Starting phenix.real_space_refine
on Fri Jun 28 09:19:53 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/06_2024/7u6v_26381.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/06_2024/7u6v_26381.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.1
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/06_2024/7u6v_26381.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/06_2024/7u6v_26381.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/06_2024/7u6v_26381.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u6v_26381/06_2024/7u6v_26381.pdb"
}
resolution = 4.1
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
qi {
qm_restraints {
package {
program = *test
}
}
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.000 sd= 0.001
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Anisotropic ADP refinement not supported. Converting 5073 atoms to isotropic.
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 23 5.16 5
C 3168 2.51 5
N 854 2.21 5
O 1051 1.98 5
H 4901 0.53 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A GLU 167": "OE1" <-> "OE2"
Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B ASP 2": "OD1" <-> "OD2"
Residue "B TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B GLU 15": "OE1" <-> "OE2"
Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 10":
Residue "C PHE 10":
Residue "C ASP 17": "OD1" <-> "OD2"
Residue "D PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E ASP 17": "OD1" <-> "OD2"
Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Time to flip residues: 0.02s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib"
Total number of atoms: 9997
Number of models: 1
Model: ""
Number of chains: 14
Chain: "A"
Number of atoms: 4485
Number of conformers: 2
Conformer: "A"
Number of residues, atoms: 282, 4416
Classifications: {'peptide': 282}
Modifications used: {'NH3': 1}
Link IDs: {'PTRANS': 9, 'TRANS': 272}
Chain breaks: 1
Conformer: "B"
Number of residues, atoms: 282, 4416
Classifications: {'peptide': 282}
Modifications used: {'NH3': 1}
Link IDs: {'PTRANS': 9, 'TRANS': 272}
Chain breaks: 1
bond proxies already assigned to first conformer: 4386
Chain: "B"
Number of atoms: 1083
Number of conformers: 2
Conformer: "A"
Number of residues, atoms: 70, 1066
Classifications: {'peptide': 70}
Modifications used: {'NH3': 1}
Link IDs: {'PTRANS': 1, 'TRANS': 68}
Conformer: "B"
Number of residues, atoms: 70, 1066
Classifications: {'peptide': 70}
Modifications used: {'NH3': 1}
Link IDs: {'PTRANS': 1, 'TRANS': 68}
bond proxies already assigned to first conformer: 1058
Chain: "C"
Number of atoms: 1105
Number of conformers: 2
Conformer: "A"
Number of residues, atoms: 70, 1066
Classifications: {'peptide': 70}
Modifications used: {'NH3': 1}
Link IDs: {'PTRANS': 1, 'TRANS': 68}
Conformer: "B"
Number of residues, atoms: 70, 1066
Classifications: {'peptide': 70}
Modifications used: {'NH3': 1}
Link IDs: {'PTRANS': 1, 'TRANS': 68}
bond proxies already assigned to first conformer: 1035
Chain: "D"
Number of atoms: 1054
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 69, 1054
Classifications: {'peptide': 69}
Modifications used: {'NH3': 1}
Link IDs: {'PTRANS': 1, 'TRANS': 67}
Chain breaks: 1
Chain: "E"
Number of atoms: 1079
Number of conformers: 2
Conformer: "A"
Number of residues, atoms: 70, 1067
Classifications: {'peptide': 70}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 1, 'TRANS': 68}
Conformer: "B"
Number of residues, atoms: 70, 1067
Classifications: {'peptide': 70}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 1, 'TRANS': 68}
bond proxies already assigned to first conformer: 1064
Chain: "F"
Number of atoms: 1083
Number of conformers: 2
Conformer: "A"
Number of residues, atoms: 70, 1067
Classifications: {'peptide': 70}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 1, 'TRANS': 68}
Conformer: "B"
Number of residues, atoms: 70, 1068
Classifications: {'peptide': 70}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 1, 'TRANS': 68}
bond proxies already assigned to first conformer: 1061
Chain: "P"
Number of atoms: 85
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 6, 85
Classifications: {'peptide': 6}
Modifications used: {'COO': 1}
Link IDs: {'TRANS': 5}
Chain: "A"
Number of atoms: 8
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 8, 8
Classifications: {'water': 8}
Link IDs: {None: 7}
Chain: "B"
Number of atoms: 2
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 2
Classifications: {'water': 2}
Link IDs: {None: 1}
Chain: "C"
Number of atoms: 5
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 5, 5
Classifications: {'water': 5}
Link IDs: {None: 4}
Chain: "D"
Number of atoms: 4
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 4, 4
Classifications: {'water': 4}
Link IDs: {None: 3}
Chain: "E"
Number of atoms: 1
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 1
Classifications: {'water': 1}
Chain: "F"
Number of atoms: 2
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 2
Classifications: {'water': 2}
Link IDs: {None: 1}
Chain: "P"
Number of atoms: 1
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 1
Classifications: {'water': 1}
Residues with excluded nonbonded symmetry interactions: 8
residue:
pdb=" N ASER A 99 " occ=0.38
... (20 atoms not shown)
pdb=" HG BSER A 99 " occ=0.62
residue:
pdb=" N AARG A 119 " occ=0.59
... (46 atoms not shown)
pdb="HH22BARG A 119 " occ=0.41
residue:
pdb=" N ASER A 278 " occ=0.27
... (20 atoms not shown)
pdb=" HG BSER A 278 " occ=0.73
residue:
pdb=" N AVAL B 65 " occ=0.74
... (30 atoms not shown)
pdb="HG23BVAL B 65 " occ=0.26
residue:
pdb=" N AGLU C 9 " occ=0.47
... (28 atoms not shown)
pdb=" HG3BGLU C 9 " occ=0.53
residue:
pdb=" N ASER C 60 " occ=0.61
... (20 atoms not shown)
pdb=" HG BSER C 60 " occ=0.39
residue:
pdb=" N ASER E 60 " occ=0.38
... (20 atoms not shown)
pdb=" HG BSER E 60 " occ=0.62
residue:
pdb=" N ACYS F 3 " occ=0.68
... (19 atoms not shown)
pdb=" HG BCYS F 3 " occ=0.32
Time building chain proxies: 8.17, per 1000 atoms: 0.82
Number of scatterers: 9997
At special positions: 0
Unit cell: (78.356, 97.3264, 109.698, 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 23 16.00
O 1051 8.00
N 854 7.00
C 3168 6.00
H 4901 1.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=6, symmetry=0
Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 260 " distance=2.03
Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 56 " distance=2.03
Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 56 " distance=2.03
Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 56 " distance=2.03
Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 56 " distance=2.03
Simple disulfide: pdb=" SG ACYS F 3 " - pdb=" SG CYS F 56 " distance=2.04
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: 8.23
Conformation dependent library (CDL) restraints added in 1.7 seconds
1286 Ramachandran restraints generated.
643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 1206
Finding SS restraints...
Secondary structure from input PDB file:
19 helices and 13 sheets defined
28.9% alpha, 24.6% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.82
Creating SS restraints...
Processing helix chain 'A' and resid 9 through 24
Processing helix chain 'A' and resid 93 through 96
Processing helix chain 'A' and resid 113 through 122
Processing helix chain 'A' and resid 131 through 145
Processing helix chain 'A' and resid 151 through 164
Processing helix chain 'A' and resid 165 through 171
Processing helix chain 'A' and resid 171 through 179
removed outlier: 4.366A pdb=" N GLN A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A)
Processing helix chain 'A' and resid 180 through 183
Processing helix chain 'A' and resid 192 through 201
Processing helix chain 'A' and resid 201 through 209
Processing helix chain 'A' and resid 210 through 212
No H-bonds generated for 'chain 'A' and resid 210 through 212'
Processing helix chain 'A' and resid 227 through 235
removed outlier: 4.042A pdb=" N VAL A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A)
Processing helix chain 'A' and resid 278 through 285
removed outlier: 4.079A pdb=" N PHE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A)
Processing helix chain 'A' and resid 290 through 296
removed outlier: 3.600A pdb=" N TYR A 293 " --> pdb=" O GLN A 290 " (cutoff:3.500A)
Processing helix chain 'B' and resid 34 through 44
removed outlier: 3.940A pdb=" N LEU B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A)
removed outlier: 4.727A pdb=" N SER B 41 " --> pdb=" O PRO B 37 " (cutoff:3.500A)
removed outlier: 3.573A pdb=" N LEU B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A)
Processing helix chain 'C' and resid 34 through 45
removed outlier: 4.522A pdb=" N LEU C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A)
Processing helix chain 'D' and resid 35 through 46
removed outlier: 3.695A pdb=" N LEU D 39 " --> pdb=" O LEU D 35 " (cutoff:3.500A)
Processing helix chain 'E' and resid 35 through 45
Processing helix chain 'F' and resid 34 through 46
removed outlier: 4.578A pdb=" N LEU F 38 " --> pdb=" O ASN F 34 " (cutoff:3.500A)
removed outlier: 4.192A pdb=" N GLN F 40 " --> pdb=" O GLN F 36 " (cutoff:3.500A)
removed outlier: 4.155A pdb=" N SER F 41 " --> pdb=" O PRO F 37 " (cutoff:3.500A)
removed outlier: 4.089A pdb=" N ALA F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A)
removed outlier: 3.595A pdb=" N GLY F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A)
Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6
removed outlier: 5.105A pdb=" N LEU A 67 " --> pdb=" O ILE A 54 " (cutoff:3.500A)
removed outlier: 6.334A pdb=" N GLU A 72 " --> pdb=" O VAL A 78 " (cutoff:3.500A)
removed outlier: 6.498A pdb=" N VAL A 78 " --> pdb=" O GLU A 72 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27
Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 130
removed outlier: 3.570A pdb=" N TYR A 189 " --> pdb=" O ILE A 130 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 225
removed outlier: 6.849A pdb=" N GLY A 217 " --> pdb=" O LEU A 275 " (cutoff:3.500A)
removed outlier: 7.777A pdb=" N GLU A 277 " --> pdb=" O GLY A 217 " (cutoff:3.500A)
removed outlier: 7.644A pdb=" N ARG A 219 " --> pdb=" O GLU A 277 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 6
removed outlier: 6.485A pdb=" N ILE B 51 " --> pdb=" O CYS B 3 " (cutoff:3.500A)
removed outlier: 4.428A pdb=" N LYS B 5 " --> pdb=" O VAL B 49 " (cutoff:3.500A)
removed outlier: 6.757A pdb=" N VAL B 49 " --> pdb=" O LYS B 5 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 14
Processing sheet with id=AA7, first strand: chain 'C' and resid 26 through 30
removed outlier: 3.944A pdb=" N PHE C 10 " --> pdb=" O LYS C 22 " (cutoff:3.500A)
removed outlier: 4.078A pdb=" N GLU C 64 " --> pdb=" O LYS C 52 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'D' and resid 4 through 6
removed outlier: 3.667A pdb=" N GLU D 64 " --> pdb=" O LYS D 52 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 14
removed outlier: 3.742A pdb=" N THR D 18 " --> pdb=" O ASN D 14 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 6
Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 13
removed outlier: 4.614A pdb=" N PHE E 10 " --> pdb=" O LYS E 22 " (cutoff:3.500A)
removed outlier: 3.631A pdb=" N VAL E 23 " --> pdb=" O LYS E 26 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'F' and resid 4 through 6
removed outlier: 4.213A pdb=" N ALA F 4 " --> pdb=" O ILE F 51 " (cutoff:3.500A)
Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 13
removed outlier: 4.439A pdb=" N PHE F 10 " --> pdb=" O LYS F 22 " (cutoff:3.500A)
214 hydrogen bonds defined for protein.
575 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: 3.32
Time building geometry restraints manager: 8.65 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.84 - 1.03: 4900
1.03 - 1.23: 25
1.23 - 1.43: 2212
1.43 - 1.62: 2904
1.62 - 1.82: 33
Bond restraints: 10074
Sorted by residual:
bond pdb=" C SER A 37 "
pdb=" N VAL A 38 "
ideal model delta sigma weight residual
1.335 1.325 0.010 1.41e-02 5.03e+03 5.00e-01
bond pdb=" N THR C 20 "
pdb=" CA THR C 20 "
ideal model delta sigma weight residual
1.463 1.454 0.009 1.28e-02 6.10e+03 4.60e-01
bond pdb=" CA VAL C 21 "
pdb=" C VAL C 21 "
ideal model delta sigma weight residual
1.526 1.520 0.006 1.04e-02 9.25e+03 3.69e-01
bond pdb=" CA VAL A 38 "
pdb=" CB VAL A 38 "
ideal model delta sigma weight residual
1.538 1.544 -0.007 1.10e-02 8.26e+03 3.50e-01
bond pdb=" CA GLU C 64 "
pdb=" C GLU C 64 "
ideal model delta sigma weight residual
1.529 1.523 0.006 1.04e-02 9.25e+03 3.43e-01
... (remaining 10069 not shown)
Histogram of bond angle deviations from ideal:
98.59 - 105.67: 50
105.67 - 112.75: 11412
112.75 - 119.83: 2660
119.83 - 126.91: 3909
126.91 - 133.99: 53
Bond angle restraints: 18084
Sorted by residual:
angle pdb=" CB ARG A 156 "
pdb=" CG ARG A 156 "
pdb=" CD ARG A 156 "
ideal model delta sigma weight residual
111.30 117.77 -6.47 2.30e+00 1.89e-01 7.91e+00
angle pdb=" CB ARG A 21 "
pdb=" CG ARG A 21 "
pdb=" CD ARG A 21 "
ideal model delta sigma weight residual
111.30 117.34 -6.04 2.30e+00 1.89e-01 6.89e+00
angle pdb=" N VAL C 21 "
pdb=" CA VAL C 21 "
pdb=" C VAL C 21 "
ideal model delta sigma weight residual
110.05 107.66 2.39 1.09e+00 8.42e-01 4.79e+00
angle pdb=" N VAL A 38 "
pdb=" CA VAL A 38 "
pdb=" C VAL A 38 "
ideal model delta sigma weight residual
110.21 107.80 2.41 1.13e+00 7.83e-01 4.56e+00
angle pdb=" N ARG A 156 "
pdb=" CA ARG A 156 "
pdb=" CB ARG A 156 "
ideal model delta sigma weight residual
110.12 113.12 -3.00 1.47e+00 4.63e-01 4.15e+00
... (remaining 18079 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.97: 4365
17.97 - 35.94: 329
35.94 - 53.91: 73
53.91 - 71.88: 20
71.88 - 89.85: 5
Dihedral angle restraints: 4792
sinusoidal: 2567
harmonic: 2225
Sorted by residual:
dihedral pdb=" CB CYS E 3 "
pdb=" SG CYS E 3 "
pdb=" SG CYS E 56 "
pdb=" CB CYS E 56 "
ideal model delta sinusoidal sigma weight residual
-86.00 -56.34 -29.66 1 1.00e+01 1.00e-02 1.26e+01
dihedral pdb=" CB CYS C 3 "
pdb=" SG CYS C 3 "
pdb=" SG CYS C 56 "
pdb=" CB CYS C 56 "
ideal model delta sinusoidal sigma weight residual
-86.00 -57.64 -28.36 1 1.00e+01 1.00e-02 1.15e+01
dihedral pdb=" CA CYS D 3 "
pdb=" CB CYS D 3 "
pdb=" SG CYS D 3 "
pdb=" SG CYS D 56 "
ideal model delta sinusoidal sigma weight residual
79.00 22.66 56.34 1 2.00e+01 2.50e-03 1.07e+01
... (remaining 4789 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.028: 482
0.028 - 0.056: 202
0.056 - 0.085: 41
0.085 - 0.113: 48
0.113 - 0.141: 14
Chirality restraints: 787
Sorted by residual:
chirality pdb=" CA VAL C 65 "
pdb=" N VAL C 65 "
pdb=" C VAL C 65 "
pdb=" CB VAL C 65 "
both_signs ideal model delta sigma weight residual
False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.98e-01
chirality pdb=" CA ILE A 31 "
pdb=" N ILE A 31 "
pdb=" C ILE A 31 "
pdb=" CB ILE A 31 "
both_signs ideal model delta sigma weight residual
False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01
chirality pdb=" CA ILE D 51 "
pdb=" N ILE D 51 "
pdb=" C ILE D 51 "
pdb=" CB ILE D 51 "
both_signs ideal model delta sigma weight residual
False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01
... (remaining 784 not shown)
Planarity restraints: 1539
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C LEU A 209 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00
pdb=" N PRO A 210 " -0.063 5.00e-02 4.00e+02
pdb=" CA PRO A 210 " 0.019 5.00e-02 4.00e+02
pdb=" CD PRO A 210 " 0.020 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" CD ARG A 156 " -0.010 9.50e-02 1.11e+02 6.87e-03 8.19e-01
pdb=" NE ARG A 156 " 0.008 2.00e-02 2.50e+03
pdb=" CZ ARG A 156 " -0.015 2.00e-02 2.50e+03
pdb=" NH1 ARG A 156 " 0.001 2.00e-02 2.50e+03
pdb=" NH2 ARG A 156 " -0.001 2.00e-02 2.50e+03
pdb="HH11 ARG A 156 " 0.001 2.00e-02 2.50e+03
pdb="HH12 ARG A 156 " 0.003 2.00e-02 2.50e+03
pdb="HH21 ARG A 156 " 0.002 2.00e-02 2.50e+03
pdb="HH22 ARG A 156 " 0.003 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA GLN E 36 " -0.005 2.00e-02 2.50e+03 8.94e-03 7.99e-01
pdb=" C GLN E 36 " 0.015 2.00e-02 2.50e+03
pdb=" O GLN E 36 " -0.006 2.00e-02 2.50e+03
pdb=" N PRO E 37 " -0.005 2.00e-02 2.50e+03
... (remaining 1536 not shown)
Histogram of nonbonded interaction distances:
1.53 - 2.15: 562
2.15 - 2.76: 20224
2.76 - 3.37: 29497
3.37 - 3.99: 37774
3.99 - 4.60: 57473
Nonbonded interactions: 145530
Sorted by model distance:
nonbonded pdb=" OE2 GLU A 72 "
pdb=" H TYR A 77 "
model vdw
1.531 1.850
nonbonded pdb=" H HIS A 66 "
pdb=" OH TYR A 139 "
model vdw
1.550 1.850
nonbonded pdb=" OD1 ASP E 16 "
pdb=" HG1 THR E 18 "
model vdw
1.572 1.850
nonbonded pdb=" O ILE A 54 "
pdb="HH11 ARG A 55 "
model vdw
1.584 1.850
nonbonded pdb=" OD1 ASN C 14 "
pdb=" H GLU C 15 "
model vdw
1.591 1.850
... (remaining 145525 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 'B' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \
resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \
and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \
through 64 or resid 67 through 70))
selection = (chain 'C' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \
resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \
and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \
through 64 or resid 67 through 70))
selection = (chain 'D' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \
resid 42 through 44 or resid 46 through 53 or resid 55 through 59 or resid 62 t \
hrough 64 or resid 67 through 70))
selection = (chain 'E' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \
resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \
and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \
through 64 or resid 67 through 69 or (resid 70 and (name N or name CA or name C \
or name O or name CB or name CG or name OD1 or name OD2 or name H or name HA or \
name HB2 or name HB3))))
selection = (chain 'F' and (resid 1 through 2 or resid 5 through 8 or resid 11 through 40 or \
resid 42 through 44 or resid 46 through 53 or resid 55 through 57 or (resid 59 \
and (name N or name CA or name C or name O or name HA2 or name HA3)) or resid 62 \
through 64 or resid 67 through 69 or (resid 70 and (name N or name CA or name C \
or name O or name CB or name CG or name OD1 or name OD2 or name H or name HA or \
name HB2 or name HB3))))
}
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=0.12 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 2.060
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.100
Construct map_model_manager: 0.190
Extract box with map and model: 5.710
Check model and map are aligned: 0.070
Set scattering table: 0.090
Process input model: 39.200
Find NCS groups from input model: 0.350
Set up NCS constraints: 0.050
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:2.870
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 50.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3344
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 : 0.002 0.016 5173 Z= 0.146
Angle : 0.524 6.467 7012 Z= 0.315
Chirality : 0.041 0.141 787
Planarity : 0.002 0.037 908
Dihedral : 13.786 88.086 1861
Min Nonbonded Distance : 1.948
Molprobity Statistics.
All-atom Clashscore : 13.74
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.68 %
Favored : 95.32 %
Rotamer:
Outliers : 1.57 %
Allowed : 0.52 %
Favored : 97.90 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.16 (0.34), residues: 643
helix: 1.06 (0.47), residues: 159
sheet: -0.12 (0.42), residues: 150
loop : -0.62 (0.33), residues: 334
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP C 33
HIS 0.004 0.001 HIS A 66
PHE 0.009 0.001 PHE A 81
TYR 0.013 0.001 TYR A 139
ARG 0.013 0.001 ARG A 156
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1286 Ramachandran restraints generated.
643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1286 Ramachandran restraints generated.
643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
99 residues out of total 537 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 99
time to evaluate : 0.850
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: A 108 MET cc_start: 0.0664 (tpp) cc_final: 0.0400 (tpp)
outliers start: 0
outliers final: 0
residues processed: 99
average time/residue: 0.3320
time to fit residues: 42.9959
Evaluate side-chains
84 residues out of total 537 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 84
time to evaluate : 0.813
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
run_program(real_space_refine.Program)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
task.run()
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run
log = self.logger)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
log = log)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
self.caller(self.refine_xyz)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
func()
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz
self.minimization_no_ncs()
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs
log = self.log)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
gradients_method = gradients_method)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
rms_angles_limit = rms_angles_limit)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
rms_angles_limit = rms_angles_limit)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
weight = weight)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
states_collector = self.states_accumulator)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
exception_handling_params=lbfgs_exception_handling_params)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
line_search)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
f, g = target_evaluator.compute_functional_and_gradients()
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
compute_gradients=True)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites
flags=flags, sites_cart=sites_cart, site_labels=site_labels)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies
check_bonded_distance_cutoff(sites_frac=sites_frac)
File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff
raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 57.2705 > 50:
distance: 118 - 146: 9.726
distance: 133 - 146: 9.738
distance: 146 - 147: 11.981
distance: 146 - 166: 3.118
distance: 147 - 148: 17.601
distance: 147 - 150: 14.918
distance: 147 - 157: 10.407
distance: 148 - 149: 13.290
distance: 148 - 167: 11.864
distance: 149 - 336: 22.799
distance: 150 - 151: 15.606
distance: 150 - 158: 14.033
distance: 151 - 152: 19.045
distance: 151 - 153: 6.324
distance: 152 - 154: 11.706
distance: 152 - 160: 12.333
distance: 153 - 155: 23.442
distance: 153 - 161: 8.644
distance: 154 - 156: 22.524
distance: 154 - 162: 13.670
distance: 155 - 156: 17.647
distance: 155 - 163: 3.852
distance: 156 - 164: 6.114
distance: 167 - 168: 11.399
distance: 167 - 173: 25.093
distance: 168 - 169: 19.602
distance: 168 - 171: 27.663
distance: 168 - 174: 31.827
distance: 169 - 170: 10.211
distance: 169 - 178: 20.607
distance: 171 - 172: 18.660
distance: 171 - 175: 37.365
distance: 171 - 176: 29.134
distance: 172 - 177: 53.754
distance: 178 - 179: 20.228
distance: 178 - 187: 17.445
distance: 178 - 311: 30.235
distance: 179 - 180: 3.671
distance: 179 - 182: 12.424
distance: 179 - 188: 20.246
distance: 180 - 181: 25.342
distance: 180 - 200: 21.077
distance: 181 - 308: 26.028
distance: 182 - 183: 13.125
distance: 182 - 189: 16.611
distance: 182 - 190: 11.718
distance: 183 - 184: 16.183
distance: 183 - 192: 4.426
distance: 184 - 185: 4.289
distance: 184 - 193: 13.363
distance: 184 - 194: 10.736
distance: 185 - 186: 7.527
distance: 185 - 195: 5.864
distance: 185 - 196: 10.450
distance: 186 - 197: 9.647
distance: 186 - 198: 14.339
distance: 186 - 199: 13.692
distance: 200 - 212: 4.661
distance: 201 - 202: 6.740
distance: 201 - 204: 4.165
distance: 201 - 213: 7.182
distance: 204 - 205: 8.555
distance: 204 - 214: 11.976
distance: 204 - 215: 19.301
distance: 205 - 206: 6.842
distance: 205 - 207: 4.486
distance: 206 - 208: 9.758
distance: 206 - 216: 4.759
distance: 207 - 209: 11.888
distance: 208 - 210: 12.411
distance: 208 - 218: 18.501
distance: 209 - 210: 7.944
distance: 210 - 211: 12.128
distance: 211 - 220: 23.989
distance: 221 - 229: 12.708
distance: 222 - 223: 13.054
distance: 222 - 225: 40.101
distance: 222 - 230: 5.128
distance: 223 - 224: 28.587
distance: 223 - 235: 19.585
distance: 225 - 226: 8.676
distance: 225 - 231: 12.896
distance: 225 - 232: 13.060
distance: 226 - 227: 20.601
distance: 226 - 228: 27.287
distance: 228 - 233: 12.790
distance: 235 - 236: 35.708
distance: 235 - 244: 24.892
distance: 236 - 237: 16.051
distance: 236 - 239: 18.840
distance: 236 - 245: 17.542
distance: 237 - 238: 3.741
distance: 237 - 250: 16.140
distance: 239 - 240: 18.177
distance: 239 - 246: 12.556
distance: 239 - 247: 11.005
distance: 240 - 241: 18.629
distance: 240 - 248: 17.897
distance: 240 - 249: 29.277
distance: 241 - 242: 21.850
distance: 241 - 243: 30.564
distance: 250 - 251: 10.666
distance: 250 - 258: 15.053
distance: 251 - 252: 14.776
distance: 251 - 254: 26.177
distance: 251 - 259: 36.067
distance: 252 - 253: 23.025
distance: 252 - 262: 18.087
distance: 254 - 255: 29.583
distance: 254 - 260: 20.024
distance: 254 - 261: 30.891
distance: 255 - 256: 24.816
distance: 255 - 257: 36.892
distance: 262 - 263: 17.458
distance: 262 - 270: 17.862
distance: 263 - 264: 11.050
distance: 263 - 266: 23.877
distance: 263 - 271: 16.862
distance: 264 - 265: 4.440
distance: 264 - 274: 13.985
distance: 266 - 267: 36.392
distance: 266 - 272: 29.027
distance: 266 - 273: 14.071
distance: 267 - 268: 21.632
distance: 267 - 269: 24.642
distance: 274 - 275: 4.086
distance: 274 - 281: 6.650
distance: 275 - 276: 21.214
distance: 275 - 278: 37.032
distance: 275 - 282: 30.138
distance: 276 - 277: 12.427
distance: 276 - 288: 21.007
distance: 278 - 279: 7.557
distance: 278 - 280: 29.446
distance: 278 - 283: 3.717
distance: 279 - 284: 51.587
distance: 280 - 285: 28.412
distance: 280 - 286: 10.424
distance: 280 - 287: 4.952
distance: 288 - 289: 21.043
distance: 288 - 299: 32.773
distance: 288 - 375: 26.201
distance: 289 - 290: 40.060
distance: 289 - 292: 5.795
distance: 289 - 300: 16.119
distance: 290 - 291: 19.707
distance: 290 - 308: 25.380
distance: 291 - 372: 11.154
distance: 292 - 293: 15.575
distance: 292 - 301: 27.833
distance: 292 - 302: 8.318
distance: 293 - 294: 24.905
distance: 293 - 295: 20.490
distance: 294 - 296: 19.471
distance: 294 - 303: 16.142
distance: 295 - 297: 13.528
distance: 295 - 304: 4.472
distance: 296 - 298: 27.972
distance: 296 - 305: 7.633
distance: 297 - 298: 13.258
distance: 297 - 306: 10.320
distance: 298 - 307: 25.613