Starting phenix.real_space_refine on Mon Mar 11 13:12:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr2_30445/03_2024/7cr2_30445_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr2_30445/03_2024/7cr2_30445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr2_30445/03_2024/7cr2_30445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr2_30445/03_2024/7cr2_30445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr2_30445/03_2024/7cr2_30445_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr2_30445/03_2024/7cr2_30445_trim_updated.pdb" } resolution = 3.2 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= 0.003 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 36 5.16 5 C 5500 2.51 5 N 1392 2.21 5 O 1344 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 322": "OE1" <-> "OE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 322": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8276 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Chain: "B" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Chain: "C" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Chain: "D" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2047 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'FBX': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'FBX': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'FBX': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'FBX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.43, per 1000 atoms: 0.54 Number of scatterers: 8276 At special positions: 0 Unit cell: (130.806, 130.806, 75.036, 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 36 16.00 F 4 9.00 O 1344 8.00 N 1392 7.00 C 5500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.4 seconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 0 sheets defined 79.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 91 through 114 removed outlier: 3.690A pdb=" N VAL A 99 " --> pdb=" O HIS A 96 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 103 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 105 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 109 " --> pdb=" O CYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 150 removed outlier: 3.827A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N CYS A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 165 removed outlier: 4.485A pdb=" N ALA A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ARG A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 253 Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 288 through 304 removed outlier: 3.657A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 329 Processing helix chain 'B' and resid 72 through 84 Processing helix chain 'B' and resid 91 through 114 removed outlier: 3.689A pdb=" N VAL B 99 " --> pdb=" O HIS B 96 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 103 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 105 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 109 " --> pdb=" O CYS B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 150 removed outlier: 3.827A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N CYS B 150 " --> pdb=" O TRP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 removed outlier: 4.486A pdb=" N ALA B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ARG B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 196 through 211 Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 229 through 253 Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 288 through 304 removed outlier: 3.657A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 329 Processing helix chain 'C' and resid 72 through 84 Processing helix chain 'C' and resid 91 through 114 removed outlier: 3.689A pdb=" N VAL C 99 " --> pdb=" O HIS C 96 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 103 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 105 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 109 " --> pdb=" O CYS C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 150 removed outlier: 3.827A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY C 149 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N CYS C 150 " --> pdb=" O TRP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 165 removed outlier: 4.486A pdb=" N ALA C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ARG C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 182 Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 229 through 253 Processing helix chain 'C' and resid 264 through 275 Processing helix chain 'C' and resid 288 through 304 removed outlier: 3.657A pdb=" N THR C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 329 Processing helix chain 'D' and resid 72 through 84 Processing helix chain 'D' and resid 91 through 114 removed outlier: 3.689A pdb=" N VAL D 99 " --> pdb=" O HIS D 96 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 103 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 105 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 109 " --> pdb=" O CYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 150 removed outlier: 3.827A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N CYS D 150 " --> pdb=" O TRP D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 165 removed outlier: 4.486A pdb=" N ALA D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 182 Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 216 through 227 Processing helix chain 'D' and resid 229 through 253 Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 288 through 304 removed outlier: 3.657A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 329 580 hydrogen bonds defined for protein. 1536 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: 2.03 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1204 1.30 - 1.43: 2635 1.43 - 1.56: 4617 1.56 - 1.68: 0 1.68 - 1.81: 48 Bond restraints: 8504 Sorted by residual: bond pdb=" C17 FBX A 801 " pdb=" C19 FBX A 801 " ideal model delta sigma weight residual 1.381 1.519 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C17 FBX D 801 " pdb=" C19 FBX D 801 " ideal model delta sigma weight residual 1.381 1.519 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C17 FBX C 801 " pdb=" C19 FBX C 801 " ideal model delta sigma weight residual 1.381 1.519 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C17 FBX B 801 " pdb=" C19 FBX B 801 " ideal model delta sigma weight residual 1.381 1.519 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" C13 FBX A 801 " pdb=" C14 FBX A 801 " ideal model delta sigma weight residual 1.385 1.510 -0.125 2.00e-02 2.50e+03 3.91e+01 ... (remaining 8499 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.14: 153 107.14 - 113.85: 4807 113.85 - 120.56: 3848 120.56 - 127.27: 2600 127.27 - 133.98: 100 Bond angle restraints: 11508 Sorted by residual: angle pdb=" CA TRP A 157 " pdb=" CB TRP A 157 " pdb=" CG TRP A 157 " ideal model delta sigma weight residual 113.60 118.68 -5.08 1.90e+00 2.77e-01 7.15e+00 angle pdb=" CA TRP B 157 " pdb=" CB TRP B 157 " pdb=" CG TRP B 157 " ideal model delta sigma weight residual 113.60 118.67 -5.07 1.90e+00 2.77e-01 7.11e+00 angle pdb=" CA TRP D 157 " pdb=" CB TRP D 157 " pdb=" CG TRP D 157 " ideal model delta sigma weight residual 113.60 118.67 -5.07 1.90e+00 2.77e-01 7.11e+00 angle pdb=" CA TRP C 157 " pdb=" CB TRP C 157 " pdb=" CG TRP C 157 " ideal model delta sigma weight residual 113.60 118.67 -5.07 1.90e+00 2.77e-01 7.11e+00 angle pdb=" N5 FBX D 801 " pdb=" C20 FBX D 801 " pdb=" O2 FBX D 801 " ideal model delta sigma weight residual 110.60 118.59 -7.99 3.00e+00 1.11e-01 7.09e+00 ... (remaining 11503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.33: 4656 32.33 - 64.65: 132 64.65 - 96.98: 16 96.98 - 129.30: 0 129.30 - 161.63: 4 Dihedral angle restraints: 4808 sinusoidal: 1900 harmonic: 2908 Sorted by residual: dihedral pdb=" C8 FBX A 801 " pdb=" C7 FBX A 801 " pdb=" N4 FBX A 801 " pdb=" C9 FBX A 801 " ideal model delta sinusoidal sigma weight residual -75.46 86.17 -161.63 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C8 FBX C 801 " pdb=" C7 FBX C 801 " pdb=" N4 FBX C 801 " pdb=" C9 FBX C 801 " ideal model delta sinusoidal sigma weight residual -75.46 86.13 -161.59 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C8 FBX B 801 " pdb=" C7 FBX B 801 " pdb=" N4 FBX B 801 " pdb=" C9 FBX B 801 " ideal model delta sinusoidal sigma weight residual -75.46 86.13 -161.59 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 4805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 561 0.030 - 0.060: 452 0.060 - 0.091: 163 0.091 - 0.121: 67 0.121 - 0.151: 9 Chirality restraints: 1252 Sorted by residual: chirality pdb=" CA PRO B 308 " pdb=" N PRO B 308 " pdb=" C PRO B 308 " pdb=" CB PRO B 308 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA PRO D 308 " pdb=" N PRO D 308 " pdb=" C PRO D 308 " pdb=" CB PRO D 308 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA PRO C 308 " pdb=" N PRO C 308 " pdb=" C PRO C 308 " pdb=" CB PRO C 308 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 1249 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 127 " -0.016 2.00e-02 2.50e+03 1.13e-02 2.54e+00 pdb=" CG TYR A 127 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 127 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 127 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 127 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 127 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 127 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 127 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 127 " 0.016 2.00e-02 2.50e+03 1.12e-02 2.49e+00 pdb=" CG TYR D 127 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR D 127 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR D 127 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 127 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 127 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR D 127 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 127 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 127 " 0.016 2.00e-02 2.50e+03 1.12e-02 2.49e+00 pdb=" CG TYR C 127 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR C 127 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 127 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 127 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 127 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 127 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 127 " 0.002 2.00e-02 2.50e+03 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 112 2.62 - 3.19: 8574 3.19 - 3.76: 12553 3.76 - 4.33: 17887 4.33 - 4.90: 27833 Nonbonded interactions: 66959 Sorted by model distance: nonbonded pdb=" O LEU C 107 " pdb=" OG SER C 110 " model vdw 2.052 2.440 nonbonded pdb=" O LEU B 107 " pdb=" OG SER B 110 " model vdw 2.052 2.440 nonbonded pdb=" O LEU D 107 " pdb=" OG SER D 110 " model vdw 2.052 2.440 nonbonded pdb=" O LEU A 107 " pdb=" OG SER A 110 " model vdw 2.053 2.440 nonbonded pdb=" O LEU C 176 " pdb=" OG SER C 179 " model vdw 2.255 2.440 ... (remaining 66954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.380 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.090 Find NCS groups from input model: 0.480 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 : 0.014 0.138 8504 Z= 0.880 Angle : 0.977 8.909 11508 Z= 0.510 Chirality : 0.048 0.151 1252 Planarity : 0.004 0.020 1392 Dihedral : 16.204 161.628 2952 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 39.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.48 % Allowed : 9.17 % Favored : 90.36 % 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: -2.81 (0.23), residues: 988 helix: -1.64 (0.15), residues: 776 sheet: None (None), residues: 0 loop : -1.88 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 157 HIS 0.004 0.002 HIS C 96 PHE 0.022 0.003 PHE A 297 TYR 0.027 0.003 TYR A 127 ARG 0.008 0.001 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.1887 (ttp) cc_final: 0.1496 (tmm) REVERT: B 174 MET cc_start: 0.1883 (ttp) cc_final: 0.1501 (tmm) REVERT: C 174 MET cc_start: 0.1872 (ttp) cc_final: 0.1495 (tmm) REVERT: D 174 MET cc_start: 0.1874 (ttp) cc_final: 0.1496 (tmm) outliers start: 4 outliers final: 0 residues processed: 148 average time/residue: 0.3486 time to fit residues: 62.8434 Evaluate side-chains 120 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 204 GLN A 228 HIS B 78 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS C 78 GLN ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 HIS D 78 GLN D 204 GLN D 228 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8504 Z= 0.249 Angle : 0.574 5.926 11508 Z= 0.304 Chirality : 0.039 0.121 1252 Planarity : 0.004 0.039 1392 Dihedral : 11.272 158.895 1140 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.67 % Allowed : 16.90 % Favored : 81.43 % 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: -0.07 (0.27), residues: 988 helix: 0.41 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -1.69 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 157 HIS 0.002 0.001 HIS D 324 PHE 0.015 0.002 PHE D 316 TYR 0.023 0.002 TYR D 82 ARG 0.003 0.001 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 0.958 Fit side-chains outliers start: 14 outliers final: 14 residues processed: 157 average time/residue: 0.3031 time to fit residues: 59.2635 Evaluate side-chains 131 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.2980 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 96 HIS B 83 ASN B 204 GLN C 83 ASN C 204 GLN D 83 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8504 Z= 0.174 Angle : 0.510 6.993 11508 Z= 0.268 Chirality : 0.036 0.115 1252 Planarity : 0.003 0.038 1392 Dihedral : 11.050 158.227 1140 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.86 % Allowed : 17.98 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 988 helix: 1.29 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -1.89 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 157 HIS 0.002 0.001 HIS C 328 PHE 0.018 0.001 PHE A 316 TYR 0.016 0.001 TYR B 141 ARG 0.004 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 0.911 Fit side-chains REVERT: A 86 GLU cc_start: 0.6793 (tp30) cc_final: 0.6541 (tp30) REVERT: A 327 LYS cc_start: 0.7472 (ttpp) cc_final: 0.6997 (mttt) REVERT: B 86 GLU cc_start: 0.6887 (tp30) cc_final: 0.6649 (tp30) REVERT: B 162 LYS cc_start: 0.5877 (pttt) cc_final: 0.5610 (pttp) REVERT: B 327 LYS cc_start: 0.7471 (ttpp) cc_final: 0.6991 (mttt) REVERT: C 86 GLU cc_start: 0.6886 (tp30) cc_final: 0.6655 (tp30) REVERT: C 327 LYS cc_start: 0.7467 (ttpp) cc_final: 0.6988 (mttt) REVERT: D 86 GLU cc_start: 0.6891 (tp30) cc_final: 0.6658 (tp30) REVERT: D 327 LYS cc_start: 0.7469 (ttpp) cc_final: 0.6993 (mttt) outliers start: 24 outliers final: 12 residues processed: 149 average time/residue: 0.2742 time to fit residues: 51.8738 Evaluate side-chains 130 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 0.0010 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS B 96 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8504 Z= 0.236 Angle : 0.520 5.322 11508 Z= 0.277 Chirality : 0.038 0.137 1252 Planarity : 0.003 0.025 1392 Dihedral : 11.011 156.865 1140 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.74 % Allowed : 20.36 % Favored : 76.90 % 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: 1.30 (0.27), residues: 988 helix: 1.49 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -2.08 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 157 HIS 0.002 0.001 HIS A 260 PHE 0.013 0.002 PHE B 297 TYR 0.013 0.001 TYR A 74 ARG 0.004 0.000 ARG D 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 0.956 Fit side-chains REVERT: B 162 LYS cc_start: 0.5892 (pttt) cc_final: 0.5645 (pttp) outliers start: 23 outliers final: 19 residues processed: 146 average time/residue: 0.2748 time to fit residues: 51.1607 Evaluate side-chains 141 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0060 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS B 96 HIS C 96 HIS D 96 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8504 Z= 0.156 Angle : 0.475 5.588 11508 Z= 0.250 Chirality : 0.036 0.115 1252 Planarity : 0.003 0.034 1392 Dihedral : 10.890 156.234 1140 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.02 % Allowed : 21.19 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.28), residues: 988 helix: 1.89 (0.19), residues: 812 sheet: None (None), residues: 0 loop : -2.06 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 157 HIS 0.002 0.001 HIS A 324 PHE 0.010 0.001 PHE A 240 TYR 0.012 0.001 TYR B 141 ARG 0.005 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.872 Fit side-chains REVERT: B 174 MET cc_start: 0.1991 (tmm) cc_final: 0.0840 (ttp) REVERT: C 174 MET cc_start: 0.1985 (tmm) cc_final: 0.0835 (ttp) REVERT: D 174 MET cc_start: 0.1986 (tmm) cc_final: 0.0843 (ttp) outliers start: 17 outliers final: 16 residues processed: 146 average time/residue: 0.2769 time to fit residues: 51.2749 Evaluate side-chains 141 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS B 96 HIS C 96 HIS D 96 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8504 Z= 0.169 Angle : 0.490 8.829 11508 Z= 0.254 Chirality : 0.036 0.115 1252 Planarity : 0.003 0.033 1392 Dihedral : 10.842 155.873 1140 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.26 % Allowed : 21.90 % Favored : 75.83 % 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: 2.08 (0.28), residues: 988 helix: 2.08 (0.19), residues: 812 sheet: None (None), residues: 0 loop : -2.09 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 146 HIS 0.002 0.001 HIS A 324 PHE 0.014 0.001 PHE C 137 TYR 0.010 0.001 TYR A 141 ARG 0.006 0.000 ARG D 207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 0.963 Fit side-chains REVERT: A 207 ARG cc_start: 0.6846 (tpp80) cc_final: 0.6491 (mpt180) outliers start: 19 outliers final: 15 residues processed: 158 average time/residue: 0.2833 time to fit residues: 56.7933 Evaluate side-chains 142 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 0.0270 chunk 54 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 321 GLN B 96 HIS B 321 GLN C 96 HIS C 321 GLN D 96 HIS D 321 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8504 Z= 0.162 Angle : 0.499 8.736 11508 Z= 0.254 Chirality : 0.036 0.162 1252 Planarity : 0.003 0.024 1392 Dihedral : 10.802 155.442 1140 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.26 % Allowed : 23.10 % Favored : 74.64 % 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: 2.08 (0.28), residues: 988 helix: 2.17 (0.19), residues: 816 sheet: None (None), residues: 0 loop : -2.72 (0.40), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 146 HIS 0.002 0.001 HIS A 324 PHE 0.010 0.001 PHE A 240 TYR 0.012 0.001 TYR B 141 ARG 0.005 0.000 ARG D 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 0.939 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 149 average time/residue: 0.2836 time to fit residues: 53.6978 Evaluate side-chains 140 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 321 GLN B 96 HIS B 321 GLN C 96 HIS C 321 GLN D 96 HIS D 321 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8504 Z= 0.203 Angle : 0.528 7.710 11508 Z= 0.269 Chirality : 0.038 0.147 1252 Planarity : 0.003 0.023 1392 Dihedral : 10.833 154.573 1140 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.38 % Allowed : 23.45 % Favored : 74.17 % 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: 2.03 (0.28), residues: 988 helix: 2.13 (0.19), residues: 820 sheet: None (None), residues: 0 loop : -2.84 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 146 HIS 0.002 0.001 HIS A 324 PHE 0.025 0.001 PHE A 137 TYR 0.010 0.001 TYR D 141 ARG 0.006 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 0.912 Fit side-chains REVERT: A 210 ARG cc_start: 0.7695 (tmm160) cc_final: 0.7455 (ttp80) REVERT: B 210 ARG cc_start: 0.7652 (tmm160) cc_final: 0.7367 (ttp80) REVERT: D 210 ARG cc_start: 0.7680 (tmm160) cc_final: 0.7357 (ttp80) outliers start: 20 outliers final: 16 residues processed: 144 average time/residue: 0.2727 time to fit residues: 50.0040 Evaluate side-chains 137 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 94 optimal weight: 0.0970 chunk 57 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 321 GLN B 96 HIS B 321 GLN C 96 HIS C 321 GLN D 96 HIS D 321 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8504 Z= 0.157 Angle : 0.509 6.968 11508 Z= 0.256 Chirality : 0.036 0.157 1252 Planarity : 0.003 0.024 1392 Dihedral : 10.776 154.310 1140 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.43 % Allowed : 24.05 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.28), residues: 988 helix: 2.20 (0.19), residues: 816 sheet: None (None), residues: 0 loop : -2.75 (0.39), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 146 HIS 0.002 0.001 HIS A 324 PHE 0.023 0.001 PHE A 137 TYR 0.011 0.001 TYR D 141 ARG 0.004 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 0.831 Fit side-chains REVERT: A 210 ARG cc_start: 0.7684 (tmm160) cc_final: 0.7478 (ttp80) REVERT: A 211 MET cc_start: 0.5778 (ttp) cc_final: 0.5521 (ttt) REVERT: B 210 ARG cc_start: 0.7661 (tmm160) cc_final: 0.7394 (ttp80) REVERT: C 210 ARG cc_start: 0.7696 (tmm160) cc_final: 0.7384 (ttp80) outliers start: 12 outliers final: 12 residues processed: 144 average time/residue: 0.2606 time to fit residues: 48.1155 Evaluate side-chains 147 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 61 optimal weight: 0.0000 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 321 GLN B 96 HIS B 321 GLN C 96 HIS C 321 GLN D 96 HIS D 321 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8504 Z= 0.173 Angle : 0.564 10.359 11508 Z= 0.275 Chirality : 0.038 0.161 1252 Planarity : 0.003 0.023 1392 Dihedral : 10.771 153.981 1140 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.55 % Allowed : 24.76 % Favored : 73.69 % 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: 2.09 (0.28), residues: 988 helix: 2.18 (0.19), residues: 816 sheet: None (None), residues: 0 loop : -2.75 (0.38), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 146 HIS 0.002 0.001 HIS A 324 PHE 0.012 0.001 PHE A 137 TYR 0.010 0.001 TYR D 141 ARG 0.004 0.000 ARG D 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 0.899 Fit side-chains REVERT: A 87 ARG cc_start: 0.7760 (ppt170) cc_final: 0.6976 (tpp80) REVERT: A 210 ARG cc_start: 0.7648 (tmm160) cc_final: 0.7413 (ttp80) REVERT: B 210 ARG cc_start: 0.7661 (tmm160) cc_final: 0.7414 (ttp80) REVERT: C 210 ARG cc_start: 0.7714 (tmm160) cc_final: 0.7315 (ttp80) REVERT: D 210 ARG cc_start: 0.7715 (tmm160) cc_final: 0.7320 (ttp80) outliers start: 13 outliers final: 13 residues processed: 145 average time/residue: 0.2593 time to fit residues: 48.2795 Evaluate side-chains 143 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.0040 chunk 22 optimal weight: 0.3980 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 321 GLN B 96 HIS B 321 GLN C 96 HIS C 321 GLN D 96 HIS D 321 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.203251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134614 restraints weight = 10227.357| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.92 r_work: 0.3441 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8504 Z= 0.171 Angle : 0.592 9.888 11508 Z= 0.289 Chirality : 0.038 0.161 1252 Planarity : 0.003 0.024 1392 Dihedral : 10.742 153.997 1140 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.90 % Allowed : 25.12 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.28), residues: 988 helix: 2.23 (0.19), residues: 816 sheet: None (None), residues: 0 loop : -2.79 (0.37), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 146 HIS 0.002 0.001 HIS B 324 PHE 0.011 0.001 PHE A 137 TYR 0.014 0.001 TYR D 141 ARG 0.004 0.000 ARG D 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.20 seconds wall clock time: 37 minutes 49.11 seconds (2269.11 seconds total)