D5203 " Not linked: pdbres="HOH D5203 " pdbres="HOH D5204 " ... (remaining 35 not shown) Conformer: "B" Number of residues, atoms: 155, 931 Classifications: {'peptide': 120, 'water': 35} Link IDs: {'PTRANS': 1, 'TRANS': 118, None: 35} Not linked: pdbres="LYS D 134 " pdbres="HOH D5201 " Not linked: pdbres="HOH D5201 " pdbres="HOH D5202 " Not linked: pdbres="HOH D5202 " pdbres="HOH D5203 " Not linked: pdbres="HOH D5203 " pdbres="HOH D5204 " Not linked: pdbres="HOH D5204 " pdbres="HOH D5205 " ... (remaining 30 not shown) bond proxies already assigned to first conformer: 867 Residues with excluded nonbonded symmetry interactions: 56 residue: pdb=" N ASER A 45 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 45 " occ=0.50 residue: pdb=" N AALA A 46 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 46 " occ=0.50 residue: pdb=" N AVAL A 47 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 47 " occ=0.50 residue: pdb=" N AGLY A 48 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 48 " occ=0.50 residue: pdb=" N AASN A 49 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 49 " occ=0.50 residue: pdb=" N AALA A 50 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 50 " occ=0.50 residue: pdb=" N AGLU A 51 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 51 " occ=0.50 residue: pdb=" N ASER A 52 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 52 " occ=0.50 residue: pdb=" C10ABTN A5100 " occ=0.50 ... (14 atoms not shown) pdb=" S1 ABTN A5100 " occ=0.50 residue: pdb=" O HOH A5223 " occ=0.50 residue: pdb=" O AHOH A5225 " occ=0.50 residue: pdb=" O AHOH A5226 " occ=0.50 ... (remaining 44 not shown) Time building chain proxies: 4.13, per 1000 atoms: 1.03 Number of scatterers: 4004 At special positions: 0 Unit cell: (68.8516, 64.4096, 58.4869, 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 4 16.00 O 940 8.00 N 668 7.00 C 2392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 5.8% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP A 120 " --> pdb=" O ALA A 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP B 120 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP C 120 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 121 removed outlier: 5.020A pdb=" N TRP D 120 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG A 53 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS A 80 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG B 53 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS B 80 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG C 53 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS C 80 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 19 through 23 removed outlier: 8.257A pdb=" N ARG D 53 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS D 80 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 540 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: 1.11 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 540 1.28 - 1.42: 876 1.42 - 1.55: 2196 1.55 - 1.68: 324 1.68 - 1.82: 8 Bond restraints: 3944 Sorted by residual: bond pdb=" C THR A 42 " pdb=" O THR A 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR B 42 " pdb=" O THR B 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR D 42 " pdb=" O THR D 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C THR C 42 " pdb=" O THR C 42 " ideal model delta sigma weight residual 1.235 1.353 -0.119 1.22e-02 6.72e+03 9.44e+01 bond pdb=" C GLY D 94 " pdb=" O GLY D 94 " ideal model delta sigma weight residual 1.232 1.313 -0.082 1.05e-02 9.07e+03 6.03e+01 ... (remaining 3939 not shown) Histogram of bond angle deviations from ideal: 94.81 - 103.65: 52 103.65 - 112.49: 1516 112.49 - 121.33: 2412 121.33 - 130.17: 1340 130.17 - 139.02: 80 Bond angle restraints: 5400 Sorted by residual: angle pdb=" CA PHE A 29 " pdb=" CB PHE A 29 " pdb=" CG PHE A 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE C 29 " pdb=" CB PHE C 29 " pdb=" CG PHE C 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " pdb=" CG PHE B 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA PHE D 29 " pdb=" CB PHE D 29 " pdb=" CG PHE D 29 " ideal model delta sigma weight residual 113.80 124.75 -10.95 1.00e+00 1.00e+00 1.20e+02 angle pdb=" CA ILE A 17 " pdb=" C ILE A 17 " pdb=" O ILE A 17 " ideal model delta sigma weight residual 120.85 110.32 10.53 1.06e+00 8.90e-01 9.87e+01 ... (remaining 5395 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.60: 1956 16.60 - 33.19: 144 33.19 - 49.79: 28 49.79 - 66.38: 12 66.38 - 82.98: 12 Dihedral angle restraints: 2152 sinusoidal: 728 harmonic: 1424 Sorted by residual: dihedral pdb=" CA ASER C 52 " pdb=" C ASER C 52 " pdb=" N ARG C 53 " pdb=" CA ARG C 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASER B 52 " pdb=" C ASER B 52 " pdb=" N ARG B 53 " pdb=" CA ARG B 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASER D 52 " pdb=" C ASER D 52 " pdb=" N ARG D 53 " pdb=" CA ARG D 53 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 2149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 424 0.083 - 0.166: 152 0.166 - 0.248: 20 0.248 - 0.331: 0 0.331 - 0.414: 8 Chirality restraints: 604 Sorted by residual: chirality pdb=" CB VAL D 125 " pdb=" CA VAL D 125 " pdb=" CG1 VAL D 125 " pdb=" CG2 VAL D 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB VAL A 125 " pdb=" CA VAL A 125 " pdb=" CG1 VAL A 125 " pdb=" CG2 VAL A 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB VAL C 125 " pdb=" CA VAL C 125 " pdb=" CG1 VAL C 125 " pdb=" CG2 VAL C 125 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 601 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 ABTN D5100 " 0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN D5100 " -0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN D5100 " -0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN D5100 " 0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN D5100 " 0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN D5100 " -0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN B5100 " 0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN B5100 " -0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN B5100 " -0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN B5100 " 0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN B5100 " 0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN B5100 " -0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN A5100 " -0.059 2.00e-02 2.50e+03 2.01e-01 6.08e+02 pdb=" C4 ABTN A5100 " 0.164 2.00e-02 2.50e+03 pdb=" C5 ABTN A5100 " 0.156 2.00e-02 2.50e+03 pdb=" N1 ABTN A5100 " -0.250 2.00e-02 2.50e+03 pdb=" N2 ABTN A5100 " -0.257 2.00e-02 2.50e+03 pdb=" O3 ABTN A5100 " 0.245 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 2 0.98 - 1.96: 0 1.96 - 2.94: 1410 2.94 - 3.92: 11570 3.92 - 4.90: 22800 Warning: very small nonbonded interaction distances. Nonbonded interactions: 35782 Sorted by model distance: nonbonded pdb=" O HOH A5223 " pdb=" O HOH C5223 " model vdw 0.001 2.440 nonbonded pdb=" O HOH B5223 " pdb=" O HOH D5223 " model vdw 0.001 2.440 nonbonded pdb=" O AASN A 49 " pdb=" OD1AASN A 49 " model vdw 2.212 3.040 nonbonded pdb=" O AASN B 49 " pdb=" OD1AASN B 49 " model vdw 2.212 3.040 nonbonded pdb=" O AASN D 49 " pdb=" OD1AASN D 49 " model vdw 2.212 3.040 ... (remaining 35777 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' and (resid 15 through 44 or resid 53 through 134)) selection = (chain 'B' and (resid 15 through 44 or resid 53 through 134)) selection = (chain 'C' and (resid 15 through 44 or resid 53 through 134)) selection = (chain 'D' and (resid 15 through 44 or resid 53 through 134)) } 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=0.50 max=1.00 mean=0.94 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 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: 1.070 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.080 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.033 0.119 3944 Z= 2.153 Angle : 3.163 13.767 5400 Z= 2.200 Chirality : 0.091 0.414 604 Planarity : 0.015 0.201 684 Dihedral : 15.471 82.977 1264 Min Nonbonded Distance : 0.001 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.85 % Allowed : 1.69 % Favored : 97.46 % Rotamer Outliers : 2.15 % Cbeta Deviations : 2.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.34), residues: 512 helix: None (None), residues: 0 sheet: 0.53 (0.31), residues: 224 loop : -1.12 (0.33), residues: 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 1.3243 time to fit residues: 87.3240 Evaluate side-chains 60 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0339 time to fit residues: 0.6253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 50.0000 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 0.0050 overall best weight: 2.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 118 ASN B 107 GLN B 118 ASN ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN D 107 GLN D 118 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.124 3944 Z= 0.709 Angle : 1.757 26.399 5400 Z= 0.957 Chirality : 0.076 0.400 604 Planarity : 0.025 0.385 684 Dihedral : 9.265 57.998 572 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.85 % Allowed : 2.33 % Favored : 96.82 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.34), residues: 512 helix: -4.51 (0.28), residues: 24 sheet: -0.07 (0.28), residues: 264 loop : -1.31 (0.41), residues: 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 64 average time/residue: 1.4475 time to fit residues: 95.4324 Evaluate side-chains 58 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 50.0000 chunk 51 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 0.0170 chunk 46 optimal weight: 50.0000 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 3944 Z= 0.233 Angle : 0.740 8.645 5400 Z= 0.399 Chirality : 0.045 0.144 604 Planarity : 0.004 0.051 684 Dihedral : 7.309 45.517 572 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.64 % Allowed : 2.75 % Favored : 96.61 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.38), residues: 512 helix: None (None), residues: 0 sheet: -0.09 (0.25), residues: 328 loop : 0.85 (0.59), residues: 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 69 average time/residue: 1.3863 time to fit residues: 98.5264 Evaluate side-chains 64 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.0060 chunk 43 optimal weight: 5.9990 chunk 30 optimal weight: 50.0000 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 61 optimal weight: 50.0000 chunk 55 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.022 3944 Z= 0.234 Angle : 0.700 6.735 5400 Z= 0.382 Chirality : 0.045 0.157 604 Planarity : 0.004 0.025 684 Dihedral : 7.280 45.280 572 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.64 % Allowed : 3.39 % Favored : 95.97 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.37), residues: 512 helix: None (None), residues: 0 sheet: 0.64 (0.25), residues: 292 loop : 0.56 (0.49), residues: 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 1.4595 time to fit residues: 99.2128 Evaluate side-chains 60 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 50.0000 chunk 25 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 31 optimal weight: 50.0000 chunk 55 optimal weight: 9.9990 chunk 15 optimal weight: 50.0000 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 40.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.038 3944 Z= 0.419 Angle : 0.836 5.349 5400 Z= 0.465 Chirality : 0.053 0.194 604 Planarity : 0.006 0.042 684 Dihedral : 8.338 55.582 572 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.39 % Favored : 95.76 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.59 (0.25), residues: 300 loop : 0.23 (0.48), residues: 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 68 average time/residue: 1.6246 time to fit residues: 113.3227 Evaluate side-chains 68 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 10.0000 chunk 15 optimal weight: 50.0000 chunk 61 optimal weight: 50.0000 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 50.0000 chunk 5 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 GLN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.027 3944 Z= 0.304 Angle : 0.734 5.105 5400 Z= 0.408 Chirality : 0.047 0.146 604 Planarity : 0.005 0.030 684 Dihedral : 7.797 52.398 572 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.39 % Favored : 95.76 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.72 (0.25), residues: 292 loop : 0.28 (0.46), residues: 220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 68 average time/residue: 1.5642 time to fit residues: 109.3425 Evaluate side-chains 70 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.6223 time to fit residues: 3.8497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 50.0000 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 50.0000 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 50.0000 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 3944 Z= 0.151 Angle : 0.591 5.658 5400 Z= 0.324 Chirality : 0.042 0.144 604 Planarity : 0.003 0.015 684 Dihedral : 6.608 40.554 572 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.79 (0.26), residues: 296 loop : 0.66 (0.46), residues: 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 1.5397 time to fit residues: 109.2235 Evaluate side-chains 64 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 50.0000 chunk 11 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 42 optimal weight: 0.5980 chunk 30 optimal weight: 50.0000 chunk 5 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3944 Z= 0.261 Angle : 0.692 6.229 5400 Z= 0.380 Chirality : 0.045 0.148 604 Planarity : 0.004 0.027 684 Dihedral : 7.290 46.560 572 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.24 % Favored : 95.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.83 (0.26), residues: 292 loop : 0.52 (0.47), residues: 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 1.6740 time to fit residues: 116.7809 Evaluate side-chains 68 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 45 optimal weight: 50.0000 chunk 17 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 28 optimal weight: 30.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 3944 Z= 0.268 Angle : 0.703 6.850 5400 Z= 0.386 Chirality : 0.045 0.154 604 Planarity : 0.004 0.027 684 Dihedral : 7.341 47.318 572 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.45 % Favored : 95.13 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.77 (0.25), residues: 300 loop : 0.41 (0.48), residues: 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 1.7285 time to fit residues: 118.7971 Evaluate side-chains 67 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 50.0000 chunk 58 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 31 optimal weight: 50.0000 chunk 40 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 15 optimal weight: 50.0000 chunk 46 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.034 3944 Z= 0.368 Angle : 0.783 5.916 5400 Z= 0.433 Chirality : 0.050 0.192 604 Planarity : 0.006 0.035 684 Dihedral : 7.706 49.718 572 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.81 % Favored : 95.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.68 (0.25), residues: 300 loop : 0.24 (0.48), residues: 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 1.7345 time to fit residues: 115.5500 Evaluate side-chains 65 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 20.0000 chunk 14 optimal weight: 50.0000 chunk 50 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 50.0000 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 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 = 0.4114 r_free = 0.4114 target = 0.173804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.150552 restraints weight = 4127.184| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.14 r_work: 0.3760 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 3944 Z= 0.237 Angle : 0.674 6.089 5400 Z= 0.370 Chirality : 0.045 0.158 604 Planarity : 0.004 0.022 684 Dihedral : 7.264 47.252 572 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.64 % Allowed : 3.39 % Favored : 95.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.84 (0.26), residues: 292 loop : 0.41 (0.47), residues: 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2126.34 seconds wall clock time: 38 minutes 24.12 seconds (2304.12 seconds total)