Starting phenix.real_space_refine on Wed Mar 4 12:11:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oxr_13104/03_2026/7oxr_13104.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oxr_13104/03_2026/7oxr_13104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7oxr_13104/03_2026/7oxr_13104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oxr_13104/03_2026/7oxr_13104.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oxr_13104/03_2026/7oxr_13104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oxr_13104/03_2026/7oxr_13104.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 8670 2.51 5 N 2270 2.21 5 O 2670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13670 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "B" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "C" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "D" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "E" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "F" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "G" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "I" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "J" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Time building chain proxies: 2.93, per 1000 atoms: 0.21 Number of scatterers: 13670 At special positions: 0 Unit cell: (150.592, 157.248, 49.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2670 8.00 N 2270 7.00 C 8670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 113 " - pdb=" SG CYS H 159 " distance=2.03 Simple disulfide: pdb=" SG CYS I 113 " - pdb=" SG CYS I 159 " distance=2.03 Simple disulfide: pdb=" SG CYS J 113 " - pdb=" SG CYS J 159 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.75 Conformation dependent library (CDL) restraints added in 507.2 milliseconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 12.9% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 167 through 175 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 167 through 175 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 167 through 175 Processing helix chain 'D' and resid 177 through 186 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 167 through 175 Processing helix chain 'E' and resid 177 through 186 Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 167 through 175 Processing helix chain 'F' and resid 177 through 186 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'G' and resid 167 through 175 Processing helix chain 'G' and resid 177 through 186 Processing helix chain 'H' and resid 56 through 58 No H-bonds generated for 'chain 'H' and resid 56 through 58' Processing helix chain 'H' and resid 167 through 175 Processing helix chain 'H' and resid 177 through 186 Processing helix chain 'I' and resid 56 through 58 No H-bonds generated for 'chain 'I' and resid 56 through 58' Processing helix chain 'I' and resid 167 through 175 Processing helix chain 'I' and resid 177 through 186 Processing helix chain 'J' and resid 56 through 58 No H-bonds generated for 'chain 'J' and resid 56 through 58' Processing helix chain 'J' and resid 167 through 175 Processing helix chain 'J' and resid 177 through 186 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 54 current: chain 'A' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 95 through 98 current: chain 'A' and resid 148 through 160 Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 51 through 54 current: chain 'B' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 95 through 98 current: chain 'B' and resid 148 through 160 Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 54 current: chain 'C' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 95 through 98 current: chain 'C' and resid 148 through 160 Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 51 through 54 current: chain 'D' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 95 through 98 current: chain 'D' and resid 148 through 160 Processing sheet with id=AA5, first strand: chain 'E' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 51 through 54 current: chain 'E' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 95 through 98 current: chain 'E' and resid 148 through 160 Processing sheet with id=AA6, first strand: chain 'F' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 51 through 54 current: chain 'F' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 95 through 98 current: chain 'F' and resid 148 through 160 Processing sheet with id=AA7, first strand: chain 'G' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 54 current: chain 'G' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 95 through 98 current: chain 'G' and resid 148 through 160 Processing sheet with id=AA8, first strand: chain 'H' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 51 through 54 current: chain 'H' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 95 through 98 current: chain 'H' and resid 148 through 160 Processing sheet with id=AA9, first strand: chain 'I' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 51 through 54 current: chain 'I' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 95 through 98 current: chain 'I' and resid 148 through 160 Processing sheet with id=AB1, first strand: chain 'J' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 51 through 54 current: chain 'J' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 95 through 98 current: chain 'J' and resid 148 through 160 150 hydrogen bonds defined for protein. 420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4510 1.34 - 1.46: 2585 1.46 - 1.57: 6705 1.57 - 1.69: 0 1.69 - 1.80: 100 Bond restraints: 13900 Sorted by residual: bond pdb=" CB PRO J 78 " pdb=" CG PRO J 78 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.63e+00 bond pdb=" CB PRO E 78 " pdb=" CG PRO E 78 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.63e+00 bond pdb=" CB PRO B 78 " pdb=" CG PRO B 78 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.62e+00 bond pdb=" CB PRO I 78 " pdb=" CG PRO I 78 " ideal model delta sigma weight residual 1.492 1.555 -0.063 5.00e-02 4.00e+02 1.60e+00 bond pdb=" CB PRO H 78 " pdb=" CG PRO H 78 " ideal model delta sigma weight residual 1.492 1.555 -0.063 5.00e-02 4.00e+02 1.60e+00 ... (remaining 13895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 17514 0.98 - 1.95: 1035 1.95 - 2.93: 161 2.93 - 3.91: 50 3.91 - 4.88: 50 Bond angle restraints: 18810 Sorted by residual: angle pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N GLN D 65 " ideal model delta sigma weight residual 116.60 119.95 -3.35 1.45e+00 4.76e-01 5.35e+00 angle pdb=" CA VAL I 64 " pdb=" C VAL I 64 " pdb=" N GLN I 65 " ideal model delta sigma weight residual 116.60 119.95 -3.35 1.45e+00 4.76e-01 5.32e+00 angle pdb=" CA VAL E 64 " pdb=" C VAL E 64 " pdb=" N GLN E 65 " ideal model delta sigma weight residual 116.60 119.94 -3.34 1.45e+00 4.76e-01 5.32e+00 angle pdb=" CA VAL G 64 " pdb=" C VAL G 64 " pdb=" N GLN G 65 " ideal model delta sigma weight residual 116.60 119.94 -3.34 1.45e+00 4.76e-01 5.31e+00 angle pdb=" CA VAL H 64 " pdb=" C VAL H 64 " pdb=" N GLN H 65 " ideal model delta sigma weight residual 116.60 119.94 -3.34 1.45e+00 4.76e-01 5.31e+00 ... (remaining 18805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7670 17.97 - 35.94: 732 35.94 - 53.91: 98 53.91 - 71.88: 30 71.88 - 89.86: 60 Dihedral angle restraints: 8590 sinusoidal: 3600 harmonic: 4990 Sorted by residual: dihedral pdb=" CB GLU A 184 " pdb=" CG GLU A 184 " pdb=" CD GLU A 184 " pdb=" OE1 GLU A 184 " ideal model delta sinusoidal sigma weight residual 0.00 79.73 -79.73 1 3.00e+01 1.11e-03 8.77e+00 dihedral pdb=" CB GLU E 184 " pdb=" CG GLU E 184 " pdb=" CD GLU E 184 " pdb=" OE1 GLU E 184 " ideal model delta sinusoidal sigma weight residual 0.00 79.71 -79.71 1 3.00e+01 1.11e-03 8.76e+00 dihedral pdb=" CB GLU D 184 " pdb=" CG GLU D 184 " pdb=" CD GLU D 184 " pdb=" OE1 GLU D 184 " ideal model delta sinusoidal sigma weight residual 0.00 79.69 -79.69 1 3.00e+01 1.11e-03 8.76e+00 ... (remaining 8587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1156 0.024 - 0.048: 515 0.048 - 0.071: 271 0.071 - 0.095: 95 0.095 - 0.119: 153 Chirality restraints: 2190 Sorted by residual: chirality pdb=" CA ILE C 219 " pdb=" N ILE C 219 " pdb=" C ILE C 219 " pdb=" CB ILE C 219 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA ILE G 219 " pdb=" N ILE G 219 " pdb=" C ILE G 219 " pdb=" CB ILE G 219 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA ILE B 219 " pdb=" N ILE B 219 " pdb=" C ILE B 219 " pdb=" CB ILE B 219 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.46e-01 ... (remaining 2187 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER H 167 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO H 168 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 168 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 168 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 167 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO C 168 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 168 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 168 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 167 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO G 168 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO G 168 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 168 " 0.041 5.00e-02 4.00e+02 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 61 2.58 - 3.16: 10589 3.16 - 3.74: 19984 3.74 - 4.32: 29423 4.32 - 4.90: 50855 Nonbonded interactions: 110912 Sorted by model distance: nonbonded pdb=" OH TYR I 182 " pdb=" ND2 ASN J 121 " model vdw 1.998 3.120 nonbonded pdb=" O PRO D 78 " pdb=" NH1 ARG D 98 " model vdw 2.307 3.120 nonbonded pdb=" O PRO I 78 " pdb=" NH1 ARG I 98 " model vdw 2.308 3.120 nonbonded pdb=" O PRO F 78 " pdb=" NH1 ARG F 98 " model vdw 2.308 3.120 nonbonded pdb=" O PRO H 78 " pdb=" NH1 ARG H 98 " model vdw 2.308 3.120 ... (remaining 110907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 8.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 11.650 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.003 0.064 13910 Z= 0.134 Angle : 0.581 4.882 18830 Z= 0.332 Chirality : 0.043 0.119 2190 Planarity : 0.007 0.075 2420 Dihedral : 16.460 89.855 5300 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.19), residues: 1660 helix: -0.87 (0.38), residues: 150 sheet: -0.76 (0.18), residues: 730 loop : -0.90 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 229 TYR 0.012 0.002 TYR I 182 PHE 0.007 0.001 PHE E 70 TRP 0.005 0.002 TRP J 186 HIS 0.001 0.001 HIS F 221 Details of bonding type rmsd covalent geometry : bond 0.00312 (13900) covalent geometry : angle 0.58145 (18810) SS BOND : bond 0.00028 ( 10) SS BOND : angle 0.49919 ( 20) hydrogen bonds : bond 0.38563 ( 150) hydrogen bonds : angle 11.51287 ( 420) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 465 time to evaluate : 0.513 Fit side-chains REVERT: C 106 ASP cc_start: 0.7820 (m-30) cc_final: 0.7576 (m-30) REVERT: C 108 ASN cc_start: 0.8111 (t0) cc_final: 0.7821 (t0) REVERT: C 148 GLU cc_start: 0.7961 (pt0) cc_final: 0.7758 (pt0) REVERT: E 52 VAL cc_start: 0.9206 (t) cc_final: 0.9000 (t) REVERT: F 103 TYR cc_start: 0.8637 (m-80) cc_final: 0.8139 (m-80) REVERT: F 215 GLN cc_start: 0.7493 (tt0) cc_final: 0.7012 (tt0) REVERT: G 148 GLU cc_start: 0.7976 (pt0) cc_final: 0.7724 (pt0) REVERT: H 103 TYR cc_start: 0.8645 (m-80) cc_final: 0.8136 (m-80) REVERT: H 106 ASP cc_start: 0.7904 (m-30) cc_final: 0.7664 (m-30) REVERT: H 108 ASN cc_start: 0.8133 (t0) cc_final: 0.7838 (t0) REVERT: H 215 GLN cc_start: 0.7508 (tt0) cc_final: 0.7189 (tt0) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.1274 time to fit residues: 82.6102 Evaluate side-chains 370 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 215 GLN C 121 ASN C 215 GLN D 121 ASN E 121 ASN E 215 GLN F 110 GLN F 114 GLN F 121 ASN G 121 ASN G 173 GLN G 215 GLN H 121 ASN I 114 GLN I 121 ASN I 215 GLN J 215 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.113471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.087732 restraints weight = 15176.323| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.09 r_work: 0.2653 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13910 Z= 0.189 Angle : 0.555 5.941 18830 Z= 0.285 Chirality : 0.046 0.132 2190 Planarity : 0.005 0.069 2420 Dihedral : 4.706 13.169 1800 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.99 % Allowed : 12.11 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.20), residues: 1660 helix: -0.05 (0.39), residues: 170 sheet: -0.41 (0.20), residues: 660 loop : -0.88 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 229 TYR 0.015 0.002 TYR F 182 PHE 0.011 0.001 PHE I 58 TRP 0.008 0.002 TRP B 186 HIS 0.003 0.001 HIS I 221 Details of bonding type rmsd covalent geometry : bond 0.00465 (13900) covalent geometry : angle 0.55493 (18810) SS BOND : bond 0.00053 ( 10) SS BOND : angle 0.16565 ( 20) hydrogen bonds : bond 0.03873 ( 150) hydrogen bonds : angle 8.03722 ( 420) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 358 time to evaluate : 0.537 Fit side-chains REVERT: B 98 ARG cc_start: 0.8849 (tpp-160) cc_final: 0.8506 (tpp-160) REVERT: B 199 GLU cc_start: 0.8675 (tt0) cc_final: 0.8447 (tt0) REVERT: C 98 ARG cc_start: 0.8927 (tpp-160) cc_final: 0.8572 (tpp-160) REVERT: C 103 TYR cc_start: 0.9205 (m-80) cc_final: 0.8957 (m-80) REVERT: C 106 ASP cc_start: 0.8518 (m-30) cc_final: 0.8251 (m-30) REVERT: D 98 ARG cc_start: 0.8838 (tpp-160) cc_final: 0.8467 (tpp-160) REVERT: E 103 TYR cc_start: 0.9246 (m-80) cc_final: 0.9045 (m-80) REVERT: E 227 LYS cc_start: 0.8855 (ttmm) cc_final: 0.8516 (ttpt) REVERT: F 98 ARG cc_start: 0.8785 (tpp-160) cc_final: 0.8438 (tpp-160) REVERT: F 199 GLU cc_start: 0.8622 (tt0) cc_final: 0.8190 (tt0) REVERT: F 201 SER cc_start: 0.8737 (m) cc_final: 0.8296 (m) REVERT: G 98 ARG cc_start: 0.8827 (tpp-160) cc_final: 0.8456 (tpp-160) REVERT: G 148 GLU cc_start: 0.8540 (pt0) cc_final: 0.8241 (pt0) REVERT: G 195 LYS cc_start: 0.8464 (mmtm) cc_final: 0.8243 (mmtp) REVERT: G 199 GLU cc_start: 0.8692 (tt0) cc_final: 0.8480 (tt0) REVERT: H 98 ARG cc_start: 0.8880 (tpp-160) cc_final: 0.8535 (mmt180) REVERT: H 195 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8351 (mmtp) REVERT: H 199 GLU cc_start: 0.8468 (tt0) cc_final: 0.8030 (tm-30) REVERT: I 98 ARG cc_start: 0.8849 (tpp-160) cc_final: 0.8461 (tpp-160) REVERT: I 103 TYR cc_start: 0.9260 (m-80) cc_final: 0.9009 (m-80) REVERT: I 195 LYS cc_start: 0.8587 (mmtm) cc_final: 0.8353 (mmtp) REVERT: J 102 GLU cc_start: 0.8106 (tt0) cc_final: 0.7896 (tt0) REVERT: J 130 TYR cc_start: 0.9424 (m-80) cc_final: 0.9181 (m-80) REVERT: J 166 MET cc_start: 0.8183 (mtm) cc_final: 0.7958 (mtt) REVERT: J 184 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7493 (mm-30) REVERT: J 193 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8094 (mt-10) outliers start: 32 outliers final: 12 residues processed: 382 average time/residue: 0.1301 time to fit residues: 68.9124 Evaluate side-chains 348 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 336 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain J residue 211 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 75 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 169 GLN B 173 GLN B 215 GLN C 215 GLN D 114 GLN D 215 GLN E 110 GLN E 114 GLN E 215 GLN F 110 GLN F 217 ASN G 114 GLN G 169 GLN G 215 GLN H 215 GLN I 215 GLN J 100 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.111443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.085927 restraints weight = 15467.821| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.09 r_work: 0.2623 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13910 Z= 0.187 Angle : 0.523 6.183 18830 Z= 0.267 Chirality : 0.045 0.132 2190 Planarity : 0.005 0.059 2420 Dihedral : 4.666 13.488 1800 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.24 % Allowed : 14.04 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.21), residues: 1660 helix: 0.43 (0.43), residues: 170 sheet: -0.20 (0.19), residues: 770 loop : -0.93 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 229 TYR 0.012 0.002 TYR A 103 PHE 0.009 0.001 PHE G 58 TRP 0.005 0.002 TRP C 186 HIS 0.003 0.001 HIS B 221 Details of bonding type rmsd covalent geometry : bond 0.00461 (13900) covalent geometry : angle 0.52281 (18810) SS BOND : bond 0.00045 ( 10) SS BOND : angle 0.14322 ( 20) hydrogen bonds : bond 0.04111 ( 150) hydrogen bonds : angle 7.59850 ( 420) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 348 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8534 (tt0) cc_final: 0.8194 (tp30) REVERT: B 195 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8416 (mmtp) REVERT: B 199 GLU cc_start: 0.8622 (tt0) cc_final: 0.8187 (tt0) REVERT: B 201 SER cc_start: 0.8801 (m) cc_final: 0.8313 (m) REVERT: C 98 ARG cc_start: 0.8863 (tpp-160) cc_final: 0.8470 (mmt180) REVERT: E 199 GLU cc_start: 0.8493 (tt0) cc_final: 0.8289 (tt0) REVERT: E 227 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8463 (ttpt) REVERT: F 199 GLU cc_start: 0.8567 (tt0) cc_final: 0.8166 (tt0) REVERT: F 201 SER cc_start: 0.8876 (m) cc_final: 0.8460 (m) REVERT: G 195 LYS cc_start: 0.8625 (mmtm) cc_final: 0.8373 (mmtp) REVERT: H 98 ARG cc_start: 0.8823 (tpp-160) cc_final: 0.8361 (mmt180) REVERT: H 195 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8418 (mmtp) REVERT: I 195 LYS cc_start: 0.8745 (mmtm) cc_final: 0.8486 (mmtp) REVERT: J 193 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8094 (mt-10) REVERT: J 194 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7976 (m-30) REVERT: J 229 ARG cc_start: 0.8620 (mtm110) cc_final: 0.8242 (mtm110) outliers start: 36 outliers final: 17 residues processed: 369 average time/residue: 0.1380 time to fit residues: 70.4878 Evaluate side-chains 364 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 346 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain J residue 194 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 6 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 110 GLN A 215 GLN B 173 GLN B 215 GLN C 100 ASN C 114 GLN C 215 GLN D 215 GLN E 110 GLN G 215 GLN H 114 GLN H 215 GLN I 215 GLN J 72 GLN J 100 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.110748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.085345 restraints weight = 15249.266| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.07 r_work: 0.2616 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13910 Z= 0.177 Angle : 0.514 6.100 18830 Z= 0.262 Chirality : 0.045 0.131 2190 Planarity : 0.005 0.053 2420 Dihedral : 4.592 14.005 1800 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.48 % Allowed : 13.42 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1660 helix: 0.62 (0.43), residues: 170 sheet: -0.14 (0.19), residues: 780 loop : -0.90 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 191 TYR 0.011 0.002 TYR E 182 PHE 0.009 0.001 PHE G 58 TRP 0.006 0.002 TRP D 186 HIS 0.003 0.001 HIS F 152 Details of bonding type rmsd covalent geometry : bond 0.00434 (13900) covalent geometry : angle 0.51383 (18810) SS BOND : bond 0.00033 ( 10) SS BOND : angle 0.09911 ( 20) hydrogen bonds : bond 0.03448 ( 150) hydrogen bonds : angle 7.26986 ( 420) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 348 time to evaluate : 0.451 Fit side-chains REVERT: A 102 GLU cc_start: 0.8566 (tt0) cc_final: 0.8283 (tp30) REVERT: E 227 LYS cc_start: 0.8855 (ttmm) cc_final: 0.8472 (ttpt) REVERT: E 230 MET cc_start: 0.5374 (tpt) cc_final: 0.5050 (tpt) REVERT: F 98 ARG cc_start: 0.8725 (tpp-160) cc_final: 0.8404 (mmt-90) REVERT: F 199 GLU cc_start: 0.8476 (tt0) cc_final: 0.7996 (tt0) REVERT: F 201 SER cc_start: 0.8854 (m) cc_final: 0.8376 (m) REVERT: G 148 GLU cc_start: 0.8589 (pt0) cc_final: 0.8278 (pt0) REVERT: G 195 LYS cc_start: 0.8640 (mmtm) cc_final: 0.8340 (mmtp) REVERT: G 199 GLU cc_start: 0.8584 (tt0) cc_final: 0.8232 (tt0) REVERT: G 201 SER cc_start: 0.8878 (m) cc_final: 0.8520 (m) REVERT: G 230 MET cc_start: 0.5128 (tpt) cc_final: 0.4857 (tpt) REVERT: H 195 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8337 (mmtp) REVERT: I 195 LYS cc_start: 0.8747 (mmtm) cc_final: 0.8465 (mmtp) REVERT: J 102 GLU cc_start: 0.8570 (tt0) cc_final: 0.8217 (tp30) REVERT: J 191 ARG cc_start: 0.8746 (mtt-85) cc_final: 0.8541 (mtt-85) REVERT: J 193 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8114 (mt-10) REVERT: J 229 ARG cc_start: 0.8641 (mtm110) cc_final: 0.8292 (mtm110) outliers start: 40 outliers final: 18 residues processed: 371 average time/residue: 0.1288 time to fit residues: 67.1168 Evaluate side-chains 356 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 338 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain J residue 211 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 150 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 173 GLN B 114 GLN B 173 GLN C 100 ASN C 215 GLN D 215 GLN E 110 GLN F 110 GLN G 114 GLN H 100 ASN H 215 GLN I 114 GLN I 215 GLN J 100 ASN J 114 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.110346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.084218 restraints weight = 15382.153| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.15 r_work: 0.2589 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13910 Z= 0.177 Angle : 0.516 5.314 18830 Z= 0.264 Chirality : 0.045 0.129 2190 Planarity : 0.005 0.050 2420 Dihedral : 4.554 14.131 1800 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.73 % Allowed : 14.41 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.22), residues: 1660 helix: 0.69 (0.44), residues: 170 sheet: -0.19 (0.20), residues: 790 loop : -0.78 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 191 TYR 0.013 0.002 TYR A 103 PHE 0.009 0.001 PHE B 58 TRP 0.006 0.002 TRP D 186 HIS 0.003 0.001 HIS F 152 Details of bonding type rmsd covalent geometry : bond 0.00434 (13900) covalent geometry : angle 0.51667 (18810) SS BOND : bond 0.00029 ( 10) SS BOND : angle 0.07384 ( 20) hydrogen bonds : bond 0.03376 ( 150) hydrogen bonds : angle 7.17798 ( 420) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 347 time to evaluate : 0.399 Fit side-chains REVERT: A 102 GLU cc_start: 0.8594 (tt0) cc_final: 0.8316 (tp30) REVERT: B 195 LYS cc_start: 0.8743 (mmtm) cc_final: 0.8455 (mmtp) REVERT: D 98 ARG cc_start: 0.8648 (tpp-160) cc_final: 0.8269 (mmt180) REVERT: E 98 ARG cc_start: 0.8545 (tpp-160) cc_final: 0.8325 (mmt-90) REVERT: E 199 GLU cc_start: 0.8367 (tt0) cc_final: 0.8155 (tt0) REVERT: E 227 LYS cc_start: 0.8829 (ttmm) cc_final: 0.8495 (ttpt) REVERT: F 98 ARG cc_start: 0.8662 (tpp-160) cc_final: 0.8267 (mmt-90) REVERT: F 201 SER cc_start: 0.8920 (m) cc_final: 0.8718 (m) REVERT: G 195 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8330 (mmtp) REVERT: G 201 SER cc_start: 0.8922 (m) cc_final: 0.8562 (m) REVERT: H 98 ARG cc_start: 0.8772 (tpp-160) cc_final: 0.8288 (mmt180) REVERT: H 195 LYS cc_start: 0.8668 (mmtm) cc_final: 0.8312 (mmtp) REVERT: I 195 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8473 (mmtp) REVERT: J 99 ASP cc_start: 0.7771 (t0) cc_final: 0.7433 (t0) REVERT: J 102 GLU cc_start: 0.8672 (tt0) cc_final: 0.8329 (tp30) outliers start: 44 outliers final: 23 residues processed: 370 average time/residue: 0.1228 time to fit residues: 64.5582 Evaluate side-chains 362 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 339 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 173 GLN C 100 ASN C 215 GLN D 215 GLN E 110 GLN E 215 GLN F 110 GLN H 100 ASN H 215 GLN I 114 GLN I 215 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.108208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.082406 restraints weight = 15493.360| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.12 r_work: 0.2570 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2385 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 13910 Z= 0.228 Angle : 0.563 8.769 18830 Z= 0.281 Chirality : 0.047 0.129 2190 Planarity : 0.005 0.048 2420 Dihedral : 4.728 15.357 1800 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.36 % Allowed : 15.16 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.22), residues: 1660 helix: 0.56 (0.43), residues: 170 sheet: -0.03 (0.20), residues: 780 loop : -0.89 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 229 TYR 0.014 0.002 TYR A 103 PHE 0.010 0.002 PHE I 58 TRP 0.006 0.002 TRP D 186 HIS 0.004 0.002 HIS F 152 Details of bonding type rmsd covalent geometry : bond 0.00557 (13900) covalent geometry : angle 0.56291 (18810) SS BOND : bond 0.00043 ( 10) SS BOND : angle 0.13221 ( 20) hydrogen bonds : bond 0.03648 ( 150) hydrogen bonds : angle 7.18970 ( 420) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 346 time to evaluate : 0.425 Fit side-chains REVERT: A 98 ARG cc_start: 0.8108 (tpp-160) cc_final: 0.7740 (mmt180) REVERT: A 102 GLU cc_start: 0.8612 (tt0) cc_final: 0.8346 (tp30) REVERT: A 199 GLU cc_start: 0.8284 (tt0) cc_final: 0.8078 (tt0) REVERT: B 195 LYS cc_start: 0.8808 (mmtm) cc_final: 0.8499 (mmtp) REVERT: E 98 ARG cc_start: 0.8570 (tpp-160) cc_final: 0.8331 (mmt-90) REVERT: E 184 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7911 (mm-30) REVERT: E 199 GLU cc_start: 0.8350 (tt0) cc_final: 0.8127 (tt0) REVERT: E 227 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8479 (ttpt) REVERT: F 98 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.8209 (mmt-90) REVERT: F 201 SER cc_start: 0.8962 (m) cc_final: 0.8749 (m) REVERT: G 85 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8742 (mm-40) REVERT: G 148 GLU cc_start: 0.8583 (pt0) cc_final: 0.8273 (pt0) REVERT: G 195 LYS cc_start: 0.8711 (mmtm) cc_final: 0.8345 (mmtp) REVERT: G 199 GLU cc_start: 0.8486 (tt0) cc_final: 0.8154 (tt0) REVERT: G 201 SER cc_start: 0.8960 (m) cc_final: 0.8646 (m) REVERT: H 195 LYS cc_start: 0.8713 (mmtm) cc_final: 0.8321 (mmtp) REVERT: I 195 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8492 (mmtp) REVERT: J 102 GLU cc_start: 0.8647 (tt0) cc_final: 0.8285 (tp30) REVERT: J 184 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7875 (mm-30) REVERT: J 229 ARG cc_start: 0.8571 (mtp-110) cc_final: 0.8341 (mtm110) outliers start: 38 outliers final: 24 residues processed: 367 average time/residue: 0.1254 time to fit residues: 64.8319 Evaluate side-chains 351 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 327 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 114 optimal weight: 0.1980 chunk 154 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 173 GLN C 100 ASN C 215 GLN D 114 GLN D 215 GLN E 110 GLN E 215 GLN H 100 ASN H 215 GLN I 114 GLN I 215 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.108354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.082666 restraints weight = 15526.798| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.11 r_work: 0.2574 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2394 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13910 Z= 0.200 Angle : 0.544 10.088 18830 Z= 0.271 Chirality : 0.046 0.128 2190 Planarity : 0.005 0.048 2420 Dihedral : 4.646 14.821 1800 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.17 % Allowed : 15.47 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.22), residues: 1660 helix: 0.62 (0.43), residues: 170 sheet: 0.02 (0.20), residues: 780 loop : -0.92 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 191 TYR 0.016 0.002 TYR A 103 PHE 0.009 0.001 PHE B 58 TRP 0.006 0.002 TRP D 186 HIS 0.004 0.001 HIS F 152 Details of bonding type rmsd covalent geometry : bond 0.00489 (13900) covalent geometry : angle 0.54404 (18810) SS BOND : bond 0.00028 ( 10) SS BOND : angle 0.11401 ( 20) hydrogen bonds : bond 0.03461 ( 150) hydrogen bonds : angle 7.08519 ( 420) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 338 time to evaluate : 0.514 Fit side-chains REVERT: A 98 ARG cc_start: 0.8158 (tpp-160) cc_final: 0.7706 (mmt180) REVERT: A 199 GLU cc_start: 0.8297 (tt0) cc_final: 0.8075 (tt0) REVERT: A 229 ARG cc_start: 0.8749 (mtm110) cc_final: 0.8530 (mtm110) REVERT: B 121 ASN cc_start: 0.8942 (t0) cc_final: 0.8731 (t0) REVERT: B 195 LYS cc_start: 0.8823 (mmtm) cc_final: 0.8500 (mmtp) REVERT: C 98 ARG cc_start: 0.8817 (tpp-160) cc_final: 0.8348 (mmt180) REVERT: E 98 ARG cc_start: 0.8573 (tpp-160) cc_final: 0.8356 (mmt-90) REVERT: E 184 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7916 (mm-30) REVERT: E 199 GLU cc_start: 0.8283 (tt0) cc_final: 0.8066 (tt0) REVERT: E 227 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8471 (ttpt) REVERT: F 98 ARG cc_start: 0.8608 (tpp-160) cc_final: 0.8378 (mmt-90) REVERT: G 195 LYS cc_start: 0.8709 (mmtm) cc_final: 0.8340 (mmtp) REVERT: G 201 SER cc_start: 0.8961 (m) cc_final: 0.8578 (m) REVERT: H 98 ARG cc_start: 0.8719 (tpp-160) cc_final: 0.8474 (mmt-90) REVERT: H 195 LYS cc_start: 0.8704 (mmtm) cc_final: 0.8279 (mmtp) REVERT: I 195 LYS cc_start: 0.8843 (mmtm) cc_final: 0.8492 (mmtp) outliers start: 35 outliers final: 27 residues processed: 355 average time/residue: 0.1293 time to fit residues: 64.7945 Evaluate side-chains 354 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 327 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain J residue 77 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 117 optimal weight: 0.3980 chunk 107 optimal weight: 0.5980 chunk 115 optimal weight: 0.0870 chunk 30 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 153 optimal weight: 0.0470 chunk 166 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN C 100 ASN C 215 GLN D 114 GLN D 215 GLN E 110 GLN E 215 GLN F 110 GLN G 114 GLN H 100 ASN H 215 GLN I 114 GLN I 215 GLN J 114 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.112164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.087881 restraints weight = 15363.353| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 1.96 r_work: 0.2661 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13910 Z= 0.097 Angle : 0.483 10.014 18830 Z= 0.242 Chirality : 0.044 0.126 2190 Planarity : 0.004 0.048 2420 Dihedral : 4.194 14.983 1800 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.49 % Allowed : 16.71 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.22), residues: 1660 helix: 1.00 (0.44), residues: 170 sheet: -0.07 (0.20), residues: 790 loop : -0.78 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 191 TYR 0.012 0.001 TYR A 103 PHE 0.007 0.001 PHE B 228 TRP 0.008 0.002 TRP D 186 HIS 0.001 0.001 HIS E 221 Details of bonding type rmsd covalent geometry : bond 0.00239 (13900) covalent geometry : angle 0.48353 (18810) SS BOND : bond 0.00021 ( 10) SS BOND : angle 0.18930 ( 20) hydrogen bonds : bond 0.02713 ( 150) hydrogen bonds : angle 6.81669 ( 420) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 358 time to evaluate : 0.521 Fit side-chains REVERT: A 98 ARG cc_start: 0.7890 (tpp-160) cc_final: 0.7656 (mmt180) REVERT: A 103 TYR cc_start: 0.9115 (m-80) cc_final: 0.8863 (m-80) REVERT: A 212 GLU cc_start: 0.8206 (tt0) cc_final: 0.7923 (tt0) REVERT: B 98 ARG cc_start: 0.8492 (tpp-160) cc_final: 0.8195 (mmt-90) REVERT: B 195 LYS cc_start: 0.8701 (mmtm) cc_final: 0.8372 (mmtp) REVERT: D 98 ARG cc_start: 0.8526 (tpp-160) cc_final: 0.8198 (mmt180) REVERT: D 215 GLN cc_start: 0.8136 (tt0) cc_final: 0.7854 (tt0) REVERT: E 227 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8467 (ttpt) REVERT: F 199 GLU cc_start: 0.8405 (tt0) cc_final: 0.8159 (tt0) REVERT: G 98 ARG cc_start: 0.8466 (tpp-160) cc_final: 0.8149 (mmt-90) REVERT: G 195 LYS cc_start: 0.8595 (mmtm) cc_final: 0.8269 (mmtp) REVERT: G 201 SER cc_start: 0.8923 (m) cc_final: 0.8686 (m) REVERT: H 195 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8245 (mmtp) REVERT: I 98 ARG cc_start: 0.8487 (tpp-160) cc_final: 0.8123 (mmt180) REVERT: I 195 LYS cc_start: 0.8769 (mmtm) cc_final: 0.8418 (mmtp) REVERT: J 102 GLU cc_start: 0.8569 (tt0) cc_final: 0.8253 (tp30) REVERT: J 215 GLN cc_start: 0.8550 (tt0) cc_final: 0.8284 (mm-40) outliers start: 24 outliers final: 17 residues processed: 371 average time/residue: 0.1264 time to fit residues: 66.6499 Evaluate side-chains 373 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 356 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 100 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 159 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 140 optimal weight: 0.3980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 173 GLN B 114 GLN B 173 GLN C 215 GLN D 114 GLN E 110 GLN E 215 GLN F 110 GLN G 114 GLN H 215 GLN I 114 GLN I 215 GLN J 114 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.108851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.083176 restraints weight = 15587.769| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.10 r_work: 0.2665 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13910 Z= 0.193 Angle : 0.546 10.248 18830 Z= 0.270 Chirality : 0.046 0.127 2190 Planarity : 0.005 0.049 2420 Dihedral : 4.500 15.682 1800 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.61 % Allowed : 16.34 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.22), residues: 1660 helix: 0.78 (0.44), residues: 170 sheet: 0.09 (0.20), residues: 780 loop : -0.88 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 191 TYR 0.013 0.002 TYR A 103 PHE 0.009 0.001 PHE G 58 TRP 0.005 0.002 TRP D 186 HIS 0.004 0.001 HIS E 152 Details of bonding type rmsd covalent geometry : bond 0.00473 (13900) covalent geometry : angle 0.54591 (18810) SS BOND : bond 0.00032 ( 10) SS BOND : angle 0.09046 ( 20) hydrogen bonds : bond 0.03300 ( 150) hydrogen bonds : angle 7.02215 ( 420) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 349 time to evaluate : 0.340 Fit side-chains REVERT: A 98 ARG cc_start: 0.8039 (tpp-160) cc_final: 0.7629 (mmt180) REVERT: A 199 GLU cc_start: 0.8231 (tt0) cc_final: 0.7973 (tt0) REVERT: B 195 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8429 (mmtp) REVERT: D 98 ARG cc_start: 0.8578 (tpp-160) cc_final: 0.8215 (mmt180) REVERT: E 227 LYS cc_start: 0.8868 (ttmm) cc_final: 0.8507 (ttpt) REVERT: F 98 ARG cc_start: 0.8431 (mmt-90) cc_final: 0.8096 (mmt180) REVERT: F 199 GLU cc_start: 0.8403 (tt0) cc_final: 0.8186 (tt0) REVERT: G 195 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8365 (mmtp) REVERT: I 195 LYS cc_start: 0.8821 (mmtm) cc_final: 0.8479 (mmtp) REVERT: J 102 GLU cc_start: 0.8581 (tt0) cc_final: 0.8233 (tp30) outliers start: 26 outliers final: 20 residues processed: 364 average time/residue: 0.1234 time to fit residues: 63.4700 Evaluate side-chains 366 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 346 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain J residue 77 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 163 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 173 GLN C 100 ASN C 215 GLN E 110 GLN E 215 GLN F 110 GLN G 215 GLN H 100 ASN H 215 GLN I 215 GLN J 114 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.110755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.085182 restraints weight = 15451.138| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.09 r_work: 0.2698 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13910 Z= 0.129 Angle : 0.510 11.535 18830 Z= 0.254 Chirality : 0.044 0.124 2190 Planarity : 0.004 0.048 2420 Dihedral : 4.323 20.663 1800 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.12 % Allowed : 17.39 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.22), residues: 1660 helix: 0.85 (0.44), residues: 170 sheet: 0.00 (0.20), residues: 790 loop : -0.77 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 191 TYR 0.012 0.001 TYR A 103 PHE 0.007 0.001 PHE B 58 TRP 0.006 0.002 TRP A 186 HIS 0.002 0.001 HIS F 152 Details of bonding type rmsd covalent geometry : bond 0.00316 (13900) covalent geometry : angle 0.51070 (18810) SS BOND : bond 0.00020 ( 10) SS BOND : angle 0.12799 ( 20) hydrogen bonds : bond 0.02950 ( 150) hydrogen bonds : angle 6.90109 ( 420) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 366 time to evaluate : 0.466 Fit side-chains REVERT: A 98 ARG cc_start: 0.7976 (tpp-160) cc_final: 0.7619 (mmt180) REVERT: A 103 TYR cc_start: 0.9161 (m-80) cc_final: 0.8936 (m-80) REVERT: B 195 LYS cc_start: 0.8709 (mmtm) cc_final: 0.8323 (mmtp) REVERT: D 98 ARG cc_start: 0.8547 (tpp-160) cc_final: 0.8190 (mmt180) REVERT: E 199 GLU cc_start: 0.8342 (tt0) cc_final: 0.7977 (tt0) REVERT: E 201 SER cc_start: 0.8949 (m) cc_final: 0.8611 (p) REVERT: E 227 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8512 (ttpt) REVERT: F 98 ARG cc_start: 0.8346 (mmt-90) cc_final: 0.8142 (mmt180) REVERT: F 199 GLU cc_start: 0.8423 (tt0) cc_final: 0.8206 (tt0) REVERT: G 195 LYS cc_start: 0.8685 (mmtm) cc_final: 0.8340 (mmtp) REVERT: I 98 ARG cc_start: 0.8532 (tpp-160) cc_final: 0.8290 (mmt180) REVERT: I 195 LYS cc_start: 0.8793 (mmtm) cc_final: 0.8448 (mmtp) REVERT: J 102 GLU cc_start: 0.8544 (tt0) cc_final: 0.8228 (tp30) REVERT: J 215 GLN cc_start: 0.8579 (tt0) cc_final: 0.8345 (mm-40) outliers start: 18 outliers final: 18 residues processed: 375 average time/residue: 0.1222 time to fit residues: 65.1340 Evaluate side-chains 370 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 352 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain J residue 77 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 18 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 82 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 114 GLN B 173 GLN C 100 ASN C 215 GLN E 110 GLN E 215 GLN F 110 GLN G 215 GLN H 215 GLN I 215 GLN J 114 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.109119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.083501 restraints weight = 15560.270| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.09 r_work: 0.2586 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2402 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13910 Z= 0.179 Angle : 0.553 11.755 18830 Z= 0.272 Chirality : 0.045 0.126 2190 Planarity : 0.004 0.049 2420 Dihedral : 4.501 21.327 1800 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.37 % Allowed : 17.02 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.22), residues: 1660 helix: 0.68 (0.43), residues: 170 sheet: 0.03 (0.20), residues: 790 loop : -0.79 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 191 TYR 0.014 0.002 TYR E 103 PHE 0.009 0.001 PHE B 58 TRP 0.005 0.002 TRP C 186 HIS 0.003 0.001 HIS E 152 Details of bonding type rmsd covalent geometry : bond 0.00438 (13900) covalent geometry : angle 0.55306 (18810) SS BOND : bond 0.00025 ( 10) SS BOND : angle 0.08743 ( 20) hydrogen bonds : bond 0.03306 ( 150) hydrogen bonds : angle 6.94988 ( 420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3212.73 seconds wall clock time: 55 minutes 41.11 seconds (3341.11 seconds total)