Starting phenix.real_space_refine on Wed Jan 17 15:01:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/01_2024/7efc_31083.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/01_2024/7efc_31083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/01_2024/7efc_31083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/01_2024/7efc_31083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/01_2024/7efc_31083.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/01_2024/7efc_31083.pdb" } resolution = 1.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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-1.21-5211/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 AHOH A5221 " occ=0.50 residue: pdb=" O HOH A5223 " occ=0.50 residue: pdb=" O AHOH A5231 " occ=0.50 ... (remaining 44 not shown) Time building chain proxies: 4.30, per 1000 atoms: 1.07 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: 1.45 Conformation dependent library (CDL) restraints added in 1.2 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 3.3% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'D' and resid 118 through 121 Processing sheet with id= 1, first strand: chain 'A' and resid 19 through 23 removed outlier: 8.184A pdb=" N ARG A 53 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS A 80 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR A 71 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY A 94 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU A 73 " --> pdb=" O TRP A 92 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP A 92 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TRP A 75 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 90 " --> pdb=" O TRP A 75 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL A 77 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER A 88 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP A 79 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 19 through 23 removed outlier: 8.184A pdb=" N ARG B 53 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS B 80 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR B 71 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY B 94 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU B 73 " --> pdb=" O TRP B 92 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP B 92 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TRP B 75 " --> pdb=" O THR B 90 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR B 90 " --> pdb=" O TRP B 75 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL B 77 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER B 88 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP B 79 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 19 through 23 removed outlier: 8.184A pdb=" N ARG C 53 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS C 80 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR C 71 " --> pdb=" O GLY C 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY C 94 " --> pdb=" O THR C 71 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU C 73 " --> pdb=" O TRP C 92 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP C 92 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TRP C 75 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR C 90 " --> pdb=" O TRP C 75 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL C 77 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER C 88 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP C 79 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 19 through 23 removed outlier: 8.184A pdb=" N ARG D 53 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LYS D 80 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR D 71 " --> pdb=" O GLY D 94 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY D 94 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU D 73 " --> pdb=" O TRP D 92 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TRP D 92 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TRP D 75 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR D 90 " --> pdb=" O TRP D 75 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL D 77 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER D 88 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TRP D 79 " --> pdb=" O ALA D 86 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 456 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: 1.03 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 548 1.29 - 1.42: 880 1.42 - 1.55: 2192 1.55 - 1.68: 316 1.68 - 1.81: 8 Bond restraints: 3944 Sorted by residual: bond pdb=" C GLY C 94 " pdb=" O GLY C 94 " ideal model delta sigma weight residual 1.232 1.307 -0.075 1.05e-02 9.07e+03 5.12e+01 bond pdb=" C GLY D 94 " pdb=" O GLY D 94 " ideal model delta sigma weight residual 1.232 1.307 -0.075 1.05e-02 9.07e+03 5.12e+01 bond pdb=" C GLY B 94 " pdb=" O GLY B 94 " ideal model delta sigma weight residual 1.232 1.307 -0.075 1.05e-02 9.07e+03 5.12e+01 bond pdb=" C GLY A 94 " pdb=" O GLY A 94 " ideal model delta sigma weight residual 1.232 1.307 -0.075 1.05e-02 9.07e+03 5.12e+01 bond pdb=" C ILE C 17 " pdb=" O ILE C 17 " ideal model delta sigma weight residual 1.237 1.154 0.083 1.19e-02 7.06e+03 4.86e+01 ... (remaining 3939 not shown) Histogram of bond angle deviations from ideal: 93.14 - 102.07: 16 102.07 - 110.99: 1152 110.99 - 119.92: 2452 119.92 - 128.84: 1668 128.84 - 137.77: 112 Bond angle restraints: 5400 Sorted by residual: angle pdb=" CA PHE D 29 " pdb=" CB PHE D 29 " pdb=" CG PHE D 29 " ideal model delta sigma weight residual 113.80 124.22 -10.42 1.00e+00 1.00e+00 1.08e+02 angle pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " pdb=" CG PHE B 29 " ideal model delta sigma weight residual 113.80 124.22 -10.42 1.00e+00 1.00e+00 1.08e+02 angle pdb=" CA PHE A 29 " pdb=" CB PHE A 29 " pdb=" CG PHE A 29 " ideal model delta sigma weight residual 113.80 124.22 -10.42 1.00e+00 1.00e+00 1.08e+02 angle pdb=" CA PHE C 29 " pdb=" CB PHE C 29 " pdb=" CG PHE C 29 " ideal model delta sigma weight residual 113.80 124.22 -10.42 1.00e+00 1.00e+00 1.08e+02 angle pdb=" CA ILE A 17 " pdb=" C ILE A 17 " pdb=" O ILE A 17 " ideal model delta sigma weight residual 120.85 110.38 10.47 1.06e+00 8.90e-01 9.75e+01 ... (remaining 5395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 2008 16.54 - 33.08: 160 33.08 - 49.62: 20 49.62 - 66.16: 12 66.16 - 82.70: 12 Dihedral angle restraints: 2212 sinusoidal: 788 harmonic: 1424 Sorted by residual: 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 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+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 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ASER A 52 " pdb=" C ASER A 52 " pdb=" N ARG A 53 " pdb=" CA ARG A 53 " ideal model delta harmonic sigma weight residual 180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 2209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 412 0.080 - 0.160: 164 0.160 - 0.241: 20 0.241 - 0.321: 0 0.321 - 0.401: 8 Chirality restraints: 604 Sorted by residual: chirality pdb=" CB VAL A 31 " pdb=" CA VAL A 31 " pdb=" CG1 VAL A 31 " pdb=" CG2 VAL A 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CB VAL C 31 " pdb=" CA VAL C 31 " pdb=" CG1 VAL C 31 " pdb=" CG2 VAL C 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CB VAL B 31 " pdb=" CA VAL B 31 " pdb=" CG1 VAL B 31 " pdb=" CG2 VAL B 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 601 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 ABTN C5100 " -0.063 2.00e-02 2.50e+03 2.15e-01 6.96e+02 pdb=" C4 ABTN C5100 " 0.172 2.00e-02 2.50e+03 pdb=" C5 ABTN C5100 " 0.172 2.00e-02 2.50e+03 pdb=" N1 ABTN C5100 " -0.270 2.00e-02 2.50e+03 pdb=" N2 ABTN C5100 " -0.272 2.00e-02 2.50e+03 pdb=" O3 ABTN C5100 " 0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN A5100 " -0.063 2.00e-02 2.50e+03 2.15e-01 6.96e+02 pdb=" C4 ABTN A5100 " 0.172 2.00e-02 2.50e+03 pdb=" C5 ABTN A5100 " 0.172 2.00e-02 2.50e+03 pdb=" N1 ABTN A5100 " -0.270 2.00e-02 2.50e+03 pdb=" N2 ABTN A5100 " -0.272 2.00e-02 2.50e+03 pdb=" O3 ABTN A5100 " 0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 ABTN B5100 " 0.063 2.00e-02 2.50e+03 2.15e-01 6.96e+02 pdb=" C4 ABTN B5100 " -0.172 2.00e-02 2.50e+03 pdb=" C5 ABTN B5100 " -0.172 2.00e-02 2.50e+03 pdb=" N1 ABTN B5100 " 0.270 2.00e-02 2.50e+03 pdb=" N2 ABTN B5100 " 0.272 2.00e-02 2.50e+03 pdb=" O3 ABTN B5100 " -0.262 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: 1438 2.94 - 3.92: 11594 3.92 - 4.90: 22880 Warning: very small nonbonded interaction distances. Nonbonded interactions: 35914 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 C 49 " pdb=" OD1AASN C 49 " model vdw 2.057 3.040 nonbonded pdb=" O AASN D 49 " pdb=" OD1AASN D 49 " model vdw 2.057 3.040 nonbonded pdb=" O AASN A 49 " pdb=" OD1AASN A 49 " model vdw 2.057 3.040 ... (remaining 35909 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: 0.110 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: 0.920 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.000 Find NCS groups from input model: 0.230 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: 0.000 Load rotamer database and sin/cos tables:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 0.032 0.090 3944 Z= 2.151 Angle : 3.162 13.316 5400 Z= 2.201 Chirality : 0.090 0.401 604 Planarity : 0.016 0.215 684 Dihedral : 14.879 82.705 1324 Min Nonbonded Distance : 0.001 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.85 % Allowed : 2.54 % Favored : 96.61 % Rotamer: Outliers : 2.15 % Allowed : 4.30 % Favored : 93.55 % Cbeta Deviations : 3.60 % 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: -0.84 (0.33), residues: 512 helix: None (None), residues: 0 sheet: 0.30 (0.29), residues: 244 loop : -1.41 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 92 HIS 0.001 0.000 HIS C 127 PHE 0.002 0.001 PHE D 130 TYR 0.002 0.001 TYR B 60 ARG 0.000 0.000 ARG D 53 *********************** 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 68 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8217 (m) cc_final: 0.7789 (p) REVERT: A 53 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7498 (ttp80) REVERT: A 69 SER cc_start: 0.7845 (m) cc_final: 0.7634 (t) REVERT: A 103 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7435 (mtm-85) REVERT: B 27 SER cc_start: 0.8218 (m) cc_final: 0.7790 (p) REVERT: B 53 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.7499 (ttp80) REVERT: B 69 SER cc_start: 0.7845 (m) cc_final: 0.7635 (t) REVERT: B 103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7434 (mtm-85) REVERT: C 27 SER cc_start: 0.8215 (m) cc_final: 0.7788 (p) REVERT: C 53 ARG cc_start: 0.7712 (ttp-110) cc_final: 0.7498 (ttp80) REVERT: C 69 SER cc_start: 0.7844 (m) cc_final: 0.7634 (t) REVERT: C 103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7433 (mtm-85) REVERT: D 27 SER cc_start: 0.8217 (m) cc_final: 0.7788 (p) REVERT: D 53 ARG cc_start: 0.7715 (ttp-110) cc_final: 0.7500 (ttp80) REVERT: D 69 SER cc_start: 0.7844 (m) cc_final: 0.7634 (t) REVERT: D 103 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7435 (mtm-85) outliers start: 4 outliers final: 4 residues processed: 64 average time/residue: 1.1196 time to fit residues: 74.3458 Evaluate side-chains 52 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 50.0000 chunk 37 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.8216 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.110 3944 Z= 0.601 Angle : 1.457 19.464 5400 Z= 0.812 Chirality : 0.072 0.450 604 Planarity : 0.014 0.105 684 Dihedral : 9.627 59.800 636 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.39 % Favored : 96.40 % Rotamer: Outliers : 1.61 % Allowed : 8.33 % Favored : 90.05 % 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: -1.78 (0.33), residues: 512 helix: -4.90 (0.26), residues: 24 sheet: -0.45 (0.26), residues: 280 loop : -1.62 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.008 TRP B 108 HIS 0.028 0.004 HIS C 87 PHE 0.119 0.019 PHE B 29 TYR 0.200 0.012 TYR B 43 ARG 0.043 0.004 ARG B 53 *********************** 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: 6 poor density : 60 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.8256 (m) cc_final: 0.7929 (p) REVERT: A 53 ARG cc_start: 0.7756 (ttp-170) cc_final: 0.7505 (ttp80) REVERT: B 27 SER cc_start: 0.8231 (m) cc_final: 0.7879 (p) REVERT: B 53 ARG cc_start: 0.7734 (ttp-170) cc_final: 0.7498 (ttp80) REVERT: C 27 SER cc_start: 0.8313 (m) cc_final: 0.7966 (p) REVERT: C 53 ARG cc_start: 0.7730 (ttp-170) cc_final: 0.7477 (ttp80) REVERT: D 27 SER cc_start: 0.8258 (m) cc_final: 0.7953 (p) outliers start: 6 outliers final: 0 residues processed: 61 average time/residue: 1.1972 time to fit residues: 75.5472 Evaluate side-chains 48 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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: 9.9990 chunk 18 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 50.0000 chunk 51 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 46 optimal weight: 50.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3944 Z= 0.381 Angle : 0.838 7.528 5400 Z= 0.460 Chirality : 0.049 0.182 604 Planarity : 0.005 0.037 684 Dihedral : 8.102 47.023 632 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.81 % Favored : 95.97 % Rotamer: Outliers : 0.27 % Allowed : 10.22 % Favored : 89.52 % 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: 0.02 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.41 (0.26), residues: 252 loop : -0.31 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP D 75 HIS 0.007 0.003 HIS C 87 PHE 0.028 0.005 PHE C 29 TYR 0.022 0.003 TYR D 43 ARG 0.008 0.002 ARG B 103 *********************** 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 62 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7347 (ttm110) REVERT: A 103 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7443 (ttm110) REVERT: B 53 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7382 (ttm110) REVERT: C 53 ARG cc_start: 0.7822 (ttp-170) cc_final: 0.7279 (ttm110) REVERT: C 103 ARG cc_start: 0.8025 (ttm-80) cc_final: 0.7448 (ttm110) REVERT: D 56 LEU cc_start: 0.8494 (tt) cc_final: 0.8191 (pp) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 1.2422 time to fit residues: 78.5420 Evaluate side-chains 57 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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: 5.9990 chunk 43 optimal weight: 7.9990 chunk 30 optimal weight: 50.0000 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 58 optimal weight: 0.4980 chunk 61 optimal weight: 50.0000 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- 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: 0.8251 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3944 Z= 0.307 Angle : 0.780 8.796 5400 Z= 0.414 Chirality : 0.046 0.143 604 Planarity : 0.005 0.034 684 Dihedral : 7.729 46.225 632 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.60 % Favored : 96.19 % Rotamer: Outliers : 0.81 % Allowed : 10.22 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.31 (0.25), residues: 296 loop : 0.22 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP B 92 HIS 0.005 0.003 HIS C 87 PHE 0.034 0.005 PHE A 29 TYR 0.015 0.002 TYR D 22 ARG 0.005 0.002 ARG C 53 *********************** 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 55 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7547 (ttp80) REVERT: A 103 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7455 (ttm110) REVERT: B 53 ARG cc_start: 0.7810 (ttp-170) cc_final: 0.7351 (ttp80) REVERT: C 53 ARG cc_start: 0.7783 (ttp-170) cc_final: 0.7440 (ttp80) REVERT: C 103 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7458 (ttm110) REVERT: D 56 LEU cc_start: 0.8468 (tt) cc_final: 0.8204 (pp) outliers start: 3 outliers final: 1 residues processed: 52 average time/residue: 1.4058 time to fit residues: 75.4021 Evaluate side-chains 52 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 50.0000 chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 42 optimal weight: 0.1980 chunk 31 optimal weight: 50.0000 chunk 55 optimal weight: 8.9990 chunk 15 optimal weight: 50.0000 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 30.0000 overall best weight: 4.3986 ------------------------------------------------------------------------------- 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: 0.8252 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3944 Z= 0.299 Angle : 0.735 8.868 5400 Z= 0.398 Chirality : 0.045 0.149 604 Planarity : 0.004 0.032 684 Dihedral : 7.756 44.815 632 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.08 % Allowed : 8.60 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.32 (0.25), residues: 296 loop : 0.45 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 92 HIS 0.005 0.002 HIS C 87 PHE 0.025 0.004 PHE A 29 TYR 0.015 0.002 TYR C 22 ARG 0.006 0.002 ARG D 103 *********************** 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 56 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7847 (ttp-170) cc_final: 0.7539 (ttp80) REVERT: A 103 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7447 (ttm110) REVERT: B 53 ARG cc_start: 0.7810 (ttp-170) cc_final: 0.7540 (ttp80) REVERT: C 53 ARG cc_start: 0.7805 (ttp-170) cc_final: 0.7453 (ttp80) REVERT: C 103 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7443 (ttm110) REVERT: D 56 LEU cc_start: 0.8449 (tt) cc_final: 0.8170 (pp) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 1.3589 time to fit residues: 74.3513 Evaluate side-chains 53 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain C residue 121 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 7.9990 chunk 15 optimal weight: 50.0000 chunk 61 optimal weight: 50.0000 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 50.0000 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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: 0.8249 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3944 Z= 0.287 Angle : 0.715 9.151 5400 Z= 0.388 Chirality : 0.045 0.146 604 Planarity : 0.004 0.026 684 Dihedral : 7.639 44.205 632 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.88 % Allowed : 8.06 % Favored : 90.05 % 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: 0.46 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.36 (0.25), residues: 296 loop : 0.45 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 92 HIS 0.005 0.002 HIS C 87 PHE 0.020 0.003 PHE D 29 TYR 0.016 0.002 TYR A 22 ARG 0.006 0.002 ARG D 103 *********************** 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 59 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7537 (ttp80) REVERT: A 103 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7445 (ttm110) REVERT: B 53 ARG cc_start: 0.7841 (ttp-170) cc_final: 0.7526 (ttp80) REVERT: C 53 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.7446 (ttp80) REVERT: C 103 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7445 (ttm110) outliers start: 7 outliers final: 6 residues processed: 55 average time/residue: 1.2998 time to fit residues: 73.9105 Evaluate side-chains 57 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 121 LYS 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: 7.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 61 optimal weight: 50.0000 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 28 optimal weight: 50.0000 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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: 0.8236 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3944 Z= 0.212 Angle : 0.666 9.245 5400 Z= 0.353 Chirality : 0.043 0.148 604 Planarity : 0.003 0.027 684 Dihedral : 7.128 43.238 632 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.88 % Allowed : 8.06 % Favored : 90.05 % 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: 0.59 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.40 (0.25), residues: 296 loop : 0.60 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 108 HIS 0.003 0.002 HIS C 87 PHE 0.014 0.002 PHE D 29 TYR 0.008 0.001 TYR D 43 ARG 0.006 0.001 ARG D 103 *********************** 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 59 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7533 (ttp80) REVERT: A 103 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7474 (ttm110) REVERT: B 53 ARG cc_start: 0.7847 (ttp-170) cc_final: 0.7526 (ttp80) REVERT: C 53 ARG cc_start: 0.7806 (ttp-170) cc_final: 0.7455 (ttp80) REVERT: C 103 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7437 (ttm110) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 1.3540 time to fit residues: 78.3594 Evaluate side-chains 57 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR 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: 10.0000 chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 30 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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: 0.8246 moved from start: 0.3092 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= 0.273 Angle : 0.708 9.542 5400 Z= 0.380 Chirality : 0.046 0.156 604 Planarity : 0.004 0.022 684 Dihedral : 7.594 43.127 632 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.15 % Allowed : 7.80 % Favored : 90.05 % 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: 0.52 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.38 (0.25), residues: 296 loop : 0.51 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 92 HIS 0.004 0.002 HIS C 87 PHE 0.008 0.002 PHE D 29 TYR 0.007 0.002 TYR D 43 ARG 0.004 0.002 ARG A 84 *********************** 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 60 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7843 (ttp-170) cc_final: 0.7535 (ttp80) REVERT: A 103 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7430 (ttm110) REVERT: B 53 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7532 (ttp80) REVERT: C 53 ARG cc_start: 0.7807 (ttp-170) cc_final: 0.7459 (ttp80) REVERT: C 103 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7449 (ttm110) outliers start: 8 outliers final: 5 residues processed: 56 average time/residue: 1.3316 time to fit residues: 77.0476 Evaluate side-chains 57 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 28 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 45 optimal weight: 50.0000 chunk 17 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.8255 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3944 Z= 0.387 Angle : 0.799 10.177 5400 Z= 0.434 Chirality : 0.050 0.174 604 Planarity : 0.005 0.028 684 Dihedral : 7.995 41.894 632 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.54 % Allowed : 9.41 % Favored : 90.05 % 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: 0.33 (0.34), residues: 512 helix: None (None), residues: 0 sheet: 0.35 (0.25), residues: 296 loop : 0.21 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP D 92 HIS 0.007 0.003 HIS C 87 PHE 0.008 0.003 PHE B 29 TYR 0.009 0.003 TYR D 43 ARG 0.007 0.002 ARG B 103 *********************** 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 54 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7853 (ttp-170) cc_final: 0.7546 (ttp80) REVERT: A 103 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7459 (ttm110) REVERT: B 53 ARG cc_start: 0.7829 (ttp-170) cc_final: 0.7521 (ttp80) REVERT: C 53 ARG cc_start: 0.7817 (ttp-170) cc_final: 0.7474 (ttp80) REVERT: C 103 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7447 (ttm110) outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 1.3935 time to fit residues: 74.7509 Evaluate side-chains 54 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain B residue 121 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 50.0000 chunk 58 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 31 optimal weight: 50.0000 chunk 40 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 50.0000 chunk 46 optimal weight: 50.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.8248 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3944 Z= 0.295 Angle : 0.735 9.895 5400 Z= 0.393 Chirality : 0.047 0.168 604 Planarity : 0.004 0.021 684 Dihedral : 7.688 43.916 632 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.54 % Allowed : 9.68 % Favored : 89.78 % 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: 0.36 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.37 (0.25), residues: 296 loop : 0.25 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 92 HIS 0.005 0.002 HIS C 87 PHE 0.006 0.002 PHE C 29 TYR 0.009 0.002 TYR B 96 ARG 0.007 0.002 ARG B 103 ********************** 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 54 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7839 (ttp-170) cc_final: 0.7536 (ttp80) REVERT: A 103 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7427 (ttm110) REVERT: B 53 ARG cc_start: 0.7834 (ttp-170) cc_final: 0.7526 (ttp80) REVERT: C 53 ARG cc_start: 0.7817 (ttp-170) cc_final: 0.7476 (ttp80) REVERT: C 103 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7446 (ttm110) outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 1.0927 time to fit residues: 58.6113 Evaluate side-chains 53 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 LYS 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: 10.0000 chunk 21 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.160322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137060 restraints weight = 4253.265| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.25 r_work: 0.3655 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3944 Z= 0.400 Angle : 0.809 10.319 5400 Z= 0.439 Chirality : 0.051 0.177 604 Planarity : 0.005 0.039 684 Dihedral : 8.066 42.111 632 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.54 % Allowed : 9.95 % Favored : 89.52 % 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: 0.14 (0.34), residues: 512 helix: None (None), residues: 0 sheet: 0.50 (0.26), residues: 272 loop : -0.30 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP D 92 HIS 0.007 0.003 HIS C 87 PHE 0.008 0.003 PHE B 29 TYR 0.009 0.003 TYR D 43 ARG 0.009 0.003 ARG D 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1888.92 seconds wall clock time: 38 minutes 27.44 seconds (2307.44 seconds total)