Starting phenix.real_space_refine on Wed Sep 17 04:54:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jt1_61788/09_2025/9jt1_61788.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jt1_61788/09_2025/9jt1_61788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jt1_61788/09_2025/9jt1_61788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jt1_61788/09_2025/9jt1_61788.map" model { file = "/net/cci-nas-00/data/ceres_data/9jt1_61788/09_2025/9jt1_61788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jt1_61788/09_2025/9jt1_61788.cif" } resolution = 3.09 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= 0.003 sd= 0.168 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 41 5.16 5 C 2908 2.51 5 N 763 2.21 5 O 877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4589 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 892 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 96} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 992 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 102} Chain: "A" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 561 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 547 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 68} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 1.39, per 1000 atoms: 0.30 Number of scatterers: 4589 At special positions: 0 Unit cell: (67.221, 99.231, 86.427, 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 41 16.00 O 877 8.00 N 763 7.00 C 2908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 137 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 138 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 149 " 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: 0.36 Conformation dependent library (CDL) restraints added in 218.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 13 sheets defined 14.9% alpha, 38.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'H' and resid 26 through 32 removed outlier: 3.676A pdb=" N PHE H 29 " --> pdb=" O GLY H 26 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG H 30 " --> pdb=" O ARG H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.561A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.650A pdb=" N THR H 91 " --> pdb=" O VAL H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.539A pdb=" N ASN L 29 " --> pdb=" O LYS L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.863A pdb=" N GLU L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.072A pdb=" N THR C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'B' and resid 89 through 102 Processing helix chain 'B' and resid 156 through 168 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.206A pdb=" N TYR H 33 " --> pdb=" O TRP H 99 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.615A pdb=" N VAL H 108 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.716A pdb=" N VAL L 10 " --> pdb=" O ARG L 102 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.716A pdb=" N VAL L 10 " --> pdb=" O ARG L 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.288A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 58 through 60 removed outlier: 5.288A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.649A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.791A pdb=" N ILE D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR D 49 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 136 through 140 Processing sheet with id=AB4, first strand: chain 'B' and resid 125 through 126 removed outlier: 4.410A pdb=" N MET B 125 " --> pdb=" O TYR B 134 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 498 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: 0.74 Time building geometry restraints manager: 0.51 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: 1439 1.34 - 1.46: 1159 1.46 - 1.58: 2048 1.58 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 4699 Sorted by residual: bond pdb=" N GLY C 100 " pdb=" CA GLY C 100 " ideal model delta sigma weight residual 1.449 1.465 -0.015 1.45e-02 4.76e+03 1.12e+00 bond pdb=" C TYR L 48 " pdb=" N GLU L 49 " ideal model delta sigma weight residual 1.332 1.320 0.013 1.40e-02 5.10e+03 7.99e-01 bond pdb=" CB ILE L 47 " pdb=" CG2 ILE L 47 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.77e-01 bond pdb=" CB CYS A 107 " pdb=" SG CYS A 107 " ideal model delta sigma weight residual 1.808 1.785 0.023 3.30e-02 9.18e+02 5.04e-01 bond pdb=" CB PRO D 95 " pdb=" CG PRO D 95 " ideal model delta sigma weight residual 1.506 1.479 0.027 3.90e-02 6.57e+02 4.88e-01 ... (remaining 4694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.87: 5848 0.87 - 1.74: 441 1.74 - 2.60: 70 2.60 - 3.47: 32 3.47 - 4.34: 6 Bond angle restraints: 6397 Sorted by residual: angle pdb=" N VAL L 46 " pdb=" CA VAL L 46 " pdb=" C VAL L 46 " ideal model delta sigma weight residual 111.81 109.04 2.77 8.60e-01 1.35e+00 1.04e+01 angle pdb=" N VAL H 61 " pdb=" CA VAL H 61 " pdb=" C VAL H 61 " ideal model delta sigma weight residual 110.05 107.40 2.65 1.09e+00 8.42e-01 5.91e+00 angle pdb=" C SER D 50 " pdb=" N THR D 51 " pdb=" CA THR D 51 " ideal model delta sigma weight residual 121.54 125.78 -4.24 1.91e+00 2.74e-01 4.93e+00 angle pdb=" N SER D 65 " pdb=" CA SER D 65 " pdb=" C SER D 65 " ideal model delta sigma weight residual 108.24 110.92 -2.68 1.32e+00 5.74e-01 4.13e+00 angle pdb=" C CYS B 149 " pdb=" N ILE B 150 " pdb=" CA ILE B 150 " ideal model delta sigma weight residual 123.04 121.33 1.71 9.20e-01 1.18e+00 3.45e+00 ... (remaining 6392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.67: 2558 13.67 - 27.35: 155 27.35 - 41.02: 40 41.02 - 54.69: 15 54.69 - 68.36: 5 Dihedral angle restraints: 2773 sinusoidal: 1044 harmonic: 1729 Sorted by residual: dihedral pdb=" CB CYS A 124 " pdb=" SG CYS A 124 " pdb=" SG CYS B 147 " pdb=" CB CYS B 147 " ideal model delta sinusoidal sigma weight residual 93.00 149.38 -56.38 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CA PHE H 32 " pdb=" C PHE H 32 " pdb=" N TYR H 33 " pdb=" CA TYR H 33 " ideal model delta harmonic sigma weight residual 180.00 162.25 17.75 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA VAL A 106 " pdb=" C VAL A 106 " pdb=" N CYS A 107 " pdb=" CA CYS A 107 " ideal model delta harmonic sigma weight residual 180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 2770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 413 0.027 - 0.054: 215 0.054 - 0.081: 40 0.081 - 0.108: 36 0.108 - 0.135: 16 Chirality restraints: 720 Sorted by residual: chirality pdb=" CA ILE D 21 " pdb=" N ILE D 21 " pdb=" C ILE D 21 " pdb=" CB ILE D 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 717 not shown) Planarity restraints: 802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 13 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO C 14 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 13 " -0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO L 14 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO L 14 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 14 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 53 " 0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO L 54 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO L 54 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 54 " 0.015 5.00e-02 4.00e+02 ... (remaining 799 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 432 2.75 - 3.28: 4414 3.28 - 3.82: 7826 3.82 - 4.36: 9499 4.36 - 4.90: 16648 Nonbonded interactions: 38819 Sorted by model distance: nonbonded pdb=" OG SER C 52 " pdb=" OD1 ASP C 106 " model vdw 2.207 3.040 nonbonded pdb=" OG SER D 65 " pdb=" OG1 THR D 72 " model vdw 2.219 3.040 nonbonded pdb=" OG SER C 52 " pdb=" OH TYR C 111 " model vdw 2.235 3.040 nonbonded pdb=" OG SER D 7 " pdb=" OG1 THR D 22 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR D 36 " pdb=" OE1 GLN D 89 " model vdw 2.242 3.040 ... (remaining 38814 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 88 and (name N or name CA or name C or name O or name CB \ )) or resid 89 through 90 or (resid 91 and (name N or name CA or name C or name \ O or name CB )) or resid 92 or (resid 93 and (name N or name CA or name C or nam \ e O or name CB )) or resid 94 through 109 or (resid 110 and (name N or name CA o \ r name C or name O or name CB )) or resid 116 through 143 or (resid 144 and (nam \ e N or name CA or name C or name O or name CB )) or resid 145 through 168)) selection = (chain 'B' and (resid 88 through 126 or resid 133 through 168)) } 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 6.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 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 0.032 4711 Z= 0.149 Angle : 0.545 4.340 6421 Z= 0.323 Chirality : 0.040 0.135 720 Planarity : 0.003 0.029 802 Dihedral : 10.522 68.363 1635 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.38 % Allowed : 6.15 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -0.26 (0.36), residues: 593 helix: 2.07 (0.71), residues: 56 sheet: -0.77 (0.37), residues: 193 loop : -0.07 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 72 TYR 0.013 0.001 TYR L 48 PHE 0.013 0.001 PHE H 29 TRP 0.013 0.001 TRP A 156 HIS 0.002 0.001 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4699) covalent geometry : angle 0.54279 ( 6397) SS BOND : bond 0.00319 ( 12) SS BOND : angle 0.98387 ( 24) hydrogen bonds : bond 0.15490 ( 175) hydrogen bonds : angle 8.12209 ( 498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 19 ARG cc_start: 0.7545 (ttp80) cc_final: 0.7314 (ttm170) REVERT: H 87 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.6512 (mtm-85) REVERT: L 102 ARG cc_start: 0.7760 (ttt180) cc_final: 0.7490 (tpt170) REVERT: C 19 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7410 (ttp80) REVERT: C 65 LYS cc_start: 0.7009 (tttp) cc_final: 0.6688 (tttm) REVERT: C 82 GLN cc_start: 0.6663 (tp40) cc_final: 0.6279 (tp40) REVERT: C 85 SER cc_start: 0.7888 (m) cc_final: 0.7278 (t) REVERT: D 42 LYS cc_start: 0.8025 (mtpp) cc_final: 0.7675 (mttt) outliers start: 12 outliers final: 7 residues processed: 115 average time/residue: 0.0965 time to fit residues: 13.3256 Evaluate side-chains 93 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.135673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.110572 restraints weight = 5233.251| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.14 r_work: 0.3002 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4711 Z= 0.179 Angle : 0.547 6.241 6421 Z= 0.287 Chirality : 0.043 0.141 720 Planarity : 0.004 0.029 802 Dihedral : 6.243 51.307 661 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.16 % Allowed : 11.31 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -0.14 (0.36), residues: 593 helix: 2.32 (0.71), residues: 56 sheet: -0.56 (0.40), residues: 184 loop : -0.13 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 122 TYR 0.014 0.002 TYR L 48 PHE 0.021 0.002 PHE H 29 TRP 0.014 0.002 TRP H 47 HIS 0.002 0.002 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 4699) covalent geometry : angle 0.54014 ( 6397) SS BOND : bond 0.00621 ( 12) SS BOND : angle 1.49064 ( 24) hydrogen bonds : bond 0.03036 ( 175) hydrogen bonds : angle 5.81452 ( 498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 4 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8651 (mt) REVERT: L 60 ARG cc_start: 0.8663 (mtm110) cc_final: 0.8397 (mtm110) REVERT: L 102 ARG cc_start: 0.8496 (ttt180) cc_final: 0.8054 (tpt170) REVERT: C 65 LYS cc_start: 0.7769 (tttp) cc_final: 0.7490 (tttm) REVERT: C 82 GLN cc_start: 0.8032 (tp40) cc_final: 0.7656 (tp40) REVERT: C 85 SER cc_start: 0.8236 (m) cc_final: 0.7837 (p) REVERT: D 42 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7862 (mttt) REVERT: D 87 TYR cc_start: 0.8932 (m-80) cc_final: 0.8573 (m-80) REVERT: A 141 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7621 (tptt) REVERT: A 164 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8809 (mm-30) outliers start: 26 outliers final: 18 residues processed: 104 average time/residue: 0.0845 time to fit residues: 10.7892 Evaluate side-chains 105 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.135671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.111043 restraints weight = 5216.105| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.12 r_work: 0.3011 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4711 Z= 0.157 Angle : 0.530 5.898 6421 Z= 0.274 Chirality : 0.042 0.142 720 Planarity : 0.004 0.029 802 Dihedral : 5.474 52.080 656 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.56 % Allowed : 11.90 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -0.11 (0.36), residues: 593 helix: 2.46 (0.71), residues: 56 sheet: -0.42 (0.39), residues: 191 loop : -0.21 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 122 TYR 0.013 0.001 TYR L 48 PHE 0.018 0.002 PHE H 29 TRP 0.013 0.001 TRP H 47 HIS 0.002 0.002 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 4699) covalent geometry : angle 0.52604 ( 6397) SS BOND : bond 0.00494 ( 12) SS BOND : angle 1.22631 ( 24) hydrogen bonds : bond 0.02627 ( 175) hydrogen bonds : angle 5.54526 ( 498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 102 ARG cc_start: 0.8520 (ttt180) cc_final: 0.8074 (tpt170) REVERT: C 13 LYS cc_start: 0.8406 (tppt) cc_final: 0.8004 (tptt) REVERT: C 19 ARG cc_start: 0.8535 (ttp80) cc_final: 0.8332 (ttt-90) REVERT: C 65 LYS cc_start: 0.7824 (tttp) cc_final: 0.7546 (tttm) REVERT: C 82 GLN cc_start: 0.8078 (tp40) cc_final: 0.7547 (tp40) REVERT: C 83 MET cc_start: 0.8658 (mtp) cc_final: 0.8417 (mtp) REVERT: C 85 SER cc_start: 0.8203 (m) cc_final: 0.7807 (p) REVERT: C 106 ASP cc_start: 0.8549 (t0) cc_final: 0.8332 (t0) REVERT: D 42 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7838 (mttt) REVERT: D 60 SER cc_start: 0.8469 (p) cc_final: 0.8269 (m) REVERT: D 87 TYR cc_start: 0.8884 (m-80) cc_final: 0.8546 (m-80) REVERT: A 141 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7654 (tptt) REVERT: A 164 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8804 (mm-30) outliers start: 28 outliers final: 21 residues processed: 108 average time/residue: 0.0935 time to fit residues: 12.3285 Evaluate side-chains 110 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 0.0070 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 0.0470 chunk 12 optimal weight: 0.0060 chunk 53 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.0870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.142570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.118408 restraints weight = 5191.141| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.07 r_work: 0.3155 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4711 Z= 0.083 Angle : 0.477 6.118 6421 Z= 0.242 Chirality : 0.040 0.145 720 Planarity : 0.003 0.029 802 Dihedral : 5.194 54.911 655 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.98 % Allowed : 14.48 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.01 (0.36), residues: 593 helix: 2.56 (0.72), residues: 57 sheet: -0.16 (0.38), residues: 190 loop : -0.27 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 56 TYR 0.009 0.001 TYR L 48 PHE 0.011 0.001 PHE H 29 TRP 0.010 0.001 TRP A 156 HIS 0.001 0.001 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 4699) covalent geometry : angle 0.47512 ( 6397) SS BOND : bond 0.00195 ( 12) SS BOND : angle 0.90017 ( 24) hydrogen bonds : bond 0.02143 ( 175) hydrogen bonds : angle 4.99658 ( 498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 102 ARG cc_start: 0.8105 (ttt180) cc_final: 0.7580 (tpt170) REVERT: C 13 LYS cc_start: 0.8298 (tppt) cc_final: 0.7931 (tppt) REVERT: C 82 GLN cc_start: 0.7780 (tp40) cc_final: 0.7281 (tp40) REVERT: C 83 MET cc_start: 0.8572 (mtp) cc_final: 0.8257 (mtp) REVERT: C 85 SER cc_start: 0.8111 (m) cc_final: 0.7534 (t) REVERT: D 42 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7538 (mttt) REVERT: D 87 TYR cc_start: 0.8702 (m-80) cc_final: 0.8417 (m-80) REVERT: A 141 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7390 (pttt) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 0.0966 time to fit residues: 10.9516 Evaluate side-chains 90 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 17 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.134419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.109559 restraints weight = 5262.070| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.09 r_work: 0.3145 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4711 Z= 0.165 Angle : 0.515 6.190 6421 Z= 0.264 Chirality : 0.041 0.144 720 Planarity : 0.003 0.029 802 Dihedral : 5.263 53.484 654 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.95 % Allowed : 13.29 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -0.02 (0.36), residues: 593 helix: 2.66 (0.71), residues: 56 sheet: -0.39 (0.38), residues: 201 loop : -0.15 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 56 TYR 0.015 0.002 TYR L 48 PHE 0.017 0.001 PHE H 29 TRP 0.013 0.001 TRP H 47 HIS 0.003 0.002 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 4699) covalent geometry : angle 0.51244 ( 6397) SS BOND : bond 0.00501 ( 12) SS BOND : angle 0.98882 ( 24) hydrogen bonds : bond 0.02464 ( 175) hydrogen bonds : angle 5.15369 ( 498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 102 ARG cc_start: 0.8301 (ttt180) cc_final: 0.7843 (tpt170) REVERT: C 13 LYS cc_start: 0.8313 (tppt) cc_final: 0.7871 (tptt) REVERT: C 83 MET cc_start: 0.8644 (mtp) cc_final: 0.8328 (mtp) REVERT: C 85 SER cc_start: 0.8244 (m) cc_final: 0.7686 (t) REVERT: D 42 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7791 (mttt) REVERT: D 87 TYR cc_start: 0.8830 (m-80) cc_final: 0.8559 (m-80) REVERT: A 141 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7635 (pttt) outliers start: 30 outliers final: 21 residues processed: 97 average time/residue: 0.0939 time to fit residues: 11.1405 Evaluate side-chains 99 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.135932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.110652 restraints weight = 5295.229| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.18 r_work: 0.3160 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4711 Z= 0.164 Angle : 0.524 6.386 6421 Z= 0.268 Chirality : 0.042 0.143 720 Planarity : 0.003 0.029 802 Dihedral : 5.373 54.171 654 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.56 % Allowed : 15.08 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.01 (0.36), residues: 593 helix: 2.67 (0.71), residues: 56 sheet: -0.47 (0.37), residues: 212 loop : -0.02 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 56 TYR 0.014 0.001 TYR L 48 PHE 0.017 0.002 PHE H 29 TRP 0.012 0.001 TRP A 156 HIS 0.002 0.002 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 4699) covalent geometry : angle 0.52139 ( 6397) SS BOND : bond 0.00494 ( 12) SS BOND : angle 1.00169 ( 24) hydrogen bonds : bond 0.02443 ( 175) hydrogen bonds : angle 5.19934 ( 498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 102 ARG cc_start: 0.8326 (ttt180) cc_final: 0.7904 (tpt170) REVERT: C 13 LYS cc_start: 0.8336 (tppt) cc_final: 0.7982 (tppt) REVERT: C 85 SER cc_start: 0.8336 (m) cc_final: 0.7789 (t) REVERT: D 42 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7775 (mttt) REVERT: D 87 TYR cc_start: 0.8855 (m-80) cc_final: 0.8600 (m-80) REVERT: A 141 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7675 (pttt) REVERT: A 164 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8831 (mm-30) outliers start: 28 outliers final: 23 residues processed: 102 average time/residue: 0.1000 time to fit residues: 12.3664 Evaluate side-chains 109 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 40 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.108388 restraints weight = 5261.256| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.11 r_work: 0.3188 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4711 Z= 0.137 Angle : 0.515 6.858 6421 Z= 0.263 Chirality : 0.041 0.141 720 Planarity : 0.003 0.029 802 Dihedral : 5.350 53.749 654 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.76 % Allowed : 15.87 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.04 (0.36), residues: 593 helix: 2.71 (0.71), residues: 56 sheet: -0.40 (0.37), residues: 212 loop : -0.04 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 19 TYR 0.013 0.001 TYR L 48 PHE 0.015 0.001 PHE H 29 TRP 0.012 0.001 TRP A 156 HIS 0.002 0.001 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4699) covalent geometry : angle 0.51267 ( 6397) SS BOND : bond 0.00418 ( 12) SS BOND : angle 0.89662 ( 24) hydrogen bonds : bond 0.02326 ( 175) hydrogen bonds : angle 5.09693 ( 498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 102 ARG cc_start: 0.8315 (ttt180) cc_final: 0.7882 (tpt170) REVERT: C 13 LYS cc_start: 0.8328 (tppt) cc_final: 0.7972 (tppt) REVERT: C 85 SER cc_start: 0.8323 (m) cc_final: 0.7759 (t) REVERT: D 42 LYS cc_start: 0.8099 (mtpp) cc_final: 0.7745 (mttt) REVERT: A 141 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7681 (pttt) outliers start: 24 outliers final: 22 residues processed: 97 average time/residue: 0.1009 time to fit residues: 11.8248 Evaluate side-chains 102 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 23 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 0.0000 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.0270 chunk 6 optimal weight: 0.9980 overall best weight: 0.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.137519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.113034 restraints weight = 5230.184| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.09 r_work: 0.3159 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4711 Z= 0.113 Angle : 0.498 7.473 6421 Z= 0.254 Chirality : 0.040 0.141 720 Planarity : 0.003 0.029 802 Dihedral : 5.266 54.162 654 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.16 % Allowed : 15.28 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.08 (0.36), residues: 593 helix: 2.75 (0.71), residues: 56 sheet: -0.32 (0.37), residues: 211 loop : -0.07 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 122 TYR 0.012 0.001 TYR L 48 PHE 0.013 0.001 PHE H 29 TRP 0.012 0.001 TRP A 156 HIS 0.002 0.001 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4699) covalent geometry : angle 0.49699 ( 6397) SS BOND : bond 0.00325 ( 12) SS BOND : angle 0.73988 ( 24) hydrogen bonds : bond 0.02225 ( 175) hydrogen bonds : angle 4.95015 ( 498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: L 102 ARG cc_start: 0.8235 (ttt180) cc_final: 0.7761 (tpt170) REVERT: C 13 LYS cc_start: 0.8295 (tppt) cc_final: 0.7938 (tppt) REVERT: C 19 ARG cc_start: 0.8303 (ttt-90) cc_final: 0.7980 (tpt-90) REVERT: C 85 SER cc_start: 0.8282 (m) cc_final: 0.7687 (t) REVERT: D 42 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7634 (mttt) REVERT: A 141 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7604 (pttt) outliers start: 26 outliers final: 24 residues processed: 94 average time/residue: 0.1005 time to fit residues: 11.4269 Evaluate side-chains 102 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 4 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.133917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.109443 restraints weight = 5257.437| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.07 r_work: 0.3128 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4711 Z= 0.153 Angle : 0.519 6.651 6421 Z= 0.266 Chirality : 0.042 0.147 720 Planarity : 0.003 0.028 802 Dihedral : 5.359 54.068 654 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.76 % Allowed : 15.87 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.07 (0.36), residues: 593 helix: 2.75 (0.71), residues: 56 sheet: -0.38 (0.38), residues: 207 loop : -0.03 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 122 TYR 0.014 0.001 TYR L 48 PHE 0.016 0.002 PHE H 29 TRP 0.012 0.001 TRP A 156 HIS 0.002 0.001 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 4699) covalent geometry : angle 0.51614 ( 6397) SS BOND : bond 0.00495 ( 12) SS BOND : angle 0.99747 ( 24) hydrogen bonds : bond 0.02412 ( 175) hydrogen bonds : angle 5.08718 ( 498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: L 102 ARG cc_start: 0.8208 (ttt180) cc_final: 0.7787 (tpt170) REVERT: C 13 LYS cc_start: 0.8307 (tppt) cc_final: 0.7950 (tppt) REVERT: C 19 ARG cc_start: 0.8377 (ttt-90) cc_final: 0.8042 (tpt-90) REVERT: C 85 SER cc_start: 0.8227 (m) cc_final: 0.7629 (t) REVERT: D 42 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7619 (mttt) REVERT: A 141 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7570 (pttt) outliers start: 24 outliers final: 23 residues processed: 92 average time/residue: 0.0953 time to fit residues: 10.6589 Evaluate side-chains 99 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.135470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110346 restraints weight = 5262.950| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.19 r_work: 0.3177 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4711 Z= 0.142 Angle : 0.512 6.438 6421 Z= 0.262 Chirality : 0.042 0.158 720 Planarity : 0.003 0.028 802 Dihedral : 5.345 53.966 654 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.56 % Allowed : 16.27 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.03 (0.36), residues: 593 helix: 2.74 (0.71), residues: 56 sheet: -0.38 (0.38), residues: 211 loop : -0.08 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 122 TYR 0.013 0.001 TYR L 48 PHE 0.015 0.002 PHE H 29 TRP 0.012 0.001 TRP A 156 HIS 0.002 0.001 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4699) covalent geometry : angle 0.50994 ( 6397) SS BOND : bond 0.00449 ( 12) SS BOND : angle 0.94558 ( 24) hydrogen bonds : bond 0.02356 ( 175) hydrogen bonds : angle 5.05772 ( 498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1186 Ramachandran restraints generated. 593 Oldfield, 0 Emsley, 593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7402 (mtmt) cc_final: 0.7153 (pttt) REVERT: L 59 GLU cc_start: 0.7680 (tt0) cc_final: 0.7460 (mp0) REVERT: L 102 ARG cc_start: 0.8281 (ttt180) cc_final: 0.7918 (tpt170) REVERT: C 13 LYS cc_start: 0.8298 (tppt) cc_final: 0.7938 (tppt) REVERT: C 19 ARG cc_start: 0.8369 (ttt-90) cc_final: 0.8048 (tpt-90) REVERT: C 85 SER cc_start: 0.8322 (m) cc_final: 0.7726 (t) REVERT: A 141 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7731 (pttt) outliers start: 23 outliers final: 22 residues processed: 89 average time/residue: 0.0941 time to fit residues: 10.1861 Evaluate side-chains 98 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 140 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.112674 restraints weight = 5224.565| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.21 r_work: 0.3027 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4711 Z= 0.133 Angle : 0.505 6.174 6421 Z= 0.259 Chirality : 0.041 0.158 720 Planarity : 0.003 0.028 802 Dihedral : 5.311 53.818 654 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.56 % Allowed : 16.27 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.02 (0.36), residues: 593 helix: 2.75 (0.71), residues: 56 sheet: -0.40 (0.37), residues: 211 loop : -0.08 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 122 TYR 0.013 0.001 TYR L 48 PHE 0.015 0.002 PHE H 29 TRP 0.012 0.001 TRP A 156 HIS 0.002 0.001 HIS L 37 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 4699) covalent geometry : angle 0.50306 ( 6397) SS BOND : bond 0.00425 ( 12) SS BOND : angle 0.90447 ( 24) hydrogen bonds : bond 0.02309 ( 175) hydrogen bonds : angle 5.02759 ( 498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1419.17 seconds wall clock time: 24 minutes 57.24 seconds (1497.24 seconds total)