Starting phenix.real_space_refine on Fri Dec 8 15:15:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/12_2023/8crb_16807.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/12_2023/8crb_16807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/12_2023/8crb_16807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/12_2023/8crb_16807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/12_2023/8crb_16807.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8crb_16807/12_2023/8crb_16807.pdb" } resolution = 4.6 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 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 13 5.16 5 C 2743 2.51 5 N 738 2.21 5 O 885 1.98 5 H 4286 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 122": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 17": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 193": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 128": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 249": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8665 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3320 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Chain: "B" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3187 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 198} Chain: "C" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2158 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131} Time building chain proxies: 4.44, per 1000 atoms: 0.51 Number of scatterers: 8665 At special positions: 0 Unit cell: (73.1, 81.6, 113.9, 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 13 16.00 O 885 8.00 N 738 7.00 C 2743 6.00 H 4286 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: 7.52 Conformation dependent library (CDL) restraints added in 968.5 milliseconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1064 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 11 sheets defined 21.8% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.666A pdb=" N ASP A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 4.321A pdb=" N SER A 146 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'C' and resid 129 through 158 removed outlier: 3.584A pdb=" N ALA C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 189 through 198 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 236 through 264 Proline residue: C 250 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.546A pdb=" N THR A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.546A pdb=" N THR A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 116 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 137 removed outlier: 3.518A pdb=" N SER A 134 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 168 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.715A pdb=" N ASP B 86 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 39 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 122 removed outlier: 6.162A pdb=" N TYR B 176 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 118 through 122 removed outlier: 6.162A pdb=" N TYR B 176 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 163 198 hydrogen bonds defined for protein. 501 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: 2.99 Time building geometry restraints manager: 7.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 4275 1.11 - 1.29: 732 1.29 - 1.46: 1380 1.46 - 1.64: 2361 1.64 - 1.81: 15 Bond restraints: 8763 Sorted by residual: bond pdb=" N SER A 49 " pdb=" H SER A 49 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N ASN A 74 " pdb=" H ASN A 74 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLY B 69 " pdb=" H GLY B 69 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N ASN B 174 " pdb=" H ASN B 174 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD1 PHE A 160 " pdb=" HD1 PHE A 160 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 8758 not shown) Histogram of bond angle deviations from ideal: 93.61 - 102.04: 27 102.04 - 110.47: 8333 110.47 - 118.89: 4046 118.89 - 127.32: 3340 127.32 - 135.75: 68 Bond angle restraints: 15814 Sorted by residual: angle pdb=" N PRO B 7 " pdb=" CA PRO B 7 " pdb=" C PRO B 7 " ideal model delta sigma weight residual 110.70 121.25 -10.55 1.22e+00 6.72e-01 7.48e+01 angle pdb=" C LYS B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta sigma weight residual 120.50 128.86 -8.36 1.34e+00 5.57e-01 3.89e+01 angle pdb=" CA PHE A 114 " pdb=" CB PHE A 114 " pdb=" CG PHE A 114 " ideal model delta sigma weight residual 113.80 119.77 -5.97 1.00e+00 1.00e+00 3.57e+01 angle pdb=" CA PHE A 27 " pdb=" CB PHE A 27 " pdb=" CG PHE A 27 " ideal model delta sigma weight residual 113.80 119.39 -5.59 1.00e+00 1.00e+00 3.13e+01 angle pdb=" C GLY B 102 " pdb=" N PRO B 103 " pdb=" CA PRO B 103 " ideal model delta sigma weight residual 119.87 125.68 -5.81 1.04e+00 9.25e-01 3.12e+01 ... (remaining 15809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 3740 17.77 - 35.55: 252 35.55 - 53.32: 64 53.32 - 71.10: 17 71.10 - 88.87: 8 Dihedral angle restraints: 4081 sinusoidal: 2157 harmonic: 1924 Sorted by residual: dihedral pdb=" CA PRO B 7 " pdb=" C PRO B 7 " pdb=" N PRO B 8 " pdb=" CA PRO B 8 " ideal model delta harmonic sigma weight residual -180.00 -150.74 -29.26 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA SER B 2 " pdb=" C SER B 2 " pdb=" N VAL B 3 " pdb=" CA VAL B 3 " ideal model delta harmonic sigma weight residual -180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASN C 234 " pdb=" C ASN C 234 " pdb=" N ASN C 235 " pdb=" CA ASN C 235 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 4078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 384 0.083 - 0.165: 226 0.165 - 0.248: 59 0.248 - 0.330: 11 0.330 - 0.412: 2 Chirality restraints: 682 Sorted by residual: chirality pdb=" CA ASN B 174 " pdb=" N ASN B 174 " pdb=" C ASN B 174 " pdb=" CB ASN B 174 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CA TYR A 108 " pdb=" N TYR A 108 " pdb=" C TYR A 108 " pdb=" CB TYR A 108 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA ASN A 218 " pdb=" N ASN A 218 " pdb=" C ASN A 218 " pdb=" CB ASN A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 679 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 37 " 0.307 2.00e-02 2.50e+03 1.40e-01 5.87e+02 pdb=" CG TYR B 37 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 37 " -0.086 2.00e-02 2.50e+03 pdb=" CD2 TYR B 37 " -0.094 2.00e-02 2.50e+03 pdb=" CE1 TYR B 37 " -0.082 2.00e-02 2.50e+03 pdb=" CE2 TYR B 37 " -0.074 2.00e-02 2.50e+03 pdb=" CZ TYR B 37 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 37 " 0.306 2.00e-02 2.50e+03 pdb=" HD1 TYR B 37 " -0.047 2.00e-02 2.50e+03 pdb=" HD2 TYR B 37 " -0.073 2.00e-02 2.50e+03 pdb=" HE1 TYR B 37 " -0.077 2.00e-02 2.50e+03 pdb=" HE2 TYR B 37 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 117 " 0.179 2.00e-02 2.50e+03 1.18e-01 5.53e+02 pdb=" CG TRP A 117 " 0.094 2.00e-02 2.50e+03 pdb=" CD1 TRP A 117 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TRP A 117 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP A 117 " -0.092 2.00e-02 2.50e+03 pdb=" CE2 TRP A 117 " -0.078 2.00e-02 2.50e+03 pdb=" CE3 TRP A 117 " -0.133 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 117 " -0.037 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 117 " -0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP A 117 " 0.078 2.00e-02 2.50e+03 pdb=" HD1 TRP A 117 " 0.101 2.00e-02 2.50e+03 pdb=" HE1 TRP A 117 " -0.153 2.00e-02 2.50e+03 pdb=" HE3 TRP A 117 " -0.188 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 117 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 117 " 0.005 2.00e-02 2.50e+03 pdb=" HH2 TRP A 117 " 0.254 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 36 " -0.175 2.00e-02 2.50e+03 7.09e-02 2.01e+02 pdb=" CG TRP A 36 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A 36 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 36 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP A 36 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 TRP A 36 " 0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP A 36 " 0.069 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 36 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 36 " 0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP A 36 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP A 36 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 TRP A 36 " 0.106 2.00e-02 2.50e+03 pdb=" HE3 TRP A 36 " 0.079 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 36 " -0.076 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 36 " 0.021 2.00e-02 2.50e+03 pdb=" HH2 TRP A 36 " -0.090 2.00e-02 2.50e+03 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 639 2.19 - 2.79: 15350 2.79 - 3.39: 23731 3.39 - 4.00: 29777 4.00 - 4.60: 43550 Nonbonded interactions: 113047 Sorted by model distance: nonbonded pdb=" OD1 ASP A 73 " pdb=" HG SER A 75 " model vdw 1.584 1.850 nonbonded pdb=" H ASP A 73 " pdb=" HG LEU A 79 " model vdw 1.586 2.270 nonbonded pdb=" OD2 ASP C 199 " pdb=" HG SER C 214 " model vdw 1.601 1.850 nonbonded pdb=" OD1 ASP C 173 " pdb=" HG1 THR C 175 " model vdw 1.622 1.850 nonbonded pdb=" HG SER A 54 " pdb=" OD2 ASP C 246 " model vdw 1.625 1.850 ... (remaining 113042 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 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: 0.250 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: 0.130 Extract box with map and model: 1.470 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 32.070 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 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 : 0.013 0.043 4477 Z= 0.858 Angle : 1.985 10.554 6092 Z= 1.299 Chirality : 0.105 0.412 682 Planarity : 0.016 0.162 789 Dihedral : 14.753 88.871 1621 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 1.91 % Allowed : 10.07 % Favored : 88.02 % Rotamer: Outliers : 1.23 % Allowed : 5.33 % Favored : 93.44 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 11.11 % 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: -2.65 (0.30), residues: 576 helix: -1.56 (0.40), residues: 109 sheet: -1.03 (0.52), residues: 98 loop : -2.13 (0.28), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.144 0.030 TRP A 117 HIS 0.013 0.007 HIS A 214 PHE 0.079 0.017 PHE A 114 TYR 0.279 0.029 TYR B 37 ARG 0.004 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 0.742 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 outliers start: 6 outliers final: 3 residues processed: 150 average time/residue: 0.4817 time to fit residues: 85.1825 Evaluate side-chains 101 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1217 time to fit residues: 1.5003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN B 174 ASN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN C 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 4477 Z= 0.370 Angle : 0.905 6.903 6092 Z= 0.507 Chirality : 0.047 0.180 682 Planarity : 0.007 0.078 789 Dihedral : 8.884 33.455 630 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.15 % Favored : 87.33 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: -2.88 (0.31), residues: 576 helix: -0.72 (0.44), residues: 107 sheet: -1.44 (0.40), residues: 148 loop : -2.65 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 47 HIS 0.003 0.002 HIS A 178 PHE 0.020 0.003 PHE A 29 TYR 0.039 0.003 TYR B 37 ARG 0.005 0.001 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.696 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 outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.4132 time to fit residues: 57.4655 Evaluate side-chains 85 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.666 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4477 Z= 0.208 Angle : 0.713 6.109 6092 Z= 0.394 Chirality : 0.045 0.177 682 Planarity : 0.007 0.072 789 Dihedral : 7.461 31.211 630 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.81 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.61 (0.32), residues: 576 helix: 0.23 (0.48), residues: 101 sheet: -1.39 (0.40), residues: 155 loop : -2.68 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 47 HIS 0.003 0.001 HIS A 178 PHE 0.020 0.002 PHE A 68 TYR 0.014 0.002 TYR B 181 ARG 0.003 0.000 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.782 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 outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.3931 time to fit residues: 54.1180 Evaluate side-chains 90 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4477 Z= 0.224 Angle : 0.686 5.658 6092 Z= 0.377 Chirality : 0.044 0.167 682 Planarity : 0.007 0.073 789 Dihedral : 7.200 31.523 630 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.28 % Favored : 88.37 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.70 (0.33), residues: 576 helix: 0.05 (0.47), residues: 107 sheet: -1.66 (0.39), residues: 160 loop : -2.61 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 36 HIS 0.004 0.001 HIS A 178 PHE 0.016 0.002 PHE A 68 TYR 0.019 0.002 TYR B 37 ARG 0.004 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.733 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 outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.4094 time to fit residues: 49.8559 Evaluate side-chains 88 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.710 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4477 Z= 0.267 Angle : 0.698 5.340 6092 Z= 0.385 Chirality : 0.044 0.165 682 Planarity : 0.007 0.070 789 Dihedral : 7.182 32.267 630 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.06 % Favored : 85.76 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.69 (0.33), residues: 576 helix: 0.25 (0.48), residues: 102 sheet: -1.72 (0.41), residues: 147 loop : -2.58 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 47 HIS 0.004 0.002 HIS A 178 PHE 0.020 0.002 PHE A 68 TYR 0.017 0.002 TYR A 60 ARG 0.004 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.741 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 outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.3904 time to fit residues: 45.7304 Evaluate side-chains 83 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4477 Z= 0.258 Angle : 0.685 5.277 6092 Z= 0.377 Chirality : 0.044 0.162 682 Planarity : 0.007 0.068 789 Dihedral : 7.047 32.589 630 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.89 % Favored : 85.94 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.75 (0.33), residues: 576 helix: 0.22 (0.47), residues: 102 sheet: -1.92 (0.41), residues: 146 loop : -2.55 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 47 HIS 0.004 0.002 HIS A 178 PHE 0.026 0.002 PHE B 101 TYR 0.016 0.002 TYR B 37 ARG 0.003 0.000 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.670 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 outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3695 time to fit residues: 44.4837 Evaluate side-chains 80 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.758 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN B 28 ASN C 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4477 Z= 0.175 Angle : 0.620 5.591 6092 Z= 0.336 Chirality : 0.043 0.156 682 Planarity : 0.006 0.072 789 Dihedral : 6.470 32.302 630 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.50 % Favored : 87.15 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.52 (0.33), residues: 576 helix: 0.43 (0.49), residues: 104 sheet: -1.73 (0.45), residues: 133 loop : -2.44 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 36 HIS 0.003 0.001 HIS A 178 PHE 0.014 0.001 PHE A 68 TYR 0.016 0.001 TYR A 60 ARG 0.003 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.671 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 outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3744 time to fit residues: 50.6191 Evaluate side-chains 87 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.636 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 7.9990 chunk 5 optimal weight: 0.0030 chunk 42 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 overall best weight: 4.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4477 Z= 0.301 Angle : 0.705 5.257 6092 Z= 0.388 Chirality : 0.043 0.159 682 Planarity : 0.007 0.071 789 Dihedral : 6.921 32.605 630 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.93 % Favored : 84.72 % Rotamer: Outliers : 0.20 % Allowed : 0.82 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.82 (0.33), residues: 576 helix: 0.20 (0.48), residues: 104 sheet: -1.91 (0.43), residues: 140 loop : -2.64 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 168 HIS 0.004 0.002 HIS A 178 PHE 0.025 0.003 PHE A 68 TYR 0.014 0.002 TYR B 99 ARG 0.009 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.751 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 outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.4056 time to fit residues: 46.8228 Evaluate side-chains 83 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1164 time to fit residues: 1.2128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 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 : 0.003 0.029 4477 Z= 0.164 Angle : 0.604 5.177 6092 Z= 0.324 Chirality : 0.043 0.151 682 Planarity : 0.007 0.073 789 Dihedral : 6.120 30.665 630 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.69 % Allowed : 10.42 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.36 (0.34), residues: 576 helix: 0.81 (0.51), residues: 99 sheet: -1.49 (0.44), residues: 145 loop : -2.46 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 36 HIS 0.003 0.001 HIS A 214 PHE 0.015 0.002 PHE A 29 TYR 0.015 0.001 TYR A 60 ARG 0.016 0.001 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.672 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 outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.4056 time to fit residues: 53.6050 Evaluate side-chains 88 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.6859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4477 Z= 0.209 Angle : 0.622 5.267 6092 Z= 0.336 Chirality : 0.042 0.149 682 Planarity : 0.007 0.071 789 Dihedral : 6.167 30.507 630 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.69 % Allowed : 12.67 % Favored : 86.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.36 (0.34), residues: 576 helix: 0.89 (0.51), residues: 98 sheet: -1.55 (0.45), residues: 137 loop : -2.43 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP A 36 HIS 0.003 0.001 HIS A 214 PHE 0.021 0.002 PHE A 68 TYR 0.012 0.001 TYR B 99 ARG 0.006 0.001 ARG A 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.702 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 outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.3839 time to fit residues: 48.3010 Evaluate side-chains 88 residues out of total 488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.660 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 29 optimal weight: 0.0970 chunk 38 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.125869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.103500 restraints weight = 47832.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.108330 restraints weight = 28406.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.111707 restraints weight = 19040.105| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4477 Z= 0.284 Angle : 0.685 5.158 6092 Z= 0.374 Chirality : 0.043 0.157 682 Planarity : 0.007 0.069 789 Dihedral : 6.662 31.418 630 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.93 % Favored : 84.55 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.77 (0.33), residues: 576 helix: 0.58 (0.50), residues: 98 sheet: -1.92 (0.42), residues: 139 loop : -2.66 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 36 HIS 0.004 0.002 HIS A 178 PHE 0.028 0.003 PHE A 68 TYR 0.016 0.002 TYR A 59 ARG 0.006 0.001 ARG A 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2479.97 seconds wall clock time: 44 minutes 47.22 seconds (2687.22 seconds total)