Starting phenix.real_space_refine (version: 1.21rc1)
on Tue Oct 10 13:19:04 2023 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/10_2023/3j9j_5778.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/10_2023/3j9j_5778.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.275
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/10_2023/3j9j_5778.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/10_2023/3j9j_5778.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/10_2023/3j9j_5778.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9j_5778/10_2023/3j9j_5778.pdb"
}
resolution = 3.275
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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= -0.000 sd= 1.000
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 5
Type Number sf(0) Gaussians
S 80 5.16 5
C 6952 2.51 5
N 1608 2.21 5
O 1804 1.98 5
H 10624 0.53 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
Residue "A TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Time to flip residues: 0.05s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib"
Total number of atoms: 21068
Number of models: 1
Model: ""
Number of chains: 4
Chain: "A"
Number of atoms: 5267
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 315, 5267
Classifications: {'peptide': 315}
Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 308}
Chain: "B"
Number of atoms: 5267
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 315, 5267
Classifications: {'peptide': 315}
Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 308}
Chain: "C"
Number of atoms: 5267
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 315, 5267
Classifications: {'peptide': 315}
Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 308}
Chain: "D"
Number of atoms: 5267
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 315, 5267
Classifications: {'peptide': 315}
Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 308}
Time building chain proxies: 9.40, per 1000 atoms: 0.45
Number of scatterers: 21068
At special positions: 0
Unit cell: (117.913, 117.913, 82.6608, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 5
Type Number sf(0)
S 80 16.00
O 1804 8.00
N 1608 7.00
C 6952 6.00
H 10624 1.00
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: 17.75
Conformation dependent library (CDL) restraints added in 1.8 seconds
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 2408
Finding SS restraints...
Secondary structure from input PDB file:
60 helices and 0 sheets defined
80.3% alpha, 0.0% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.51
Creating SS restraints...
Processing helix chain 'A' and resid 14 through 21
Processing helix chain 'A' and resid 30 through 34
Processing helix chain 'A' and resid 35 through 49
Processing helix chain 'A' and resid 49 through 74
Processing helix chain 'A' and resid 88 through 119
Processing helix chain 'A' and resid 120 through 125
Processing helix chain 'A' and resid 130 through 152
removed outlier: 4.391A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A)
Processing helix chain 'A' and resid 156 through 172
Processing helix chain 'A' and resid 173 through 179
Processing helix chain 'A' and resid 181 through 195
Processing helix chain 'A' and resid 195 through 219
removed outlier: 3.772A pdb=" N VAL A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A)
removed outlier: 3.982A pdb=" N VAL A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A)
Processing helix chain 'A' and resid 226 through 240
removed outlier: 3.851A pdb=" N PHE A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A)
removed outlier: 3.988A pdb=" N THR A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A)
Processing helix chain 'A' and resid 252 through 268
Processing helix chain 'A' and resid 269 through 287
Processing helix chain 'A' and resid 287 through 309
Processing helix chain 'B' and resid 14 through 21
Processing helix chain 'B' and resid 30 through 34
Processing helix chain 'B' and resid 35 through 49
Processing helix chain 'B' and resid 49 through 74
Processing helix chain 'B' and resid 88 through 119
Processing helix chain 'B' and resid 120 through 125
Processing helix chain 'B' and resid 130 through 152
removed outlier: 4.390A pdb=" N PHE B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A)
Processing helix chain 'B' and resid 156 through 172
Processing helix chain 'B' and resid 173 through 179
Processing helix chain 'B' and resid 181 through 195
Processing helix chain 'B' and resid 195 through 219
removed outlier: 3.771A pdb=" N VAL B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A)
removed outlier: 3.981A pdb=" N VAL B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A)
Processing helix chain 'B' and resid 226 through 240
removed outlier: 3.850A pdb=" N PHE B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A)
removed outlier: 3.988A pdb=" N THR B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A)
Processing helix chain 'B' and resid 252 through 268
Processing helix chain 'B' and resid 269 through 287
Processing helix chain 'B' and resid 287 through 309
Processing helix chain 'C' and resid 14 through 21
Processing helix chain 'C' and resid 30 through 34
Processing helix chain 'C' and resid 35 through 49
Processing helix chain 'C' and resid 49 through 74
Processing helix chain 'C' and resid 88 through 119
Processing helix chain 'C' and resid 120 through 125
Processing helix chain 'C' and resid 130 through 152
removed outlier: 4.391A pdb=" N PHE C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A)
Processing helix chain 'C' and resid 156 through 172
Processing helix chain 'C' and resid 173 through 179
Processing helix chain 'C' and resid 181 through 195
Processing helix chain 'C' and resid 195 through 219
removed outlier: 3.771A pdb=" N VAL C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A)
removed outlier: 3.982A pdb=" N VAL C 206 " --> pdb=" O PHE C 202 " (cutoff:3.500A)
Processing helix chain 'C' and resid 226 through 240
removed outlier: 3.852A pdb=" N PHE C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A)
removed outlier: 3.988A pdb=" N THR C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A)
Processing helix chain 'C' and resid 252 through 268
Processing helix chain 'C' and resid 269 through 287
Processing helix chain 'C' and resid 287 through 309
Processing helix chain 'D' and resid 14 through 21
Processing helix chain 'D' and resid 30 through 34
Processing helix chain 'D' and resid 35 through 49
Processing helix chain 'D' and resid 49 through 74
Processing helix chain 'D' and resid 88 through 119
Processing helix chain 'D' and resid 120 through 125
Processing helix chain 'D' and resid 130 through 152
removed outlier: 4.392A pdb=" N PHE D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A)
Processing helix chain 'D' and resid 156 through 172
Processing helix chain 'D' and resid 173 through 179
Processing helix chain 'D' and resid 181 through 195
Processing helix chain 'D' and resid 195 through 219
removed outlier: 3.771A pdb=" N VAL D 203 " --> pdb=" O ARG D 199 " (cutoff:3.500A)
removed outlier: 3.982A pdb=" N VAL D 206 " --> pdb=" O PHE D 202 " (cutoff:3.500A)
Processing helix chain 'D' and resid 226 through 240
removed outlier: 3.851A pdb=" N PHE D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A)
removed outlier: 3.987A pdb=" N THR D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A)
Processing helix chain 'D' and resid 252 through 268
Processing helix chain 'D' and resid 269 through 287
Processing helix chain 'D' and resid 287 through 309
760 hydrogen bonds defined for protein.
2208 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: 7.04
Time building geometry restraints manager: 18.46 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.96 - 1.13: 10600
1.13 - 1.30: 1564
1.30 - 1.47: 4509
1.47 - 1.64: 4515
1.64 - 1.81: 136
Bond restraints: 21324
Sorted by residual:
bond pdb=" CE1 HIS A 30 "
pdb=" HE1 HIS A 30 "
ideal model delta sigma weight residual
0.930 1.093 -0.163 2.00e-02 2.50e+03 6.66e+01
bond pdb=" CE1 HIS C 30 "
pdb=" HE1 HIS C 30 "
ideal model delta sigma weight residual
0.930 1.093 -0.163 2.00e-02 2.50e+03 6.66e+01
bond pdb=" CE1 TYR B 131 "
pdb=" HE1 TYR B 131 "
ideal model delta sigma weight residual
0.930 1.093 -0.163 2.00e-02 2.50e+03 6.62e+01
bond pdb=" CE1 TYR A 131 "
pdb=" HE1 TYR A 131 "
ideal model delta sigma weight residual
0.930 1.093 -0.163 2.00e-02 2.50e+03 6.61e+01
bond pdb=" CZ2 TRP C 294 "
pdb=" HZ2 TRP C 294 "
ideal model delta sigma weight residual
0.930 1.093 -0.163 2.00e-02 2.50e+03 6.61e+01
... (remaining 21319 not shown)
Histogram of bond angle deviations from ideal:
95.69 - 103.29: 120
103.29 - 110.89: 22012
110.89 - 118.48: 5119
118.48 - 126.08: 11102
126.08 - 133.68: 79
Bond angle restraints: 38432
Sorted by residual:
angle pdb=" C ARG B 120 "
pdb=" N PRO B 121 "
pdb=" CA PRO B 121 "
ideal model delta sigma weight residual
119.28 127.05 -7.77 1.10e+00 8.26e-01 4.99e+01
angle pdb=" C ARG D 120 "
pdb=" N PRO D 121 "
pdb=" CA PRO D 121 "
ideal model delta sigma weight residual
119.28 127.04 -7.76 1.10e+00 8.26e-01 4.98e+01
angle pdb=" C ARG A 120 "
pdb=" N PRO A 121 "
pdb=" CA PRO A 121 "
ideal model delta sigma weight residual
119.28 127.01 -7.73 1.10e+00 8.26e-01 4.93e+01
angle pdb=" C ARG C 120 "
pdb=" N PRO C 121 "
pdb=" CA PRO C 121 "
ideal model delta sigma weight residual
119.28 126.97 -7.69 1.10e+00 8.26e-01 4.89e+01
angle pdb=" C LEU D 80 "
pdb=" N PRO D 81 "
pdb=" CA PRO D 81 "
ideal model delta sigma weight residual
120.38 127.29 -6.91 1.03e+00 9.43e-01 4.50e+01
... (remaining 38427 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 13.30: 8265
13.30 - 26.61: 283
26.61 - 39.91: 48
39.91 - 53.21: 30
53.21 - 66.51: 110
Dihedral angle restraints: 8736
sinusoidal: 3948
harmonic: 4788
Sorted by residual:
dihedral pdb=" CB MET D 182 "
pdb=" CG MET D 182 "
pdb=" SD MET D 182 "
pdb=" CE MET D 182 "
ideal model delta sinusoidal sigma weight residual
60.00 99.64 -39.64 3 1.50e+01 4.44e-03 7.03e+00
dihedral pdb=" CB MET C 182 "
pdb=" CG MET C 182 "
pdb=" SD MET C 182 "
pdb=" CE MET C 182 "
ideal model delta sinusoidal sigma weight residual
60.00 99.63 -39.63 3 1.50e+01 4.44e-03 7.03e+00
dihedral pdb=" CB MET A 182 "
pdb=" CG MET A 182 "
pdb=" SD MET A 182 "
pdb=" CE MET A 182 "
ideal model delta sinusoidal sigma weight residual
60.00 99.62 -39.62 3 1.50e+01 4.44e-03 7.03e+00
... (remaining 8733 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.047: 566
0.047 - 0.093: 570
0.093 - 0.140: 323
0.140 - 0.186: 106
0.186 - 0.233: 59
Chirality restraints: 1624
Sorted by residual:
chirality pdb=" CA PHE A 309 "
pdb=" N PHE A 309 "
pdb=" C PHE A 309 "
pdb=" CB PHE A 309 "
both_signs ideal model delta sigma weight residual
False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00
chirality pdb=" CA PHE B 309 "
pdb=" N PHE B 309 "
pdb=" C PHE B 309 "
pdb=" CB PHE B 309 "
both_signs ideal model delta sigma weight residual
False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00
chirality pdb=" CA PHE D 309 "
pdb=" N PHE D 309 "
pdb=" C PHE D 309 "
pdb=" CB PHE D 309 "
both_signs ideal model delta sigma weight residual
False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00
... (remaining 1621 not shown)
Planarity restraints: 2988
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB HIS D 30 " 0.057 2.00e-02 2.50e+03 4.44e-02 4.43e+01
pdb=" CG HIS D 30 " 0.003 2.00e-02 2.50e+03
pdb=" ND1 HIS D 30 " 0.033 2.00e-02 2.50e+03
pdb=" CD2 HIS D 30 " -0.021 2.00e-02 2.50e+03
pdb=" CE1 HIS D 30 " 0.021 2.00e-02 2.50e+03
pdb=" NE2 HIS D 30 " -0.009 2.00e-02 2.50e+03
pdb=" HD1 HIS D 30 " -0.099 2.00e-02 2.50e+03
pdb=" HD2 HIS D 30 " -0.027 2.00e-02 2.50e+03
pdb=" HE1 HIS D 30 " 0.042 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB HIS A 30 " -0.057 2.00e-02 2.50e+03 4.43e-02 4.42e+01
pdb=" CG HIS A 30 " -0.003 2.00e-02 2.50e+03
pdb=" ND1 HIS A 30 " -0.033 2.00e-02 2.50e+03
pdb=" CD2 HIS A 30 " 0.021 2.00e-02 2.50e+03
pdb=" CE1 HIS A 30 " -0.021 2.00e-02 2.50e+03
pdb=" NE2 HIS A 30 " 0.009 2.00e-02 2.50e+03
pdb=" HD1 HIS A 30 " 0.099 2.00e-02 2.50e+03
pdb=" HD2 HIS A 30 " 0.027 2.00e-02 2.50e+03
pdb=" HE1 HIS A 30 " -0.042 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB HIS B 30 " 0.057 2.00e-02 2.50e+03 4.42e-02 4.40e+01
pdb=" CG HIS B 30 " 0.003 2.00e-02 2.50e+03
pdb=" ND1 HIS B 30 " 0.033 2.00e-02 2.50e+03
pdb=" CD2 HIS B 30 " -0.021 2.00e-02 2.50e+03
pdb=" CE1 HIS B 30 " 0.021 2.00e-02 2.50e+03
pdb=" NE2 HIS B 30 " -0.009 2.00e-02 2.50e+03
pdb=" HD1 HIS B 30 " -0.099 2.00e-02 2.50e+03
pdb=" HD2 HIS B 30 " -0.027 2.00e-02 2.50e+03
pdb=" HE1 HIS B 30 " 0.042 2.00e-02 2.50e+03
... (remaining 2985 not shown)
Histogram of nonbonded interaction distances:
1.36 - 2.01: 710
2.01 - 2.66: 28402
2.66 - 3.30: 66390
3.30 - 3.95: 84546
3.95 - 4.60: 128117
Nonbonded interactions: 308165
Sorted by model distance:
nonbonded pdb=" OE1 GLU D 156 "
pdb=" H GLU D 156 "
model vdw
1.360 1.850
nonbonded pdb=" OE1 GLU B 156 "
pdb=" H GLU B 156 "
model vdw
1.360 1.850
nonbonded pdb=" OE1 GLU C 156 "
pdb=" H GLU C 156 "
model vdw
1.360 1.850
nonbonded pdb=" OE1 GLU A 156 "
pdb=" H GLU A 156 "
model vdw
1.360 1.850
nonbonded pdb=" OE1 GLU A 11 "
pdb=" H GLU A 11 "
model vdw
1.522 1.850
... (remaining 308160 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'B'
selection = chain 'C'
selection = chain 'D'
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as 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: 0.940
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: 0.320
Extract box with map and model: 4.890
Check model and map are aligned: 0.350
Set scattering table: 0.210
Process input model: 66.900
Find NCS groups from input model: 0.830
Set up NCS constraints: 0.070
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:2.820
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 77.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5907
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 : 0.015 0.063 10700 Z= 0.947
Angle : 1.078 9.580 14452 Z= 0.764
Chirality : 0.089 0.233 1624
Planarity : 0.010 0.126 1756
Dihedral : 9.349 66.513 3880
Min Nonbonded Distance : 2.266
Molprobity Statistics.
All-atom Clashscore : 2.70
Ramachandran Plot:
Outliers : 2.24 %
Allowed : 3.27 %
Favored : 94.49 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.35 %
Favored : 99.65 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 16.67 %
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: -0.65 (0.22), residues: 1252
helix: -0.21 (0.15), residues: 964
sheet: None (None), residues: 0
loop : -0.67 (0.42), residues: 288
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
524 residues out of total 1152 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 524
time to evaluate : 1.771
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 524
average time/residue: 0.5428
time to fit residues: 389.8171
Evaluate side-chains
295 residues out of total 1152 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 295
time to evaluate : 1.768
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 2.1236
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 124
random chunks:
chunk 104 optimal weight: 3.9990
chunk 93 optimal weight: 0.9990
chunk 52 optimal weight: 0.8980
chunk 32 optimal weight: 0.9990
chunk 63 optimal weight: 0.9980
chunk 50 optimal weight: 0.8980
chunk 97 optimal weight: 1.9990
chunk 37 optimal weight: 0.9980
chunk 59 optimal weight: 0.9990
chunk 72 optimal weight: 1.9990
chunk 112 optimal weight: 0.9980
overall best weight: 0.9580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
D 181 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5925
moved from start: 0.4605
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.035 10700 Z= 0.224
Angle : 0.591 4.623 14452 Z= 0.333
Chirality : 0.036 0.141 1624
Planarity : 0.005 0.068 1756
Dihedral : 4.095 22.159 1408
Min Nonbonded Distance : 2.013
Molprobity Statistics.
All-atom Clashscore : 8.26
Ramachandran Plot:
Outliers : 0.64 %
Allowed : 5.99 %
Favored : 93.37 %
Rotamer:
Outliers : 2.52 %
Allowed : 11.02 %
Favored : 86.46 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 16.67 %
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: 1.29 (0.23), residues: 1252
helix: 1.27 (0.15), residues: 944
sheet: None (None), residues: 0
loop : -0.24 (0.41), residues: 308
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
408 residues out of total 1152 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 29
poor density : 379
time to evaluate : 1.869
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 29
outliers final: 14
residues processed: 387
average time/residue: 0.4614
time to fit residues: 253.2577
Evaluate side-chains
311 residues out of total 1152 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 14
poor density : 297
time to evaluate : 1.626
Switching outliers to nearest non-outliers
outliers start: 14
outliers final: 0
residues processed: 14
average time/residue: 0.3787
time to fit residues: 9.8830
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 124
random chunks:
chunk 62 optimal weight: 5.9990
chunk 34 optimal weight: 0.8980
chunk 93 optimal weight: 6.9990
chunk 76 optimal weight: 4.9990
chunk 31 optimal weight: 6.9990
chunk 112 optimal weight: 3.9990
chunk 121 optimal weight: 2.9990
chunk 100 optimal weight: 6.9990
chunk 111 optimal weight: 0.6980
chunk 38 optimal weight: 7.9990
chunk 90 optimal weight: 2.9990
overall best weight: 2.3186
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 181 GLN
** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 181 GLN
** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6025
moved from start: 0.5346
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.032 10700 Z= 0.269
Angle : 0.571 4.544 14452 Z= 0.322
Chirality : 0.036 0.134 1624
Planarity : 0.004 0.057 1756
Dihedral : 4.126 25.810 1408
Min Nonbonded Distance : 2.058
Molprobity Statistics.
All-atom Clashscore : 9.58
Ramachandran Plot:
Outliers : 0.64 %
Allowed : 6.63 %
Favored : 92.73 %
Rotamer:
Outliers : 2.17 %
Allowed : 14.15 %
Favored : 83.68 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 16.67 %
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 (0.23), residues: 1252
helix: 1.75 (0.16), residues: 944
sheet: None (None), residues: 0
loop : -0.63 (0.37), residues: 308
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
361 residues out of total 1152 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 25
poor density : 336
time to evaluate : 1.763
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 25
outliers final: 18
residues processed: 343
average time/residue: 0.4700
time to fit residues: 230.2657
Evaluate side-chains
324 residues out of total 1152 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 18
poor density : 306
time to evaluate : 1.818
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
outliers start: 18
outliers final: 2
residues processed: 18
average time/residue: 0.2740
time to fit residues: 10.7889
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 124
random chunks:
chunk 111 optimal weight: 0.6980
chunk 84 optimal weight: 5.9990
chunk 58 optimal weight: 2.9990
chunk 12 optimal weight: 4.9990
chunk 53 optimal weight: 4.9990
chunk 75 optimal weight: 3.9990
chunk 113 optimal weight: 0.9990
chunk 119 optimal weight: 2.9990
chunk 59 optimal weight: 0.9990
chunk 107 optimal weight: 2.9990
chunk 32 optimal weight: 3.9990
overall best weight: 1.7388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
B 114 GLN
C 114 GLN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6015
moved from start: 0.6018
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.028 10700 Z= 0.206
Angle : 0.528 4.474 14452 Z= 0.292
Chirality : 0.034 0.135 1624
Planarity : 0.004 0.055 1756
Dihedral : 4.050 26.074 1408
Min Nonbonded Distance : 1.953
Molprobity Statistics.
All-atom Clashscore : 8.21
Ramachandran Plot:
Outliers : 0.64 %
Allowed : 6.47 %
Favored : 92.89 %
Rotamer:
Outliers : 1.22 %
Allowed : 15.97 %
Favored : 82.81 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 16.67 %
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: 1.99 (0.23), residues: 1252
helix: 1.97 (0.16), residues: 948
sheet: None (None), residues: 0
loop : -0.76 (0.35), residues: 304
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
347 residues out of total 1152 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 14
poor density : 333
time to evaluate : 1.688
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 14
outliers final: 4
residues processed: 334
average time/residue: 0.4490
time to fit residues: 220.0091
Evaluate side-chains
300 residues out of total 1152 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 296
time to evaluate : 1.655
Switching outliers to nearest non-outliers
outliers start: 4
outliers final: 0
residues processed: 4
average time/residue: 0.2830
time to fit residues: 3.8401
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 124
random chunks:
chunk 99 optimal weight: 1.9990
chunk 68 optimal weight: 5.9990
chunk 1 optimal weight: 2.9990
chunk 89 optimal weight: 1.9990
chunk 49 optimal weight: 2.9990
chunk 102 optimal weight: 4.9990
chunk 82 optimal weight: 1.9990
chunk 0 optimal weight: 5.9990
chunk 61 optimal weight: 4.9990
chunk 107 optimal weight: 4.9990
chunk 30 optimal weight: 4.9990
overall best weight: 2.3990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
B 114 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6067
moved from start: 0.6430
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.050 10700 Z= 0.272
Angle : 0.549 5.044 14452 Z= 0.309
Chirality : 0.035 0.131 1624
Planarity : 0.004 0.054 1756
Dihedral : 4.068 26.838 1408
Min Nonbonded Distance : 1.919
Molprobity Statistics.
All-atom Clashscore : 11.48
Ramachandran Plot:
Outliers : 0.56 %
Allowed : 7.43 %
Favored : 92.01 %
Rotamer:
Outliers : 1.04 %
Allowed : 19.62 %
Favored : 79.34 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 16.67 %
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: 1.80 (0.23), residues: 1252
helix: 1.96 (0.16), residues: 968
sheet: None (None), residues: 0
loop : -1.55 (0.35), residues: 284
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
312 residues out of total 1152 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 12
poor density : 300
time to evaluate : 1.825
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 12
outliers final: 7
residues processed: 301
average time/residue: 0.4165
time to fit residues: 184.9408
Evaluate side-chains
295 residues out of total 1152 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 7
poor density : 288
time to evaluate : 1.718
Switching outliers to nearest non-outliers
outliers start: 7
outliers final: 0
residues processed: 7
average time/residue: 0.2548
time to fit residues: 5.2784
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 124
random chunks:
chunk 40 optimal weight: 6.9990
chunk 107 optimal weight: 4.9990
chunk 23 optimal weight: 1.9990
chunk 70 optimal weight: 8.9990
chunk 29 optimal weight: 1.9990
chunk 119 optimal weight: 1.9990
chunk 99 optimal weight: 3.9990
chunk 55 optimal weight: 5.9990
chunk 9 optimal weight: 1.9990
chunk 39 optimal weight: 1.9990
chunk 62 optimal weight: 5.9990
overall best weight: 1.9990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
D 118 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6061
moved from start: 0.6701
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.032 10700 Z= 0.225
Angle : 0.526 4.152 14452 Z= 0.293
Chirality : 0.035 0.139 1624
Planarity : 0.004 0.054 1756
Dihedral : 4.064 27.318 1408
Min Nonbonded Distance : 1.946
Molprobity Statistics.
All-atom Clashscore : 10.96
Ramachandran Plot:
Outliers : 0.56 %
Allowed : 7.19 %
Favored : 92.25 %
Rotamer:
Outliers : 1.82 %
Allowed : 18.23 %
Favored : 79.95 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 16.67 %
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: 1.97 (0.24), residues: 1252
helix: 2.09 (0.16), residues: 968
sheet: None (None), residues: 0
loop : -1.57 (0.35), residues: 284
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
323 residues out of total 1152 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 21
poor density : 302
time to evaluate : 1.674
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 21
outliers final: 9
residues processed: 307
average time/residue: 0.4523
time to fit residues: 198.8501
Evaluate side-chains
294 residues out of total 1152 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 9
poor density : 285
time to evaluate : 1.627
Switching outliers to nearest non-outliers
outliers start: 9
outliers final: 0
residues processed: 9
average time/residue: 0.2596
time to fit residues: 6.0570
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 124
random chunks:
chunk 115 optimal weight: 2.9990
chunk 13 optimal weight: 3.9990
chunk 68 optimal weight: 5.9990
chunk 87 optimal weight: 1.9990
chunk 67 optimal weight: 0.9990
chunk 100 optimal weight: 0.6980
chunk 66 optimal weight: 1.9990
chunk 119 optimal weight: 2.9990
chunk 74 optimal weight: 1.9990
chunk 72 optimal weight: 3.9990
chunk 55 optimal weight: 4.9990
overall best weight: 1.5388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
B 114 GLN
C 114 GLN
** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6058
moved from start: 0.7012
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.042 10700 Z= 0.199
Angle : 0.546 6.073 14452 Z= 0.297
Chirality : 0.035 0.170 1624
Planarity : 0.004 0.054 1756
Dihedral : 3.994 26.810 1408
Min Nonbonded Distance : 1.933
Molprobity Statistics.
All-atom Clashscore : 11.62
Ramachandran Plot:
Outliers : 0.56 %
Allowed : 7.03 %
Favored : 92.41 %
Rotamer:
Outliers : 1.30 %
Allowed : 19.79 %
Favored : 78.91 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 16.67 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.18 (0.24), residues: 1252
helix: 2.26 (0.16), residues: 968
sheet: None (None), residues: 0
loop : -1.55 (0.35), residues: 284
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2504 Ramachandran restraints generated.
1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
308 residues out of total 1152 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 15
poor density : 293
time to evaluate : 1.566
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 15
outliers final: 7
residues processed: 295
average time/residue: 0.4266
time to fit residues: 185.7025
Evaluate side-chains
293 residues out of total 1152 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 7
poor density : 286
time to evaluate : 1.861
Switching outliers to nearest non-outliers
outliers start: 7
outliers final: 0
residues processed: 7
average time/residue: 0.2474
time to fit residues: 5.1824
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 124
random chunks:
chunk 73 optimal weight: 3.9990
chunk 47 optimal weight: 4.9990
chunk 71 optimal weight: 5.9990
chunk 36 optimal weight: 3.9990
chunk 23 optimal weight: 0.9980
chunk 75 optimal weight: 2.9990
chunk 81 optimal weight: 2.9990
chunk 59 optimal weight: 0.8980
chunk 11 optimal weight: 3.9990
chunk 93 optimal weight: 6.9990
chunk 108 optimal weight: 4.9990
overall best weight: 2.3786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'.
Dumping stdin to file 'reduce_failure.pdb'.
Return code: -15
Dumping stderr: