Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 22:44:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/10_2023/7efc_31083.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/10_2023/7efc_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_31083/10_2023/7efc_31083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/10_2023/7efc_31083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/10_2023/7efc_31083.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7efc_31083/10_2023/7efc_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-1.21rc1-5097/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: 4.73, per 1000 atoms: 1.18 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: 1.69 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 3.3% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 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: 1.04 Time building geometry restraints manager: 1.80 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: 1952 16.54 - 33.08: 156 33.08 - 49.62: 20 49.62 - 66.16: 12 66.16 - 82.70: 12 Dihedral angle restraints: 2152 sinusoidal: 728 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 2149 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: 0.130 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: 0.000 Extract box with map and model: 0.920 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.650 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:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.050 ------------------------------------------------------------------------------- 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 : 15.028 82.705 1264 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 *********************** 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 : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 64 average time/residue: 0.9063 time to fit residues: 60.2470 Evaluate side-chains 44 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.310 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0338 time to fit residues: 0.6290 ------------------------------------------------------------------------------- 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: 0.9990 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: 10.0000 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 0.0770 chunk 30 optimal weight: 50.0000 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- 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: 0.8210 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.132 3944 Z= 0.635 Angle : 1.517 20.516 5400 Z= 0.852 Chirality : 0.074 0.453 604 Planarity : 0.026 0.383 684 Dihedral : 9.617 59.705 572 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.18 % Favored : 96.40 % Rotamer: Outliers : 1.34 % Allowed : 9.68 % Favored : 88.98 % Cbeta Deviations : 0.23 % 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: -1.75 (0.33), residues: 512 helix: -4.90 (0.27), residues: 24 sheet: -0.48 (0.26), residues: 280 loop : -1.51 (0.42), residues: 208 *********************** 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 59 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 1.3642 time to fit residues: 77.4518 Evaluate side-chains 43 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.9834 time to fit residues: 2.5386 ------------------------------------------------------------------------------- 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: 5.9990 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 50.0000 chunk 51 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 46 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.8247 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3944 Z= 0.328 Angle : 0.804 7.472 5400 Z= 0.439 Chirality : 0.048 0.165 604 Planarity : 0.005 0.060 684 Dihedral : 8.032 45.523 572 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.39 % Favored : 96.19 % Rotamer: Outliers : 0.54 % Allowed : 10.22 % Favored : 89.25 % 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: 0.04 (0.36), residues: 512 helix: None (None), residues: 0 sheet: 0.34 (0.26), residues: 260 loop : -0.21 (0.44), residues: 252 *********************** 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 61 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 1.1054 time to fit residues: 68.5699 Evaluate side-chains 54 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.301 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.3679 ------------------------------------------------------------------------------- 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: 3.9990 chunk 43 optimal weight: 10.0000 chunk 30 optimal weight: 50.0000 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 50.0000 chunk 55 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3944 Z= 0.300 Angle : 0.761 8.696 5400 Z= 0.412 Chirality : 0.047 0.165 604 Planarity : 0.004 0.030 684 Dihedral : 7.769 44.097 572 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.81 % Favored : 95.97 % Rotamer: Outliers : 0.81 % Allowed : 9.68 % 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: 0.26 (0.34), residues: 512 helix: None (None), residues: 0 sheet: 0.36 (0.24), residues: 300 loop : 0.07 (0.47), residues: 212 *********************** 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 51 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 49 average time/residue: 1.5048 time to fit residues: 76.0177 Evaluate side-chains 47 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5130 ------------------------------------------------------------------------------- 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: 5.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 50.0000 chunk 25 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 50.0000 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 50.0000 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 30.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3126 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= 0.280 Angle : 0.715 8.671 5400 Z= 0.390 Chirality : 0.045 0.154 604 Planarity : 0.004 0.024 684 Dihedral : 7.663 43.912 572 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.34 % Allowed : 9.41 % Favored : 89.25 % 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: 0.41 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.33 (0.24), residues: 304 loop : 0.40 (0.48), residues: 208 *********************** 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 53 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 1.5006 time to fit residues: 75.7980 Evaluate side-chains 51 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 1.4334 time to fit residues: 3.4271 ------------------------------------------------------------------------------- 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: 5.9990 chunk 28 optimal weight: 50.0000 chunk 5 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8255 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3944 Z= 0.430 Angle : 0.819 9.630 5400 Z= 0.456 Chirality : 0.050 0.151 604 Planarity : 0.005 0.038 684 Dihedral : 8.136 42.334 572 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.64 % Allowed : 3.18 % 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: 0.14 (0.34), residues: 512 helix: None (None), residues: 0 sheet: 0.53 (0.26), residues: 260 loop : -0.31 (0.40), residues: 252 *********************** 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 52 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 1.4424 time to fit residues: 74.3701 Evaluate side-chains 50 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.5131 time to fit residues: 2.0536 ------------------------------------------------------------------------------- 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: 0.5980 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 50.0000 chunk 38 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 40.0000 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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: 0.8238 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3944 Z= 0.225 Angle : 0.667 9.077 5400 Z= 0.361 Chirality : 0.044 0.150 604 Planarity : 0.003 0.020 684 Dihedral : 7.424 41.822 572 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.81 % Allowed : 10.48 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.38 (0.24), residues: 304 loop : 0.33 (0.47), residues: 208 *********************** 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 51 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 1.4741 time to fit residues: 74.4786 Evaluate side-chains 50 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0405 time to fit residues: 0.5739 ------------------------------------------------------------------------------- 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: 40.0000 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 50.0000 chunk 5 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.003 0.022 3944 Z= 0.228 Angle : 0.675 9.089 5400 Z= 0.362 Chirality : 0.045 0.151 604 Planarity : 0.003 0.022 684 Dihedral : 7.410 42.062 572 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.54 % Allowed : 10.75 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.42 (0.25), residues: 304 loop : 0.35 (0.47), residues: 208 *********************** 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 50 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 49 average time/residue: 1.4601 time to fit residues: 73.7351 Evaluate side-chains 49 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5335 ------------------------------------------------------------------------------- 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: 9.9990 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 45 optimal weight: 50.0000 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 0.0570 chunk 60 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 overall best weight: 3.8106 ------------------------------------------------------------------------------- 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: 0.8240 moved from start: 0.3256 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= 0.262 Angle : 0.708 9.406 5400 Z= 0.378 Chirality : 0.046 0.160 604 Planarity : 0.004 0.025 684 Dihedral : 7.543 41.194 572 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.27 % Allowed : 11.29 % Favored : 88.44 % 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: 0.41 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.39 (0.25), residues: 304 loop : 0.28 (0.47), residues: 208 *********************** 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 49 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 1.5432 time to fit residues: 77.8452 Evaluate side-chains 49 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5293 ------------------------------------------------------------------------------- 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: 0.9990 chunk 63 optimal weight: 50.0000 chunk 58 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 50.0000 chunk 40 optimal weight: 0.0050 chunk 54 optimal weight: 20.0000 chunk 15 optimal weight: 50.0000 chunk 46 optimal weight: 50.0000 overall best weight: 5.2004 ------------------------------------------------------------------------------- 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: 0.3287 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= 0.332 Angle : 0.762 9.715 5400 Z= 0.411 Chirality : 0.048 0.177 604 Planarity : 0.004 0.031 684 Dihedral : 7.801 40.944 572 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.27 % Allowed : 11.29 % Favored : 88.44 % 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: 0.27 (0.34), residues: 512 helix: None (None), residues: 0 sheet: 0.33 (0.25), residues: 304 loop : 0.14 (0.46), residues: 208 ********************** 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 49 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 1.4798 time to fit residues: 74.7304 Evaluate side-chains 49 residues out of total 332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5443 ------------------------------------------------------------------------------- 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: 0.4980 chunk 14 optimal weight: 50.0000 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.163786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140326 restraints weight = 4685.495| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.33 r_work: 0.3694 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3944 Z= 0.139 Angle : 0.625 8.692 5400 Z= 0.320 Chirality : 0.043 0.150 604 Planarity : 0.002 0.016 684 Dihedral : 6.648 39.386 572 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.27 % Allowed : 11.29 % Favored : 88.44 % 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 (0.35), residues: 512 helix: None (None), residues: 0 sheet: 0.57 (0.25), residues: 304 loop : 0.45 (0.48), residues: 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1892.72 seconds wall clock time: 40 minutes 13.93 seconds (2413.93 seconds total)