Starting phenix.real_space_refine on Sun Jun 8 18:25:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qey_13944/06_2025/7qey_13944.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qey_13944/06_2025/7qey_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qey_13944/06_2025/7qey_13944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qey_13944/06_2025/7qey_13944.map" model { file = "/net/cci-nas-00/data/ceres_data/7qey_13944/06_2025/7qey_13944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qey_13944/06_2025/7qey_13944.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.82, per 1000 atoms: 1.25 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: 3.72 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.89 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: 4.40 Time building geometry restraints manager: 4.13 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: 0.16 Found NCS groups: ncs_group { reference = (chain 'G' and (resid 9 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'H' and (resid 9 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'I' and (resid 9 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'J' and (resid 9 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'K' and (resid 9 through 217 or resid 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: 225.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 39.550 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:20.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 288.060 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (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 TRP 0.004 0.001 TRP L 77 HIS 0.001 0.000 HIS K 73 PHE 0.007 0.001 PHE L 51 TYR 0.004 0.001 TYR H 65 ARG 0.001 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.25146 ( 636) hydrogen bonds : angle 6.49950 ( 1872) SS BOND : bond 0.00173 ( 18) SS BOND : angle 0.80446 ( 36) covalent geometry : bond 0.00474 ( 9414) covalent geometry : angle 0.84797 (12690) *********************** 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 : 1.384 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: 0.8860 time to fit residues: 233.1054 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 : 0.959 ------------------------------------------------------------------------------- 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 91 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.125141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.079417 restraints weight = 12404.255| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.61 r_work: 0.2816 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9432 Z= 0.206 Angle : 0.712 10.156 12726 Z= 0.380 Chirality : 0.048 0.142 1422 Planarity : 0.004 0.019 1500 Dihedral : 9.647 59.733 1372 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.78 % Allowed : 11.45 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.25), residues: 1068 helix: 3.03 (0.17), residues: 738 sheet: 3.01 (0.60), residues: 66 loop : -1.11 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 133 HIS 0.004 0.001 HIS J 16 PHE 0.020 0.002 PHE G 51 TYR 0.020 0.002 TYR I 65 ARG 0.008 0.001 ARG L 216 Details of bonding type rmsd hydrogen bonds : bond 0.07817 ( 636) hydrogen bonds : angle 4.33507 ( 1872) SS BOND : bond 0.00486 ( 18) SS BOND : angle 1.37741 ( 36) covalent geometry : bond 0.00471 ( 9414) covalent geometry : angle 0.70921 (12690) *********************** 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 219 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 1.043 Fit side-chains REVERT: G 134 TRP cc_start: 0.7622 (OUTLIER) cc_final: 0.7297 (m100) REVERT: H 199 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8932 (m) REVERT: H 216 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7374 (tpm170) REVERT: J 138 SER cc_start: 0.8818 (m) cc_final: 0.8468 (p) REVERT: J 216 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8109 (tpm170) outliers start: 37 outliers final: 19 residues processed: 195 average time/residue: 1.0608 time to fit residues: 224.6215 Evaluate side-chains 192 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 134 TRP Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 199 SER 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 86 THR 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 54 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 95 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.0770 chunk 45 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.126844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.081249 restraints weight = 12644.975| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.64 r_work: 0.2858 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.2505 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= 0.137 Angle : 0.588 7.264 12726 Z= 0.307 Chirality : 0.042 0.138 1422 Planarity : 0.003 0.029 1500 Dihedral : 8.950 59.810 1370 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.58 % Allowed : 11.96 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.25), residues: 1068 helix: 3.34 (0.17), residues: 738 sheet: 3.04 (0.61), residues: 66 loop : -1.30 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 133 HIS 0.011 0.001 HIS J 94 PHE 0.012 0.002 PHE L 51 TYR 0.011 0.002 TYR J 65 ARG 0.010 0.001 ARG I 216 Details of bonding type rmsd hydrogen bonds : bond 0.06207 ( 636) hydrogen bonds : angle 3.98142 ( 1872) SS BOND : bond 0.00284 ( 18) SS BOND : angle 0.98595 ( 36) covalent geometry : bond 0.00280 ( 9414) covalent geometry : angle 0.58650 (12690) *********************** 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 215 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 1.240 Fit side-chains REVERT: G 134 TRP cc_start: 0.7565 (m-10) cc_final: 0.7256 (m100) REVERT: H 93 MET cc_start: 0.8170 (mmp) cc_final: 0.7881 (mmp) REVERT: I 216 ARG cc_start: 0.7820 (ttp80) cc_final: 0.7299 (tpm170) REVERT: J 138 SER cc_start: 0.8813 (m) cc_final: 0.8464 (p) REVERT: L 212 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.6676 (t80) outliers start: 35 outliers final: 17 residues processed: 193 average time/residue: 0.9718 time to fit residues: 204.8207 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 : 1.348 ------------------------------------------------------------------------------- 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 41 LYS Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 212 TYR 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 15 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 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 = 0.3794 r_free = 0.3794 target = 0.126356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.080485 restraints weight = 12423.404| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.63 r_work: 0.2839 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.2776 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= 0.144 Angle : 0.617 8.984 12726 Z= 0.316 Chirality : 0.043 0.138 1422 Planarity : 0.003 0.057 1500 Dihedral : 8.707 59.996 1370 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.37 % Allowed : 13.19 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.25), residues: 1068 helix: 3.37 (0.17), residues: 738 sheet: 2.90 (0.59), residues: 66 loop : -1.27 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 133 HIS 0.011 0.001 HIS J 94 PHE 0.015 0.002 PHE L 51 TYR 0.014 0.002 TYR L 65 ARG 0.007 0.001 ARG J 216 Details of bonding type rmsd hydrogen bonds : bond 0.05991 ( 636) hydrogen bonds : angle 3.93533 ( 1872) SS BOND : bond 0.00293 ( 18) SS BOND : angle 1.07155 ( 36) covalent geometry : bond 0.00315 ( 9414) covalent geometry : angle 0.61492 (12690) *********************** 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 206 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 1.052 Fit side-chains REVERT: G 134 TRP cc_start: 0.7501 (m-10) cc_final: 0.7141 (m100) REVERT: H 93 MET cc_start: 0.8154 (mmp) cc_final: 0.7910 (mmp) REVERT: H 132 LEU cc_start: 0.7922 (tt) cc_final: 0.7611 (mm) REVERT: H 212 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.6929 (t80) REVERT: J 132 LEU cc_start: 0.7849 (tt) cc_final: 0.7575 (mm) REVERT: J 138 SER cc_start: 0.8854 (m) cc_final: 0.8501 (p) REVERT: K 212 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6768 (t80) REVERT: L 212 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6784 (t80) outliers start: 33 outliers final: 23 residues processed: 187 average time/residue: 0.8815 time to fit residues: 180.1021 Evaluate side-chains 191 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 38 VAL 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 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 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 72 optimal weight: 9.9990 chunk 21 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.126034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.080412 restraints weight = 12570.796| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.62 r_work: 0.2832 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9432 Z= 0.148 Angle : 0.608 8.204 12726 Z= 0.313 Chirality : 0.043 0.136 1422 Planarity : 0.003 0.019 1500 Dihedral : 8.480 59.971 1370 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.07 % Allowed : 13.39 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.25), residues: 1068 helix: 3.38 (0.17), residues: 738 sheet: 2.82 (0.59), residues: 66 loop : -1.25 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 133 HIS 0.011 0.001 HIS J 94 PHE 0.015 0.002 PHE I 51 TYR 0.014 0.002 TYR L 65 ARG 0.011 0.001 ARG J 216 Details of bonding type rmsd hydrogen bonds : bond 0.05888 ( 636) hydrogen bonds : angle 3.88507 ( 1872) SS BOND : bond 0.00323 ( 18) SS BOND : angle 1.07736 ( 36) covalent geometry : bond 0.00331 ( 9414) covalent geometry : angle 0.60647 (12690) *********************** 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 194 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.997 Fit side-chains REVERT: G 134 TRP cc_start: 0.7458 (m-10) cc_final: 0.7237 (m100) REVERT: H 132 LEU cc_start: 0.7920 (tt) cc_final: 0.7648 (mm) REVERT: H 212 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.7025 (t80) REVERT: J 132 LEU cc_start: 0.7770 (tt) cc_final: 0.7495 (mm) REVERT: J 138 SER cc_start: 0.8901 (m) cc_final: 0.8558 (p) REVERT: J 212 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6795 (t80) REVERT: K 212 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6996 (t80) REVERT: L 212 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6907 (t80) outliers start: 30 outliers final: 20 residues processed: 177 average time/residue: 0.9816 time to fit residues: 189.0386 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 : 0.985 ------------------------------------------------------------------------------- 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 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 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 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 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 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 25 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 40 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.126261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.080202 restraints weight = 12497.922| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.64 r_work: 0.2833 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9432 Z= 0.148 Angle : 0.627 8.583 12726 Z= 0.318 Chirality : 0.043 0.146 1422 Planarity : 0.003 0.017 1500 Dihedral : 8.199 59.886 1370 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.99 % Allowed : 13.29 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.25), residues: 1068 helix: 3.41 (0.17), residues: 738 sheet: 2.79 (0.59), residues: 66 loop : -1.29 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 133 HIS 0.011 0.001 HIS J 94 PHE 0.015 0.002 PHE I 51 TYR 0.014 0.002 TYR G 68 ARG 0.005 0.001 ARG J 216 Details of bonding type rmsd hydrogen bonds : bond 0.05753 ( 636) hydrogen bonds : angle 3.88708 ( 1872) SS BOND : bond 0.00323 ( 18) SS BOND : angle 1.07260 ( 36) covalent geometry : bond 0.00334 ( 9414) covalent geometry : angle 0.62511 (12690) *********************** 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 207 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.949 Fit side-chains REVERT: G 134 TRP cc_start: 0.7501 (m-10) cc_final: 0.7152 (m100) REVERT: H 132 LEU cc_start: 0.7906 (tt) cc_final: 0.7649 (mm) REVERT: H 212 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.7041 (t80) REVERT: J 132 LEU cc_start: 0.7772 (tt) cc_final: 0.7514 (mm) REVERT: J 138 SER cc_start: 0.8910 (m) cc_final: 0.8587 (p) REVERT: K 212 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.7172 (t80) REVERT: L 212 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.7071 (t80) outliers start: 39 outliers final: 22 residues processed: 189 average time/residue: 0.8736 time to fit residues: 180.8420 Evaluate side-chains 184 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 151 MET 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 K residue 38 VAL 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 96 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 102 optimal weight: 0.0470 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 85 optimal weight: 0.0770 chunk 21 optimal weight: 0.0570 chunk 104 optimal weight: 1.9990 overall best weight: 0.1754 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.128821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.083846 restraints weight = 12678.990| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.63 r_work: 0.2910 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9432 Z= 0.121 Angle : 0.604 8.989 12726 Z= 0.303 Chirality : 0.041 0.146 1422 Planarity : 0.003 0.016 1500 Dihedral : 7.426 58.910 1368 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.35 % Allowed : 15.54 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.25), residues: 1068 helix: 3.51 (0.17), residues: 738 sheet: 2.93 (0.59), residues: 66 loop : -1.41 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 133 HIS 0.011 0.001 HIS J 94 PHE 0.010 0.001 PHE G 29 TYR 0.014 0.001 TYR J 158 ARG 0.004 0.000 ARG L 216 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 636) hydrogen bonds : angle 3.67219 ( 1872) SS BOND : bond 0.00145 ( 18) SS BOND : angle 0.84044 ( 36) covalent geometry : bond 0.00236 ( 9414) covalent geometry : angle 0.60311 (12690) *********************** 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 208 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.526 Fit side-chains REVERT: G 134 TRP cc_start: 0.7376 (m-10) cc_final: 0.7109 (m100) REVERT: H 132 LEU cc_start: 0.7934 (tt) cc_final: 0.7711 (mm) REVERT: H 212 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.7187 (t80) REVERT: J 132 LEU cc_start: 0.7712 (tt) cc_final: 0.7494 (mm) REVERT: K 212 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.7275 (t80) REVERT: L 212 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.7265 (t80) outliers start: 23 outliers final: 14 residues processed: 194 average time/residue: 0.9224 time to fit residues: 196.1378 Evaluate side-chains 190 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 G residue 213 LEU Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 213 LEU 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 212 TYR Chi-restraints excluded: chain K residue 38 VAL 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 212 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 31 optimal weight: 0.0870 chunk 103 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 79 optimal weight: 0.4980 chunk 30 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.128262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.083127 restraints weight = 12800.540| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.62 r_work: 0.2892 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9432 Z= 0.126 Angle : 0.624 8.886 12726 Z= 0.312 Chirality : 0.042 0.153 1422 Planarity : 0.003 0.016 1500 Dihedral : 7.070 58.818 1368 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.15 % Allowed : 16.46 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.25), residues: 1068 helix: 3.54 (0.17), residues: 738 sheet: 3.01 (0.59), residues: 66 loop : -1.33 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 133 HIS 0.011 0.001 HIS J 94 PHE 0.019 0.002 PHE L 29 TYR 0.010 0.001 TYR J 65 ARG 0.004 0.000 ARG G 216 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 636) hydrogen bonds : angle 3.67117 ( 1872) SS BOND : bond 0.00182 ( 18) SS BOND : angle 0.86250 ( 36) covalent geometry : bond 0.00268 ( 9414) covalent geometry : angle 0.62304 (12690) *********************** 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 191 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 1.062 Fit side-chains REVERT: G 134 TRP cc_start: 0.7382 (m-10) cc_final: 0.7113 (m100) REVERT: H 132 LEU cc_start: 0.7951 (tt) cc_final: 0.7730 (mm) REVERT: H 212 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7282 (t80) REVERT: J 132 LEU cc_start: 0.7696 (tt) cc_final: 0.7488 (mm) outliers start: 21 outliers final: 12 residues processed: 176 average time/residue: 0.9346 time to fit residues: 179.2891 Evaluate side-chains 179 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 42 GLU 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 212 TYR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 34 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.127520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.081892 restraints weight = 12705.385| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.63 r_work: 0.2867 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9432 Z= 0.135 Angle : 0.640 9.201 12726 Z= 0.320 Chirality : 0.043 0.183 1422 Planarity : 0.003 0.016 1500 Dihedral : 6.450 58.732 1364 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.74 % Allowed : 16.97 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.25), residues: 1068 helix: 3.50 (0.17), residues: 738 sheet: 3.00 (0.60), residues: 66 loop : -1.28 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 133 HIS 0.011 0.001 HIS J 94 PHE 0.019 0.002 PHE L 29 TYR 0.012 0.001 TYR L 65 ARG 0.003 0.000 ARG L 216 Details of bonding type rmsd hydrogen bonds : bond 0.05109 ( 636) hydrogen bonds : angle 3.72047 ( 1872) SS BOND : bond 0.00243 ( 18) SS BOND : angle 0.94251 ( 36) covalent geometry : bond 0.00297 ( 9414) covalent geometry : angle 0.63869 (12690) *********************** 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 187 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.988 Fit side-chains REVERT: G 134 TRP cc_start: 0.7390 (m-10) cc_final: 0.7116 (m100) REVERT: H 132 LEU cc_start: 0.7969 (tt) cc_final: 0.7750 (mm) REVERT: H 212 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.7302 (t80) REVERT: J 132 LEU cc_start: 0.7709 (tt) cc_final: 0.7496 (mm) outliers start: 17 outliers final: 12 residues processed: 175 average time/residue: 0.9391 time to fit residues: 179.2136 Evaluate side-chains 179 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 42 GLU Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain H residue 213 LEU 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 212 TYR Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 0.0040 chunk 107 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.126513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.080666 restraints weight = 12732.110| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.63 r_work: 0.2839 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9432 Z= 0.154 Angle : 0.672 9.511 12726 Z= 0.338 Chirality : 0.044 0.207 1422 Planarity : 0.003 0.016 1500 Dihedral : 6.351 59.035 1364 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.04 % Allowed : 17.08 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.25), residues: 1068 helix: 3.39 (0.17), residues: 738 sheet: 2.89 (0.60), residues: 66 loop : -1.26 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 133 HIS 0.011 0.001 HIS J 94 PHE 0.020 0.002 PHE L 31 TYR 0.016 0.002 TYR I 65 ARG 0.003 0.001 ARG I 216 Details of bonding type rmsd hydrogen bonds : bond 0.05549 ( 636) hydrogen bonds : angle 3.82893 ( 1872) SS BOND : bond 0.00326 ( 18) SS BOND : angle 1.08498 ( 36) covalent geometry : bond 0.00353 ( 9414) covalent geometry : angle 0.67096 (12690) ********************** 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 187 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 1.159 Fit side-chains REVERT: J 132 LEU cc_start: 0.7710 (tt) cc_final: 0.7478 (mm) REVERT: J 138 SER cc_start: 0.8877 (m) cc_final: 0.8572 (p) outliers start: 20 outliers final: 17 residues processed: 173 average time/residue: 0.9483 time to fit residues: 179.1760 Evaluate side-chains 181 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 G residue 213 LEU 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 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 212 TYR Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 30 optimal weight: 0.0170 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.128148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.082260 restraints weight = 12688.334| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.63 r_work: 0.2875 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9432 Z= 0.131 Angle : 0.646 9.567 12726 Z= 0.321 Chirality : 0.043 0.214 1422 Planarity : 0.003 0.015 1500 Dihedral : 5.944 57.337 1364 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.04 % Allowed : 17.08 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.25), residues: 1068 helix: 3.38 (0.17), residues: 738 sheet: 2.94 (0.59), residues: 66 loop : -1.34 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 134 HIS 0.011 0.001 HIS J 94 PHE 0.018 0.002 PHE L 29 TYR 0.010 0.001 TYR J 65 ARG 0.003 0.000 ARG I 216 Details of bonding type rmsd hydrogen bonds : bond 0.05023 ( 636) hydrogen bonds : angle 3.75153 ( 1872) SS BOND : bond 0.00222 ( 18) SS BOND : angle 0.90744 ( 36) covalent geometry : bond 0.00286 ( 9414) covalent geometry : angle 0.64467 (12690) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11686.53 seconds wall clock time: 203 minutes 50.15 seconds (12230.15 seconds total)