Starting phenix.real_space_refine on Wed Mar 4 01:24:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qey_13944/03_2026/7qey_13944.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qey_13944/03_2026/7qey_13944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qey_13944/03_2026/7qey_13944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qey_13944/03_2026/7qey_13944.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qey_13944/03_2026/7qey_13944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qey_13944/03_2026/7qey_13944.map" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 6198 2.51 5 N 1428 2.21 5 O 1757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9467 Number of models: 1 Model: "" Number of chains: 18 Chain: "G" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1483 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 175} Chain breaks: 1 Chain: "H" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1483 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 175} Chain breaks: 1 Chain: "I" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1483 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1483 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 175} Chain breaks: 1 Chain: "K" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1483 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 175} Chain breaks: 1 Chain: "L" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1483 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 175} Chain breaks: 1 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "K" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Time building chain proxies: 2.12, per 1000 atoms: 0.22 Number of scatterers: 9467 At special positions: 0 Unit cell: (97.75, 107.95, 85, 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 84 16.00 O 1757 8.00 N 1428 7.00 C 6198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 180 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 180 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 180 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 169 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 180 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 174 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 169 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 180 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 174 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 169 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 180 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 174 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 169 " 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: 0.63 Conformation dependent library (CDL) restraints added in 342.2 milliseconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 73.2% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'G' and resid 9 through 14 removed outlier: 4.072A pdb=" N VAL G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 39 Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.858A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 101 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 130 through 159 removed outlier: 3.554A pdb=" N THR G 135 " --> pdb=" O SER G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 217 Processing helix chain 'H' and resid 10 through 14 Processing helix chain 'H' and resid 23 through 39 Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.858A pdb=" N VAL H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 101 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 130 through 159 removed outlier: 3.555A pdb=" N THR H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 217 Processing helix chain 'I' and resid 10 through 14 Processing helix chain 'I' and resid 23 through 39 Processing helix chain 'I' and resid 39 through 44 removed outlier: 3.858A pdb=" N VAL I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 101 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 130 through 159 removed outlier: 3.555A pdb=" N THR I 135 " --> pdb=" O SER I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 217 Processing helix chain 'J' and resid 10 through 14 Processing helix chain 'J' and resid 23 through 39 Processing helix chain 'J' and resid 39 through 44 removed outlier: 3.858A pdb=" N VAL J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 101 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 130 through 159 removed outlier: 3.555A pdb=" N THR J 135 " --> pdb=" O SER J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 217 Processing helix chain 'K' and resid 10 through 14 Processing helix chain 'K' and resid 23 through 39 Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.858A pdb=" N VAL K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 101 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 130 through 159 removed outlier: 3.555A pdb=" N THR K 135 " --> pdb=" O SER K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 217 Processing helix chain 'L' and resid 10 through 14 Processing helix chain 'L' and resid 23 through 39 Processing helix chain 'L' and resid 39 through 44 removed outlier: 3.858A pdb=" N VAL L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 101 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 130 through 159 removed outlier: 3.556A pdb=" N THR L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 217 Processing sheet with id=AA1, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'H' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'I' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'J' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'K' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'L' and resid 52 through 53 636 hydrogen bonds defined for protein. 1872 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: 0.96 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2640 1.35 - 1.46: 2519 1.46 - 1.58: 4135 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 9414 Sorted by residual: bond pdb=" C1 LMT H 303 " pdb=" C2 LMT H 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 LMT G 303 " pdb=" C2 LMT G 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" C1 LMT K 305 " pdb=" C2 LMT K 305 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C1 LMT H 305 " pdb=" C2 LMT H 305 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" C1 LMT I 305 " pdb=" C2 LMT I 305 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.01e+00 ... (remaining 9409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 12343 1.61 - 3.22: 144 3.22 - 4.83: 53 4.83 - 6.44: 90 6.44 - 8.05: 60 Bond angle restraints: 12690 Sorted by residual: angle pdb=" C6 LMT H 305 " pdb=" C7 LMT H 305 " pdb=" C8 LMT H 305 " ideal model delta sigma weight residual 117.26 109.21 8.05 3.00e+00 1.11e-01 7.21e+00 angle pdb=" C6 LMT K 305 " pdb=" C7 LMT K 305 " pdb=" C8 LMT K 305 " ideal model delta sigma weight residual 117.26 109.22 8.04 3.00e+00 1.11e-01 7.18e+00 angle pdb=" C6 LMT G 305 " pdb=" C7 LMT G 305 " pdb=" C8 LMT G 305 " ideal model delta sigma weight residual 117.26 109.23 8.03 3.00e+00 1.11e-01 7.17e+00 angle pdb=" C6 LMT J 305 " pdb=" C7 LMT J 305 " pdb=" C8 LMT J 305 " ideal model delta sigma weight residual 117.26 109.23 8.03 3.00e+00 1.11e-01 7.16e+00 angle pdb=" C6 LMT I 305 " pdb=" C7 LMT I 305 " pdb=" C8 LMT I 305 " ideal model delta sigma weight residual 117.26 109.24 8.02 3.00e+00 1.11e-01 7.14e+00 ... (remaining 12685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.23: 4926 11.23 - 22.46: 372 22.46 - 33.69: 96 33.69 - 44.93: 54 44.93 - 56.16: 24 Dihedral angle restraints: 5472 sinusoidal: 2250 harmonic: 3222 Sorted by residual: dihedral pdb=" N ARG L 75 " pdb=" CA ARG L 75 " pdb=" CB ARG L 75 " pdb=" CG ARG L 75 " ideal model delta sinusoidal sigma weight residual -60.00 -104.22 44.22 3 1.50e+01 4.44e-03 7.95e+00 dihedral pdb=" N ARG K 75 " pdb=" CA ARG K 75 " pdb=" CB ARG K 75 " pdb=" CG ARG K 75 " ideal model delta sinusoidal sigma weight residual -60.00 -104.21 44.21 3 1.50e+01 4.44e-03 7.95e+00 dihedral pdb=" N ARG I 75 " pdb=" CA ARG I 75 " pdb=" CB ARG I 75 " pdb=" CG ARG I 75 " ideal model delta sinusoidal sigma weight residual -60.00 -104.20 44.20 3 1.50e+01 4.44e-03 7.95e+00 ... (remaining 5469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 714 0.021 - 0.041: 417 0.041 - 0.062: 174 0.062 - 0.083: 53 0.083 - 0.103: 64 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA PRO H 185 " pdb=" N PRO H 185 " pdb=" C PRO H 185 " pdb=" CB PRO H 185 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.67e-01 chirality pdb=" CA PRO G 185 " pdb=" N PRO G 185 " pdb=" C PRO G 185 " pdb=" CB PRO G 185 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.63e-01 chirality pdb=" CA ILE I 71 " pdb=" N ILE I 71 " pdb=" C ILE I 71 " pdb=" CB ILE I 71 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.10 2.00e-01 2.50e+01 2.63e-01 ... (remaining 1419 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP K 172 " 0.015 5.00e-02 4.00e+02 2.29e-02 8.39e-01 pdb=" N PRO K 173 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO K 173 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO K 173 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP J 172 " 0.015 5.00e-02 4.00e+02 2.28e-02 8.33e-01 pdb=" N PRO J 173 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO J 173 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO J 173 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP G 172 " -0.015 5.00e-02 4.00e+02 2.28e-02 8.33e-01 pdb=" N PRO G 173 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO G 173 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO G 173 " -0.011 5.00e-02 4.00e+02 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 685 2.74 - 3.28: 9476 3.28 - 3.82: 15551 3.82 - 4.36: 18476 4.36 - 4.90: 31785 Nonbonded interactions: 75973 Sorted by model distance: nonbonded pdb=" O ILE J 71 " pdb=" OH TYR J 158 " model vdw 2.199 3.040 nonbonded pdb=" O ILE H 71 " pdb=" OH TYR H 158 " model vdw 2.199 3.040 nonbonded pdb=" O ILE G 71 " pdb=" OH TYR G 158 " model vdw 2.199 3.040 nonbonded pdb=" O ILE L 71 " pdb=" OH TYR L 158 " model vdw 2.200 3.040 nonbonded pdb=" O ILE I 71 " pdb=" OH TYR I 158 " model vdw 2.200 3.040 ... (remaining 75968 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 9 through 301 or resid 303 through 304)) selection = (chain 'H' and (resid 9 through 301 or resid 303 through 304)) selection = (chain 'I' and (resid 9 through 301 or resid 303 through 304)) selection = (chain 'J' and (resid 9 through 301 or resid 303 through 304)) selection = (chain 'K' and (resid 9 through 301 or resid 303 through 304)) selection = (chain 'L' and (resid 9 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) } 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: 5.210 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.280 Find NCS groups from input model: 0.140 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 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 : 0.005 0.050 9432 Z= 0.237 Angle : 0.848 8.054 12726 Z= 0.339 Chirality : 0.035 0.103 1422 Planarity : 0.003 0.023 1500 Dihedral : 10.531 56.156 3330 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.35 % Allowed : 5.52 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.25), residues: 1068 helix: 1.79 (0.18), residues: 714 sheet: 4.11 (0.69), residues: 66 loop : -1.27 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 99 TYR 0.004 0.001 TYR H 65 PHE 0.007 0.001 PHE L 51 TRP 0.004 0.001 TRP L 77 HIS 0.001 0.000 HIS K 73 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9414) covalent geometry : angle 0.84797 (12690) SS BOND : bond 0.00173 ( 18) SS BOND : angle 0.80446 ( 36) hydrogen bonds : bond 0.25146 ( 636) hydrogen bonds : angle 6.49950 ( 1872) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.333 Fit side-chains REVERT: J 46 ASP cc_start: 0.8042 (p0) cc_final: 0.7715 (p0) outliers start: 23 outliers final: 5 residues processed: 240 average time/residue: 0.4096 time to fit residues: 107.2102 Evaluate side-chains 173 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 14 ASN G 206 ASN H 14 ASN I 14 ASN J 14 ASN L 14 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.126999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.081677 restraints weight = 12468.663| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.60 r_work: 0.2850 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9432 Z= 0.174 Angle : 0.671 10.630 12726 Z= 0.356 Chirality : 0.045 0.140 1422 Planarity : 0.004 0.021 1500 Dihedral : 9.342 57.360 1372 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.17 % Allowed : 11.55 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.25), residues: 1068 helix: 3.10 (0.17), residues: 738 sheet: 3.30 (0.63), residues: 66 loop : -1.19 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 216 TYR 0.016 0.002 TYR L 65 PHE 0.015 0.002 PHE G 51 TRP 0.009 0.001 TRP J 133 HIS 0.005 0.001 HIS J 16 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9414) covalent geometry : angle 0.66905 (12690) SS BOND : bond 0.00314 ( 18) SS BOND : angle 1.17787 ( 36) hydrogen bonds : bond 0.07479 ( 636) hydrogen bonds : angle 4.23089 ( 1872) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.340 Fit side-chains REVERT: G 134 TRP cc_start: 0.7632 (OUTLIER) cc_final: 0.7304 (m100) REVERT: H 216 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7395 (tpm170) REVERT: J 138 SER cc_start: 0.8758 (m) cc_final: 0.8398 (p) REVERT: J 216 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8095 (tpm170) REVERT: K 134 TRP cc_start: 0.7280 (OUTLIER) cc_final: 0.6989 (m100) outliers start: 31 outliers final: 15 residues processed: 204 average time/residue: 0.4095 time to fit residues: 90.7801 Evaluate side-chains 188 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 134 TRP Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain J residue 216 ARG Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 132 LEU Chi-restraints excluded: chain K residue 134 TRP Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 103 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.126654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.081549 restraints weight = 12521.103| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.60 r_work: 0.2856 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9432 Z= 0.138 Angle : 0.589 7.473 12726 Z= 0.305 Chirality : 0.042 0.139 1422 Planarity : 0.003 0.028 1500 Dihedral : 8.761 59.823 1370 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.78 % Allowed : 11.96 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.44 (0.25), residues: 1068 helix: 3.33 (0.17), residues: 738 sheet: 3.03 (0.59), residues: 66 loop : -1.31 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 216 TYR 0.011 0.001 TYR I 65 PHE 0.013 0.002 PHE G 51 TRP 0.009 0.001 TRP J 133 HIS 0.012 0.001 HIS J 94 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9414) covalent geometry : angle 0.58728 (12690) SS BOND : bond 0.00273 ( 18) SS BOND : angle 0.95975 ( 36) hydrogen bonds : bond 0.06092 ( 636) hydrogen bonds : angle 3.93511 ( 1872) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.242 Fit side-chains REVERT: G 134 TRP cc_start: 0.7593 (m-10) cc_final: 0.7285 (m100) REVERT: I 216 ARG cc_start: 0.7727 (ttp80) cc_final: 0.7314 (tpm170) REVERT: J 138 SER cc_start: 0.8815 (m) cc_final: 0.8457 (p) REVERT: J 212 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6706 (t80) REVERT: L 212 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6751 (t80) outliers start: 37 outliers final: 16 residues processed: 197 average time/residue: 0.4067 time to fit residues: 87.3213 Evaluate side-chains 185 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 134 TRP Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 20 optimal weight: 0.0010 chunk 81 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 99 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.125841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.079728 restraints weight = 12706.383| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.64 r_work: 0.2822 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9432 Z= 0.166 Angle : 0.634 8.051 12726 Z= 0.327 Chirality : 0.044 0.143 1422 Planarity : 0.003 0.037 1500 Dihedral : 8.747 59.415 1370 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.27 % Allowed : 13.70 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.44 (0.25), residues: 1068 helix: 3.32 (0.17), residues: 738 sheet: 2.89 (0.59), residues: 66 loop : -1.24 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 216 TYR 0.017 0.002 TYR I 65 PHE 0.016 0.002 PHE G 51 TRP 0.008 0.001 TRP G 133 HIS 0.011 0.001 HIS J 94 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9414) covalent geometry : angle 0.63214 (12690) SS BOND : bond 0.00381 ( 18) SS BOND : angle 1.15152 ( 36) hydrogen bonds : bond 0.06210 ( 636) hydrogen bonds : angle 3.98943 ( 1872) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.376 Fit side-chains REVERT: G 134 TRP cc_start: 0.7541 (m-10) cc_final: 0.7186 (m100) REVERT: H 132 LEU cc_start: 0.8009 (tt) cc_final: 0.7726 (mm) REVERT: H 212 TYR cc_start: 0.7665 (OUTLIER) cc_final: 0.6966 (t80) REVERT: J 132 LEU cc_start: 0.7898 (tt) cc_final: 0.7613 (mm) REVERT: J 138 SER cc_start: 0.8873 (m) cc_final: 0.8520 (p) REVERT: K 212 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.6874 (t80) REVERT: L 212 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.6785 (t80) outliers start: 32 outliers final: 22 residues processed: 179 average time/residue: 0.4257 time to fit residues: 83.0134 Evaluate side-chains 185 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 41 LYS Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 134 TRP Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 37 optimal weight: 0.0670 chunk 0 optimal weight: 9.9990 chunk 85 optimal weight: 0.0870 chunk 95 optimal weight: 0.7980 chunk 41 optimal weight: 0.0670 chunk 94 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.127492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.082890 restraints weight = 12724.649| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.60 r_work: 0.2879 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9432 Z= 0.117 Angle : 0.573 8.819 12726 Z= 0.290 Chirality : 0.041 0.134 1422 Planarity : 0.003 0.020 1500 Dihedral : 8.289 59.166 1370 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.27 % Allowed : 14.11 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.57 (0.25), residues: 1068 helix: 3.47 (0.17), residues: 738 sheet: 2.92 (0.59), residues: 66 loop : -1.36 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 216 TYR 0.008 0.001 TYR J 65 PHE 0.011 0.001 PHE G 194 TRP 0.008 0.001 TRP G 133 HIS 0.012 0.001 HIS J 94 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9414) covalent geometry : angle 0.57235 (12690) SS BOND : bond 0.00211 ( 18) SS BOND : angle 0.88176 ( 36) hydrogen bonds : bond 0.05162 ( 636) hydrogen bonds : angle 3.73544 ( 1872) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.272 Fit side-chains REVERT: G 134 TRP cc_start: 0.7413 (m-10) cc_final: 0.7146 (m100) REVERT: H 132 LEU cc_start: 0.7984 (tt) cc_final: 0.7712 (mm) REVERT: H 212 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.7068 (t80) REVERT: J 132 LEU cc_start: 0.7770 (tt) cc_final: 0.7504 (mm) REVERT: J 212 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.6781 (t80) REVERT: K 212 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.7096 (t80) REVERT: L 212 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.7012 (t80) outliers start: 32 outliers final: 16 residues processed: 184 average time/residue: 0.4199 time to fit residues: 84.2301 Evaluate side-chains 185 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 134 TRP Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 GLN J 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.125979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.079795 restraints weight = 12556.561| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.64 r_work: 0.2826 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9432 Z= 0.162 Angle : 0.634 8.434 12726 Z= 0.324 Chirality : 0.044 0.142 1422 Planarity : 0.003 0.017 1500 Dihedral : 8.300 59.433 1370 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.68 % Allowed : 14.11 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.54 (0.25), residues: 1068 helix: 3.42 (0.17), residues: 738 sheet: 2.85 (0.60), residues: 66 loop : -1.25 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 216 TYR 0.016 0.002 TYR L 65 PHE 0.015 0.002 PHE I 51 TRP 0.007 0.001 TRP G 133 HIS 0.011 0.001 HIS J 94 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9414) covalent geometry : angle 0.63230 (12690) SS BOND : bond 0.00373 ( 18) SS BOND : angle 1.15109 ( 36) hydrogen bonds : bond 0.05887 ( 636) hydrogen bonds : angle 3.88907 ( 1872) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.217 Fit side-chains REVERT: G 134 TRP cc_start: 0.7478 (m-10) cc_final: 0.7251 (m100) REVERT: H 212 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.7083 (t80) REVERT: J 132 LEU cc_start: 0.7794 (tt) cc_final: 0.7524 (mm) REVERT: J 138 SER cc_start: 0.8902 (m) cc_final: 0.8578 (p) REVERT: K 212 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.7197 (t80) REVERT: L 212 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.7074 (t80) outliers start: 36 outliers final: 21 residues processed: 189 average time/residue: 0.3928 time to fit residues: 81.0245 Evaluate side-chains 189 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 134 TRP Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 41 LYS Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.126374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.080736 restraints weight = 12685.432| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.62 r_work: 0.2841 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9432 Z= 0.144 Angle : 0.637 8.761 12726 Z= 0.325 Chirality : 0.043 0.150 1422 Planarity : 0.003 0.016 1500 Dihedral : 7.862 58.765 1368 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.86 % Allowed : 14.52 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.50 (0.25), residues: 1068 helix: 3.41 (0.17), residues: 738 sheet: 2.85 (0.60), residues: 66 loop : -1.34 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 216 TYR 0.013 0.002 TYR J 68 PHE 0.014 0.002 PHE I 51 TRP 0.008 0.001 TRP I 133 HIS 0.011 0.001 HIS J 94 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9414) covalent geometry : angle 0.63508 (12690) SS BOND : bond 0.00294 ( 18) SS BOND : angle 1.03367 ( 36) hydrogen bonds : bond 0.05560 ( 636) hydrogen bonds : angle 3.85912 ( 1872) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.372 Fit side-chains REVERT: G 134 TRP cc_start: 0.7513 (m-10) cc_final: 0.7230 (m100) REVERT: H 132 LEU cc_start: 0.8041 (tt) cc_final: 0.7784 (mm) REVERT: H 212 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.7194 (t80) REVERT: J 132 LEU cc_start: 0.7794 (tt) cc_final: 0.7548 (mm) REVERT: J 138 SER cc_start: 0.8889 (m) cc_final: 0.8582 (p) REVERT: K 212 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.7276 (t80) REVERT: L 212 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.7077 (t80) outliers start: 28 outliers final: 21 residues processed: 174 average time/residue: 0.4150 time to fit residues: 78.6898 Evaluate side-chains 181 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 210 LEU Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 90 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.126973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.081223 restraints weight = 12542.125| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.62 r_work: 0.2856 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9432 Z= 0.137 Angle : 0.640 8.857 12726 Z= 0.322 Chirality : 0.042 0.158 1422 Planarity : 0.003 0.015 1500 Dihedral : 7.455 57.475 1368 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.17 % Allowed : 14.42 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.51 (0.25), residues: 1068 helix: 3.42 (0.17), residues: 738 sheet: 2.86 (0.60), residues: 66 loop : -1.34 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 216 TYR 0.012 0.001 TYR G 68 PHE 0.013 0.002 PHE I 51 TRP 0.008 0.001 TRP G 133 HIS 0.011 0.001 HIS J 94 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9414) covalent geometry : angle 0.63857 (12690) SS BOND : bond 0.00266 ( 18) SS BOND : angle 0.98022 ( 36) hydrogen bonds : bond 0.05348 ( 636) hydrogen bonds : angle 3.81174 ( 1872) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.339 Fit side-chains REVERT: G 134 TRP cc_start: 0.7505 (m-10) cc_final: 0.7211 (m100) REVERT: H 132 LEU cc_start: 0.7954 (tt) cc_final: 0.7721 (mm) REVERT: H 212 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7319 (t80) REVERT: J 132 LEU cc_start: 0.7765 (tt) cc_final: 0.7550 (mm) REVERT: J 138 SER cc_start: 0.8868 (m) cc_final: 0.8575 (p) REVERT: L 212 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.7282 (t80) outliers start: 31 outliers final: 22 residues processed: 177 average time/residue: 0.4144 time to fit residues: 80.0825 Evaluate side-chains 186 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 41 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.126586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.082618 restraints weight = 12603.001| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.57 r_work: 0.2865 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9432 Z= 0.135 Angle : 0.641 9.316 12726 Z= 0.321 Chirality : 0.043 0.198 1422 Planarity : 0.003 0.015 1500 Dihedral : 6.859 57.436 1366 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.76 % Allowed : 15.34 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.48 (0.25), residues: 1068 helix: 3.40 (0.17), residues: 738 sheet: 2.87 (0.60), residues: 66 loop : -1.34 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 216 TYR 0.012 0.001 TYR G 68 PHE 0.019 0.002 PHE L 29 TRP 0.008 0.001 TRP I 133 HIS 0.011 0.001 HIS J 94 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9414) covalent geometry : angle 0.63943 (12690) SS BOND : bond 0.00267 ( 18) SS BOND : angle 0.96194 ( 36) hydrogen bonds : bond 0.05259 ( 636) hydrogen bonds : angle 3.79994 ( 1872) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.364 Fit side-chains REVERT: G 134 TRP cc_start: 0.7474 (m-10) cc_final: 0.7185 (m100) REVERT: H 132 LEU cc_start: 0.7971 (tt) cc_final: 0.7747 (mm) REVERT: H 212 TYR cc_start: 0.7684 (OUTLIER) cc_final: 0.7329 (t80) REVERT: J 132 LEU cc_start: 0.7767 (tt) cc_final: 0.7547 (mm) outliers start: 27 outliers final: 20 residues processed: 177 average time/residue: 0.4547 time to fit residues: 87.5792 Evaluate side-chains 186 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 36 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 0.0000 chunk 55 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 80 GLN J 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.126852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.080919 restraints weight = 12542.013| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.61 r_work: 0.2847 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9432 Z= 0.144 Angle : 0.662 9.611 12726 Z= 0.331 Chirality : 0.044 0.266 1422 Planarity : 0.003 0.016 1500 Dihedral : 6.465 58.036 1364 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.56 % Allowed : 15.95 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.41 (0.25), residues: 1068 helix: 3.33 (0.17), residues: 738 sheet: 2.86 (0.60), residues: 66 loop : -1.34 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 216 TYR 0.013 0.002 TYR L 65 PHE 0.018 0.002 PHE L 29 TRP 0.008 0.001 TRP I 133 HIS 0.012 0.001 HIS J 94 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9414) covalent geometry : angle 0.66090 (12690) SS BOND : bond 0.00292 ( 18) SS BOND : angle 1.00686 ( 36) hydrogen bonds : bond 0.05400 ( 636) hydrogen bonds : angle 3.84139 ( 1872) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.366 Fit side-chains REVERT: H 18 THR cc_start: 0.6435 (t) cc_final: 0.6029 (p) REVERT: H 132 LEU cc_start: 0.7956 (tt) cc_final: 0.7736 (mm) REVERT: J 132 LEU cc_start: 0.7708 (tt) cc_final: 0.7488 (mm) outliers start: 25 outliers final: 21 residues processed: 178 average time/residue: 0.3846 time to fit residues: 74.9153 Evaluate side-chains 185 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 49 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.126373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.080354 restraints weight = 12587.579| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.62 r_work: 0.2837 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9432 Z= 0.154 Angle : 0.676 10.026 12726 Z= 0.339 Chirality : 0.044 0.294 1422 Planarity : 0.003 0.016 1500 Dihedral : 6.354 58.972 1364 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.35 % Allowed : 15.95 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.36 (0.25), residues: 1068 helix: 3.29 (0.17), residues: 738 sheet: 2.84 (0.60), residues: 66 loop : -1.33 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 216 TYR 0.014 0.002 TYR L 65 PHE 0.018 0.002 PHE L 29 TRP 0.009 0.001 TRP I 134 HIS 0.012 0.001 HIS J 94 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9414) covalent geometry : angle 0.67488 (12690) SS BOND : bond 0.00336 ( 18) SS BOND : angle 1.07364 ( 36) hydrogen bonds : bond 0.05601 ( 636) hydrogen bonds : angle 3.88457 ( 1872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5161.47 seconds wall clock time: 88 minutes 5.63 seconds (5285.63 seconds total)