Starting phenix.real_space_refine on Thu Jul 31 14:51:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oxr_13104/07_2025/7oxr_13104.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oxr_13104/07_2025/7oxr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7oxr_13104/07_2025/7oxr_13104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oxr_13104/07_2025/7oxr_13104.map" model { file = "/net/cci-nas-00/data/ceres_data/7oxr_13104/07_2025/7oxr_13104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oxr_13104/07_2025/7oxr_13104.cif" } resolution = 3.3 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= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.70, per 1000 atoms: 0.71 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: 3.70 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.49 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: 2.96 Time building geometry restraints manager: 4.43 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 116.050 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: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.080 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.270 ------------------------------------------------------------------------------- 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 (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: -1.36 (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 TRP 0.005 0.002 TRP J 186 HIS 0.001 0.001 HIS F 221 PHE 0.007 0.001 PHE E 70 TYR 0.012 0.002 TYR I 182 ARG 0.010 0.001 ARG G 229 Details of bonding type rmsd hydrogen bonds : bond 0.38563 ( 150) hydrogen bonds : angle 11.51287 ( 420) SS BOND : bond 0.00028 ( 10) SS BOND : angle 0.49919 ( 20) covalent geometry : bond 0.00312 (13900) covalent geometry : angle 0.58145 (18810) *********************** 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 : 2.049 Fit side-chains REVERT: C 106 ASP cc_start: 0.7820 (m-30) cc_final: 0.7577 (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: 0.8140 (m-80) REVERT: F 215 GLN cc_start: 0.7493 (tt0) cc_final: 0.7013 (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: 0.8137 (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: 0.3544 time to fit residues: 230.9764 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 : 4.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 173 GLN B 215 GLN C 121 ASN C 215 GLN D 114 GLN D 121 ASN E 114 GLN E 121 ASN E 215 GLN F 110 GLN F 114 GLN F 121 ASN G 114 GLN G 121 ASN G 173 GLN G 215 GLN H 121 ASN I 114 GLN I 121 ASN I 215 GLN J 100 ASN J 215 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.110960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.085126 restraints weight = 15211.259| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.09 r_work: 0.2628 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2449 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13910 Z= 0.258 Angle : 0.610 6.033 18830 Z= 0.310 Chirality : 0.047 0.129 2190 Planarity : 0.005 0.066 2420 Dihedral : 4.938 14.246 1800 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.93 % Allowed : 12.80 % Favored : 85.28 % 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: -1.04 (0.20), residues: 1660 helix: -0.20 (0.40), residues: 170 sheet: -0.46 (0.20), residues: 660 loop : -0.90 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 186 HIS 0.004 0.002 HIS A 221 PHE 0.013 0.002 PHE I 58 TYR 0.019 0.003 TYR F 182 ARG 0.004 0.001 ARG F 229 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 150) hydrogen bonds : angle 7.93674 ( 420) SS BOND : bond 0.00031 ( 10) SS BOND : angle 0.19217 ( 20) covalent geometry : bond 0.00639 (13900) covalent geometry : angle 0.60988 (18810) *********************** 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 399 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 368 time to evaluate : 1.505 Fit side-chains REVERT: A 172 GLU cc_start: 0.7959 (tt0) cc_final: 0.7755 (pt0) REVERT: A 227 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8582 (ttpt) REVERT: B 98 ARG cc_start: 0.8864 (tpp-160) cc_final: 0.8504 (tpp-160) REVERT: B 193 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8286 (mt-10) REVERT: B 195 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8403 (mmtp) REVERT: B 199 GLU cc_start: 0.8682 (tt0) cc_final: 0.8260 (tt0) REVERT: B 201 SER cc_start: 0.8787 (m) cc_final: 0.8289 (m) REVERT: C 98 ARG cc_start: 0.8922 (tpp-160) cc_final: 0.8590 (tpp-160) REVERT: D 98 ARG cc_start: 0.8840 (tpp-160) cc_final: 0.8484 (tpp-160) REVERT: E 98 ARG cc_start: 0.8772 (tpp-160) cc_final: 0.8290 (tpp-160) REVERT: E 227 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8582 (ttpt) REVERT: F 98 ARG cc_start: 0.8856 (tpp-160) cc_final: 0.8581 (tpp-160) REVERT: F 199 GLU cc_start: 0.8580 (tt0) cc_final: 0.8185 (tt0) REVERT: F 201 SER cc_start: 0.8789 (m) cc_final: 0.8350 (m) REVERT: G 98 ARG cc_start: 0.8841 (tpp-160) cc_final: 0.8475 (tpp-160) REVERT: G 148 GLU cc_start: 0.8538 (pt0) cc_final: 0.8230 (pt0) REVERT: G 195 LYS cc_start: 0.8606 (mmtm) cc_final: 0.8391 (mmtp) REVERT: G 199 GLU cc_start: 0.8667 (tt0) cc_final: 0.8238 (tt0) REVERT: G 201 SER cc_start: 0.8801 (m) cc_final: 0.8303 (m) REVERT: H 195 LYS cc_start: 0.8644 (mmtm) cc_final: 0.8398 (mmtp) REVERT: H 199 GLU cc_start: 0.8499 (tt0) cc_final: 0.8296 (tt0) REVERT: I 98 ARG cc_start: 0.8850 (tpp-160) cc_final: 0.8481 (tpp-160) REVERT: I 195 LYS cc_start: 0.8704 (mmtm) cc_final: 0.8446 (mmtp) REVERT: J 172 GLU cc_start: 0.7849 (tt0) cc_final: 0.7627 (pt0) REVERT: J 193 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8082 (mt-10) outliers start: 31 outliers final: 8 residues processed: 391 average time/residue: 0.3137 time to fit residues: 168.7202 Evaluate side-chains 353 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 345 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 230 MET Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 230 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 119 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 100 ASN A 173 GLN B 173 GLN B 215 GLN C 215 GLN D 215 GLN E 110 GLN E 215 GLN F 110 GLN G 215 GLN H 215 GLN I 114 GLN I 215 GLN J 72 GLN J 100 ASN J 114 GLN J 173 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 = 0.3088 r_free = 0.3088 target = 0.108223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.082859 restraints weight = 15502.931| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.08 r_work: 0.2569 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2390 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 13910 Z= 0.284 Angle : 0.602 6.372 18830 Z= 0.303 Chirality : 0.048 0.133 2190 Planarity : 0.005 0.058 2420 Dihedral : 5.034 15.642 1800 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.73 % Allowed : 13.85 % Favored : 83.42 % 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: -0.79 (0.21), residues: 1660 helix: 0.26 (0.43), residues: 170 sheet: -0.24 (0.20), residues: 740 loop : -0.90 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 186 HIS 0.005 0.002 HIS F 152 PHE 0.013 0.002 PHE I 58 TYR 0.014 0.002 TYR E 182 ARG 0.004 0.001 ARG H 229 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 150) hydrogen bonds : angle 7.59381 ( 420) SS BOND : bond 0.00046 ( 10) SS BOND : angle 0.11349 ( 20) covalent geometry : bond 0.00695 (13900) covalent geometry : angle 0.60183 (18810) *********************** 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 391 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 347 time to evaluate : 1.538 Fit side-chains REVERT: A 99 ASP cc_start: 0.7857 (t70) cc_final: 0.7622 (t0) REVERT: A 102 GLU cc_start: 0.8586 (tt0) cc_final: 0.8308 (tt0) REVERT: A 199 GLU cc_start: 0.8226 (tt0) cc_final: 0.8011 (tt0) REVERT: B 195 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8532 (mmtp) REVERT: B 199 GLU cc_start: 0.8593 (tt0) cc_final: 0.8179 (tt0) REVERT: B 201 SER cc_start: 0.8924 (m) cc_final: 0.8497 (m) REVERT: C 204 THR cc_start: 0.9176 (m) cc_final: 0.8975 (m) REVERT: E 227 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8487 (ttpt) REVERT: F 199 GLU cc_start: 0.8575 (tt0) cc_final: 0.8127 (tt0) REVERT: F 201 SER cc_start: 0.8897 (m) cc_final: 0.8411 (m) REVERT: G 195 LYS cc_start: 0.8754 (mmtm) cc_final: 0.8501 (mmtp) REVERT: G 199 GLU cc_start: 0.8579 (tt0) cc_final: 0.8356 (tt0) REVERT: H 195 LYS cc_start: 0.8770 (mmtm) cc_final: 0.8487 (mmtp) REVERT: H 199 GLU cc_start: 0.8408 (tt0) cc_final: 0.8009 (tt0) REVERT: I 195 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8574 (mmtp) REVERT: J 193 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8098 (mt-10) REVERT: J 194 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8091 (m-30) outliers start: 44 outliers final: 16 residues processed: 361 average time/residue: 0.3088 time to fit residues: 152.2053 Evaluate side-chains 341 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 324 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LYS 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 163 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 F residue 68 THR Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain J residue 194 ASP Chi-restraints excluded: chain J residue 215 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 29 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 0.0270 chunk 46 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 215 GLN B 85 GLN B 114 GLN B 173 GLN C 100 ASN C 114 GLN C 215 GLN D 215 GLN E 110 GLN E 215 GLN H 100 ASN H 114 GLN H 215 GLN I 114 GLN I 215 GLN J 100 ASN J 114 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.111797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.086637 restraints weight = 15211.184| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.06 r_work: 0.2637 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13910 Z= 0.119 Angle : 0.467 5.963 18830 Z= 0.240 Chirality : 0.044 0.127 2190 Planarity : 0.004 0.052 2420 Dihedral : 4.499 13.435 1800 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.61 % Allowed : 14.35 % Favored : 83.04 % 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: -0.67 (0.22), residues: 1660 helix: 0.82 (0.44), residues: 170 sheet: -0.27 (0.20), residues: 790 loop : -0.84 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 186 HIS 0.002 0.001 HIS J 221 PHE 0.007 0.001 PHE E 58 TYR 0.011 0.001 TYR A 103 ARG 0.005 0.000 ARG H 191 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 150) hydrogen bonds : angle 7.22139 ( 420) SS BOND : bond 0.00021 ( 10) SS BOND : angle 0.23898 ( 20) covalent geometry : bond 0.00293 (13900) covalent geometry : angle 0.46750 (18810) *********************** 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 379 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 337 time to evaluate : 1.547 Fit side-chains REVERT: A 102 GLU cc_start: 0.8577 (tt0) cc_final: 0.8236 (tp30) REVERT: B 195 LYS cc_start: 0.8750 (mmtm) cc_final: 0.8455 (mmtp) REVERT: C 98 ARG cc_start: 0.8743 (tpp-160) cc_final: 0.8297 (mmt180) REVERT: E 227 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8469 (ttpt) REVERT: F 98 ARG cc_start: 0.8659 (tpp-160) cc_final: 0.8308 (mmt-90) REVERT: F 199 GLU cc_start: 0.8461 (tt0) cc_final: 0.7991 (tt0) REVERT: F 201 SER cc_start: 0.8909 (m) cc_final: 0.8465 (m) REVERT: G 195 LYS cc_start: 0.8697 (mmtm) cc_final: 0.8415 (mmtp) REVERT: H 98 ARG cc_start: 0.8720 (tpp-160) cc_final: 0.8235 (mmt180) REVERT: H 195 LYS cc_start: 0.8642 (mmtm) cc_final: 0.8330 (mmtp) REVERT: I 195 LYS cc_start: 0.8770 (mmtm) cc_final: 0.8463 (mmtp) REVERT: J 99 ASP cc_start: 0.7661 (t70) cc_final: 0.7235 (t0) REVERT: J 193 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8043 (mt-10) REVERT: J 194 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7878 (m-30) outliers start: 42 outliers final: 19 residues processed: 365 average time/residue: 0.3073 time to fit residues: 158.7288 Evaluate side-chains 345 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 325 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 163 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain F residue 62 ASN 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 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 194 ASP Chi-restraints excluded: chain J residue 215 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 100 optimal weight: 0.0170 chunk 64 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN B 173 GLN C 100 ASN C 215 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 = 0.3121 r_free = 0.3121 target = 0.110681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.084767 restraints weight = 15388.497| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.14 r_work: 0.2601 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13910 Z= 0.154 Angle : 0.505 5.232 18830 Z= 0.260 Chirality : 0.044 0.128 2190 Planarity : 0.005 0.050 2420 Dihedral : 4.479 13.752 1800 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.24 % Allowed : 15.47 % Favored : 82.30 % 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: -0.59 (0.22), residues: 1660 helix: 0.87 (0.44), residues: 170 sheet: -0.21 (0.20), residues: 790 loop : -0.79 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP E 186 HIS 0.003 0.001 HIS F 152 PHE 0.008 0.001 PHE G 58 TYR 0.013 0.002 TYR A 103 ARG 0.007 0.000 ARG H 229 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 150) hydrogen bonds : angle 7.17946 ( 420) SS BOND : bond 0.00020 ( 10) SS BOND : angle 0.10280 ( 20) covalent geometry : bond 0.00377 (13900) covalent geometry : angle 0.50507 (18810) *********************** 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 379 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 343 time to evaluate : 1.598 Fit side-chains REVERT: A 102 GLU cc_start: 0.8598 (tt0) cc_final: 0.8252 (tp30) REVERT: B 98 ARG cc_start: 0.8626 (tpp-160) cc_final: 0.8357 (mmt-90) REVERT: B 195 LYS cc_start: 0.8768 (mmtm) cc_final: 0.8470 (mmtp) REVERT: E 98 ARG cc_start: 0.8556 (tpp-160) cc_final: 0.8354 (mmt-90) REVERT: E 227 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8471 (ttpt) REVERT: F 98 ARG cc_start: 0.8656 (tpp-160) cc_final: 0.8425 (mmt-90) REVERT: G 195 LYS cc_start: 0.8721 (mmtm) cc_final: 0.8413 (mmtp) REVERT: H 98 ARG cc_start: 0.8668 (tpp-160) cc_final: 0.8089 (mmt180) REVERT: H 195 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8320 (mmtp) REVERT: I 195 LYS cc_start: 0.8795 (mmtm) cc_final: 0.8470 (mmtp) REVERT: J 102 GLU cc_start: 0.8669 (tt0) cc_final: 0.8298 (tp30) REVERT: J 193 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8107 (mt-10) REVERT: J 215 GLN cc_start: 0.8545 (tt0) cc_final: 0.8316 (mm-40) outliers start: 36 outliers final: 24 residues processed: 364 average time/residue: 0.2701 time to fit residues: 138.1529 Evaluate side-chains 363 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 339 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 163 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 77 ILE 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 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 201 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 81 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 85 GLN B 114 GLN B 169 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 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 = 0.3121 r_free = 0.3121 target = 0.110768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.084980 restraints weight = 15710.792| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.14 r_work: 0.2627 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13910 Z= 0.140 Angle : 0.495 8.608 18830 Z= 0.251 Chirality : 0.044 0.126 2190 Planarity : 0.004 0.048 2420 Dihedral : 4.383 13.773 1800 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.05 % Allowed : 16.02 % Favored : 81.93 % 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: -0.51 (0.22), residues: 1660 helix: 0.95 (0.44), residues: 170 sheet: -0.15 (0.20), residues: 790 loop : -0.75 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP I 186 HIS 0.003 0.001 HIS F 152 PHE 0.007 0.001 PHE G 58 TYR 0.012 0.001 TYR A 103 ARG 0.007 0.000 ARG H 229 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 150) hydrogen bonds : angle 7.06482 ( 420) SS BOND : bond 0.00019 ( 10) SS BOND : angle 0.10758 ( 20) covalent geometry : bond 0.00341 (13900) covalent geometry : angle 0.49486 (18810) *********************** 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 375 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 342 time to evaluate : 1.607 Fit side-chains REVERT: A 102 GLU cc_start: 0.8586 (tt0) cc_final: 0.8290 (tp30) REVERT: B 98 ARG cc_start: 0.8582 (tpp-160) cc_final: 0.8369 (mmt-90) REVERT: B 195 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8479 (mmtp) REVERT: C 98 ARG cc_start: 0.8745 (tpp-160) cc_final: 0.8321 (mmt180) REVERT: D 98 ARG cc_start: 0.8558 (tpp-160) cc_final: 0.8158 (mmt180) REVERT: D 199 GLU cc_start: 0.8431 (tt0) cc_final: 0.8155 (tt0) REVERT: D 201 SER cc_start: 0.8963 (m) cc_final: 0.8763 (p) REVERT: E 184 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7764 (mm-30) REVERT: E 227 LYS cc_start: 0.8863 (ttmm) cc_final: 0.8507 (ttpt) REVERT: F 98 ARG cc_start: 0.8586 (tpp-160) cc_final: 0.8379 (mmt-90) REVERT: F 199 GLU cc_start: 0.8431 (tt0) cc_final: 0.8139 (tt0) REVERT: G 195 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8235 (mmtp) REVERT: H 195 LYS cc_start: 0.8686 (mmtm) cc_final: 0.8331 (mmtp) REVERT: I 195 LYS cc_start: 0.8804 (mmtm) cc_final: 0.8484 (mmtp) REVERT: J 102 GLU cc_start: 0.8649 (tt0) cc_final: 0.8321 (tp30) REVERT: J 215 GLN cc_start: 0.8556 (tt0) cc_final: 0.8312 (mm-40) outliers start: 33 outliers final: 21 residues processed: 358 average time/residue: 0.2780 time to fit residues: 140.2113 Evaluate side-chains 359 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 338 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 68 THR Chi-restraints excluded: chain B residue 163 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 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 201 SER Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 230 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 6 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 173 GLN C 100 ASN C 114 GLN C 215 GLN D 114 GLN D 215 GLN E 110 GLN E 215 GLN F 110 GLN H 215 GLN I 215 GLN J 100 ASN J 114 GLN J 215 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.109214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.083425 restraints weight = 15698.422| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.13 r_work: 0.2596 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13910 Z= 0.184 Angle : 0.541 10.229 18830 Z= 0.269 Chirality : 0.045 0.128 2190 Planarity : 0.005 0.048 2420 Dihedral : 4.545 14.254 1800 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.36 % Allowed : 15.84 % 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 (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: -0.44 (0.22), residues: 1660 helix: 0.82 (0.44), residues: 170 sheet: 0.02 (0.20), residues: 780 loop : -0.82 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 186 HIS 0.004 0.001 HIS F 152 PHE 0.009 0.001 PHE G 58 TYR 0.015 0.002 TYR A 103 ARG 0.007 0.000 ARG H 229 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 150) hydrogen bonds : angle 7.11664 ( 420) SS BOND : bond 0.00028 ( 10) SS BOND : angle 0.09556 ( 20) covalent geometry : bond 0.00452 (13900) covalent geometry : angle 0.54117 (18810) *********************** 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 382 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 344 time to evaluate : 1.680 Fit side-chains REVERT: A 102 GLU cc_start: 0.8614 (tt0) cc_final: 0.8314 (tp30) REVERT: A 199 GLU cc_start: 0.8247 (tt0) cc_final: 0.8038 (tt0) REVERT: B 85 GLN cc_start: 0.8947 (mm-40) cc_final: 0.8628 (mm-40) REVERT: B 98 ARG cc_start: 0.8570 (tpp-160) cc_final: 0.8252 (mmt-90) REVERT: B 195 LYS cc_start: 0.8824 (mmtm) cc_final: 0.8513 (mmtp) REVERT: C 98 ARG cc_start: 0.8763 (tpp-160) cc_final: 0.8267 (mmt180) REVERT: D 98 ARG cc_start: 0.8586 (tpp-160) cc_final: 0.8339 (mmt-90) REVERT: D 199 GLU cc_start: 0.8409 (tt0) cc_final: 0.7789 (tm-30) REVERT: D 201 SER cc_start: 0.8979 (m) cc_final: 0.8539 (m) REVERT: E 199 GLU cc_start: 0.8399 (tt0) cc_final: 0.8114 (tt0) REVERT: E 201 SER cc_start: 0.8912 (m) cc_final: 0.8597 (p) REVERT: E 227 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8484 (ttpt) REVERT: F 199 GLU cc_start: 0.8488 (tt0) cc_final: 0.8251 (tt0) REVERT: G 195 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8340 (mmtp) REVERT: H 194 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: H 195 LYS cc_start: 0.8724 (mmtm) cc_final: 0.8366 (mmtp) REVERT: I 98 ARG cc_start: 0.8569 (tpp-160) cc_final: 0.8286 (mmt-90) REVERT: I 195 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8499 (mmtp) REVERT: J 102 GLU cc_start: 0.8624 (tt0) cc_final: 0.8272 (tp30) REVERT: J 215 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8326 (mm-40) outliers start: 38 outliers final: 23 residues processed: 365 average time/residue: 0.2791 time to fit residues: 143.9803 Evaluate side-chains 356 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 331 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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 A residue 230 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 205 ILE 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 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 201 SER Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain J residue 62 ASN Chi-restraints excluded: chain J residue 215 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 215 GLN E 110 GLN E 215 GLN F 110 GLN H 100 ASN H 114 GLN H 215 GLN I 215 GLN J 215 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.107460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.082434 restraints weight = 15729.806| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.04 r_work: 0.2568 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2391 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13910 Z= 0.258 Angle : 0.603 10.891 18830 Z= 0.296 Chirality : 0.047 0.128 2190 Planarity : 0.005 0.051 2420 Dihedral : 4.791 15.410 1800 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.36 % Allowed : 16.02 % 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 (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: -0.49 (0.22), residues: 1660 helix: 0.64 (0.43), residues: 170 sheet: 0.05 (0.20), residues: 780 loop : -0.89 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 186 HIS 0.005 0.002 HIS E 152 PHE 0.011 0.002 PHE G 58 TYR 0.017 0.002 TYR A 103 ARG 0.008 0.001 ARG H 229 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 150) hydrogen bonds : angle 7.18938 ( 420) SS BOND : bond 0.00048 ( 10) SS BOND : angle 0.18591 ( 20) covalent geometry : bond 0.00630 (13900) covalent geometry : angle 0.60295 (18810) *********************** 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 368 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 330 time to evaluate : 1.633 Fit side-chains REVERT: A 102 GLU cc_start: 0.8560 (tt0) cc_final: 0.8285 (tp30) REVERT: A 199 GLU cc_start: 0.8338 (tt0) cc_final: 0.8089 (tt0) REVERT: B 195 LYS cc_start: 0.8851 (mmtm) cc_final: 0.8520 (mmtp) REVERT: C 230 MET cc_start: 0.6101 (ppp) cc_final: 0.5427 (ptp) REVERT: D 199 GLU cc_start: 0.8400 (tt0) cc_final: 0.8194 (tt0) REVERT: D 201 SER cc_start: 0.8952 (m) cc_final: 0.8750 (m) REVERT: E 184 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7873 (mm-30) REVERT: E 199 GLU cc_start: 0.8356 (tt0) cc_final: 0.8074 (tt0) REVERT: E 201 SER cc_start: 0.8965 (m) cc_final: 0.8641 (p) REVERT: E 227 LYS cc_start: 0.8816 (ttmm) cc_final: 0.8440 (ttpt) REVERT: F 98 ARG cc_start: 0.8423 (mmt-90) cc_final: 0.7979 (mmt180) REVERT: F 199 GLU cc_start: 0.8481 (tt0) cc_final: 0.8233 (tt0) REVERT: G 195 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8386 (mmtp) REVERT: H 195 LYS cc_start: 0.8735 (mmtm) cc_final: 0.8367 (mmtp) REVERT: I 195 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8532 (mmtp) outliers start: 38 outliers final: 25 residues processed: 353 average time/residue: 0.2707 time to fit residues: 135.2902 Evaluate side-chains 361 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 336 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 205 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 F residue 212 GLU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain J residue 62 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 169 GLN B 173 GLN C 100 ASN C 215 GLN D 215 GLN E 110 GLN E 215 GLN H 100 ASN H 215 GLN I 215 GLN J 114 GLN J 215 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.108901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.083353 restraints weight = 15565.307| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.11 r_work: 0.2599 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2418 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13910 Z= 0.175 Angle : 0.541 10.557 18830 Z= 0.268 Chirality : 0.045 0.146 2190 Planarity : 0.004 0.048 2420 Dihedral : 4.559 15.348 1800 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.61 % Allowed : 16.83 % Favored : 81.55 % 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: -0.46 (0.22), residues: 1660 helix: 0.82 (0.44), residues: 170 sheet: -0.04 (0.20), residues: 790 loop : -0.79 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 186 HIS 0.003 0.001 HIS F 152 PHE 0.008 0.001 PHE G 58 TYR 0.015 0.002 TYR A 103 ARG 0.008 0.000 ARG H 229 Details of bonding type rmsd hydrogen bonds : bond 0.03274 ( 150) hydrogen bonds : angle 6.97894 ( 420) SS BOND : bond 0.00022 ( 10) SS BOND : angle 0.09236 ( 20) covalent geometry : bond 0.00429 (13900) covalent geometry : angle 0.54146 (18810) *********************** 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 372 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 346 time to evaluate : 1.498 Fit side-chains REVERT: A 102 GLU cc_start: 0.8582 (tt0) cc_final: 0.8331 (tp30) REVERT: A 199 GLU cc_start: 0.8320 (tt0) cc_final: 0.8084 (tt0) REVERT: B 195 LYS cc_start: 0.8851 (mmtm) cc_final: 0.8508 (mmtp) REVERT: C 98 ARG cc_start: 0.8766 (tpp-160) cc_final: 0.8533 (mmt-90) REVERT: D 98 ARG cc_start: 0.8544 (tpp-160) cc_final: 0.8234 (mmt180) REVERT: E 184 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7853 (mm-30) REVERT: E 199 GLU cc_start: 0.8327 (tt0) cc_final: 0.8030 (tt0) REVERT: E 201 SER cc_start: 0.8998 (m) cc_final: 0.8660 (p) REVERT: E 227 LYS cc_start: 0.8841 (ttmm) cc_final: 0.8471 (ttpt) REVERT: F 199 GLU cc_start: 0.8471 (tt0) cc_final: 0.8241 (tt0) REVERT: G 195 LYS cc_start: 0.8753 (mmtm) cc_final: 0.8353 (mmtp) REVERT: H 195 LYS cc_start: 0.8747 (mmtm) cc_final: 0.8374 (mmtp) REVERT: I 195 LYS cc_start: 0.8843 (mmtm) cc_final: 0.8494 (mmtp) REVERT: J 99 ASP cc_start: 0.7975 (t70) cc_final: 0.7769 (t0) REVERT: J 229 ARG cc_start: 0.8752 (mtm110) cc_final: 0.8539 (mtm110) outliers start: 26 outliers final: 23 residues processed: 364 average time/residue: 0.2825 time to fit residues: 144.9754 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 : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE 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 163 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 194 ASP 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 201 SER Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 211 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 146 optimal weight: 0.0270 chunk 79 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 167 optimal weight: 0.0770 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 169 GLN B 173 GLN C 100 ASN C 114 GLN C 215 GLN D 215 GLN E 110 GLN E 215 GLN F 110 GLN H 114 GLN H 215 GLN I 114 GLN I 215 GLN J 114 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.111014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.085682 restraints weight = 15524.571| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.09 r_work: 0.2624 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13910 Z= 0.115 Angle : 0.508 11.762 18830 Z= 0.252 Chirality : 0.044 0.123 2190 Planarity : 0.004 0.048 2420 Dihedral : 4.293 16.893 1800 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.18 % Allowed : 17.76 % Favored : 81.06 % 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: -0.36 (0.22), residues: 1660 helix: 1.08 (0.45), residues: 170 sheet: 0.01 (0.20), residues: 790 loop : -0.75 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP I 186 HIS 0.002 0.001 HIS F 152 PHE 0.006 0.001 PHE G 58 TYR 0.013 0.001 TYR F 103 ARG 0.009 0.000 ARG H 229 Details of bonding type rmsd hydrogen bonds : bond 0.02837 ( 150) hydrogen bonds : angle 6.82457 ( 420) SS BOND : bond 0.00026 ( 10) SS BOND : angle 0.15059 ( 20) covalent geometry : bond 0.00283 (13900) covalent geometry : angle 0.50850 (18810) ********************** 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 367 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 348 time to evaluate : 1.512 Fit side-chains REVERT: A 85 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8494 (mt0) REVERT: A 103 TYR cc_start: 0.9169 (m-80) cc_final: 0.8927 (m-80) REVERT: A 199 GLU cc_start: 0.8266 (tt0) cc_final: 0.8027 (tt0) REVERT: B 98 ARG cc_start: 0.8517 (tpp-160) cc_final: 0.8287 (mmt-90) REVERT: B 195 LYS cc_start: 0.8824 (mmtm) cc_final: 0.8479 (mmtp) REVERT: C 98 ARG cc_start: 0.8667 (tpp-160) cc_final: 0.8389 (mmt-90) REVERT: D 98 ARG cc_start: 0.8508 (tpp-160) cc_final: 0.8212 (mmt180) REVERT: D 215 GLN cc_start: 0.8231 (tt0) cc_final: 0.7950 (tt0) REVERT: E 193 GLU cc_start: 0.8222 (mt-10) cc_final: 0.8007 (mt-10) REVERT: E 199 GLU cc_start: 0.8295 (tt0) cc_final: 0.7982 (tt0) REVERT: E 201 SER cc_start: 0.8993 (m) cc_final: 0.8649 (p) REVERT: E 227 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8470 (ttpt) REVERT: G 98 ARG cc_start: 0.8468 (tpp-160) cc_final: 0.8158 (mmt-90) REVERT: G 195 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8274 (mmtp) REVERT: H 195 LYS cc_start: 0.8736 (mmtm) cc_final: 0.8370 (mmtp) REVERT: I 195 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8452 (mmtp) REVERT: J 229 ARG cc_start: 0.8727 (mtm110) cc_final: 0.8484 (mtm110) outliers start: 19 outliers final: 16 residues processed: 360 average time/residue: 0.2714 time to fit residues: 137.5663 Evaluate side-chains 363 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 347 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 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 I residue 122 LEU Chi-restraints excluded: chain I residue 211 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 139 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN B 173 GLN C 114 GLN C 215 GLN E 110 GLN E 215 GLN F 110 GLN F 173 GLN H 100 ASN H 215 GLN I 114 GLN I 215 GLN J 114 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.108863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.083913 restraints weight = 15697.475| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.02 r_work: 0.2591 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2415 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13910 Z= 0.194 Angle : 0.564 11.862 18830 Z= 0.277 Chirality : 0.046 0.126 2190 Planarity : 0.005 0.048 2420 Dihedral : 4.559 16.101 1800 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.24 % Allowed : 18.01 % Favored : 80.75 % 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: -0.38 (0.22), residues: 1660 helix: 0.86 (0.44), residues: 170 sheet: 0.05 (0.20), residues: 790 loop : -0.78 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 186 HIS 0.004 0.001 HIS F 152 PHE 0.009 0.001 PHE G 58 TYR 0.014 0.002 TYR A 103 ARG 0.009 0.001 ARG H 229 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 150) hydrogen bonds : angle 6.95771 ( 420) SS BOND : bond 0.00033 ( 10) SS BOND : angle 0.08988 ( 20) covalent geometry : bond 0.00473 (13900) covalent geometry : angle 0.56459 (18810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7458.19 seconds wall clock time: 129 minutes 31.87 seconds (7771.87 seconds total)