Starting phenix.real_space_refine on Wed Sep 25 07:34:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/09_2024/7qey_13944.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/09_2024/7qey_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/09_2024/7qey_13944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/09_2024/7qey_13944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/09_2024/7qey_13944.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/09_2024/7qey_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-5461/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: 7.59, per 1000 atoms: 0.80 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 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: 0.89 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: 2.33 Time building geometry restraints manager: 2.72 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: 0.00 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: 5.220 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.470 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.030 ------------------------------------------------------------------------------- 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 9414 Z= 0.304 Angle : 0.848 8.054 12690 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 *********************** 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 fitting. rotamer outliers: 23 poor density : 223 time to evaluate : 0.976 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: 0.8630 time to fit residues: 226.4686 Evaluate side-chains 173 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 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 9414 Z= 0.310 Angle : 0.709 10.156 12690 Z= 0.379 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 *********************** 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 fitting. rotamer outliers: 37 poor density : 182 time to evaluate : 1.130 Fit side-chains REVERT: H 216 ARG cc_start: 0.7782 (ttp80) cc_final: 0.7240 (tpm170) REVERT: J 138 SER cc_start: 0.8765 (m) cc_final: 0.8509 (p) outliers start: 37 outliers final: 19 residues processed: 195 average time/residue: 0.9469 time to fit residues: 200.7787 Evaluate side-chains 189 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 170 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 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 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 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 30 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9414 Z= 0.318 Angle : 0.669 7.061 12690 Z= 0.353 Chirality : 0.046 0.145 1422 Planarity : 0.004 0.062 1500 Dihedral : 9.392 59.701 1370 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.60 % Allowed : 10.63 % 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: 3.25 (0.25), residues: 1068 helix: 3.14 (0.18), residues: 738 sheet: 2.66 (0.58), residues: 66 loop : -1.10 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 172 HIS 0.012 0.001 HIS J 94 PHE 0.019 0.002 PHE G 51 TYR 0.018 0.002 TYR L 65 ARG 0.010 0.001 ARG I 216 *********************** 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 219 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 1.128 Fit side-chains REVERT: H 216 ARG cc_start: 0.7696 (ttp80) cc_final: 0.7333 (tpm170) REVERT: J 138 SER cc_start: 0.8819 (m) cc_final: 0.8577 (p) outliers start: 45 outliers final: 32 residues processed: 190 average time/residue: 0.9243 time to fit residues: 191.4169 Evaluate side-chains 199 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL 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 37 VAL 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 86 THR 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 86 THR Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 151 MET Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 86 THR 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 86 THR Chi-restraints excluded: chain L residue 132 LEU 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 97 optimal weight: 0.0470 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 93 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9414 Z= 0.182 Angle : 0.603 9.095 12690 Z= 0.306 Chirality : 0.042 0.139 1422 Planarity : 0.003 0.029 1500 Dihedral : 8.819 59.784 1370 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.27 % Allowed : 13.50 % Favored : 83.23 % 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: 3.40 (0.25), residues: 1068 helix: 3.32 (0.17), residues: 738 sheet: 2.75 (0.59), residues: 66 loop : -1.29 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 133 HIS 0.012 0.001 HIS J 94 PHE 0.013 0.002 PHE I 51 TYR 0.011 0.002 TYR G 65 ARG 0.008 0.000 ARG G 216 *********************** 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 203 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 171 time to evaluate : 1.072 Fit side-chains REVERT: J 138 SER cc_start: 0.8732 (m) cc_final: 0.8514 (p) REVERT: K 212 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.6759 (t80) REVERT: L 212 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6738 (t80) outliers start: 32 outliers final: 21 residues processed: 186 average time/residue: 0.9304 time to fit residues: 189.5370 Evaluate side-chains 191 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 212 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9414 Z= 0.246 Angle : 0.616 8.753 12690 Z= 0.322 Chirality : 0.044 0.139 1422 Planarity : 0.003 0.025 1500 Dihedral : 8.535 59.529 1370 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.58 % Allowed : 12.88 % 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: 3.42 (0.25), residues: 1068 helix: 3.32 (0.17), residues: 738 sheet: 2.67 (0.58), residues: 66 loop : -1.21 (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 0.017 0.002 PHE J 51 TYR 0.016 0.002 TYR L 65 ARG 0.007 0.001 ARG G 216 *********************** 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 206 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 0.984 Fit side-chains REVERT: H 212 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.6928 (t80) REVERT: J 138 SER cc_start: 0.8785 (m) cc_final: 0.8584 (p) REVERT: J 212 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6618 (t80) REVERT: K 212 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6926 (t80) REVERT: L 212 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.6754 (t80) outliers start: 35 outliers final: 22 residues processed: 185 average time/residue: 0.8627 time to fit residues: 175.0166 Evaluate side-chains 190 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 42 GLU Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 132 LEU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 0.0670 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 10.0000 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9414 Z= 0.203 Angle : 0.608 8.942 12690 Z= 0.311 Chirality : 0.043 0.144 1422 Planarity : 0.003 0.019 1500 Dihedral : 8.113 59.269 1370 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.89 % Allowed : 13.09 % 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 (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: 3.41 (0.17), residues: 738 sheet: 2.72 (0.59), residues: 66 loop : -1.34 (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 0.014 0.002 PHE I 51 TYR 0.012 0.002 TYR J 68 ARG 0.006 0.000 ARG G 216 *********************** 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 201 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 1.164 Fit side-chains REVERT: H 209 GLU cc_start: 0.8302 (tp30) cc_final: 0.8094 (tp30) REVERT: H 212 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.6979 (t80) REVERT: J 212 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6675 (t80) REVERT: K 212 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7035 (t80) REVERT: L 212 TYR cc_start: 0.7424 (OUTLIER) cc_final: 0.6909 (t80) outliers start: 38 outliers final: 21 residues processed: 183 average time/residue: 0.9158 time to fit residues: 183.0108 Evaluate side-chains 178 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 J residue 132 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 212 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 0.0010 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 64 optimal weight: 0.7980 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9414 Z= 0.193 Angle : 0.628 8.875 12690 Z= 0.322 Chirality : 0.042 0.142 1422 Planarity : 0.003 0.018 1500 Dihedral : 7.757 59.014 1370 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.17 % Allowed : 14.01 % Favored : 82.82 % 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: 3.43 (0.18), residues: 738 sheet: 2.71 (0.59), residues: 66 loop : -1.36 (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 0.013 0.002 PHE I 51 TYR 0.011 0.002 TYR J 68 ARG 0.005 0.000 ARG G 216 *********************** 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 194 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 1.133 Fit side-chains REVERT: H 212 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.7032 (t80) REVERT: J 212 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6861 (t80) REVERT: K 212 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.7143 (t80) REVERT: L 212 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.7036 (t80) outliers start: 31 outliers final: 19 residues processed: 174 average time/residue: 0.8955 time to fit residues: 170.4309 Evaluate side-chains 181 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.220 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 20 optimal weight: 0.0030 chunk 66 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9414 Z= 0.178 Angle : 0.630 8.859 12690 Z= 0.315 Chirality : 0.042 0.149 1422 Planarity : 0.003 0.017 1500 Dihedral : 7.255 59.489 1370 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.86 % Allowed : 14.72 % 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 (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: 3.51 (0.25), residues: 1068 helix: 3.45 (0.17), residues: 738 sheet: 2.71 (0.59), residues: 66 loop : -1.37 (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 0.012 0.002 PHE L 31 TYR 0.010 0.001 TYR G 65 ARG 0.005 0.000 ARG G 216 *********************** 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 197 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 169 time to evaluate : 1.071 Fit side-chains REVERT: H 212 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.7097 (t80) REVERT: L 212 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.7259 (t80) outliers start: 28 outliers final: 15 residues processed: 179 average time/residue: 0.9263 time to fit residues: 180.8593 Evaluate side-chains 183 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 85 SER 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 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 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 90 optimal weight: 0.0030 chunk 97 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9414 Z= 0.196 Angle : 0.634 9.198 12690 Z= 0.320 Chirality : 0.042 0.187 1422 Planarity : 0.003 0.027 1500 Dihedral : 6.767 58.359 1368 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.04 % Allowed : 15.95 % Favored : 82.00 % 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: 3.43 (0.17), residues: 738 sheet: 2.75 (0.59), residues: 66 loop : -1.36 (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 0.011 0.001 TYR J 68 ARG 0.013 0.001 ARG I 216 *********************** 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 fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 0.877 Fit side-chains REVERT: G 18 THR cc_start: 0.6355 (t) cc_final: 0.5832 (p) REVERT: H 212 TYR cc_start: 0.7578 (OUTLIER) cc_final: 0.7179 (t80) outliers start: 20 outliers final: 18 residues processed: 174 average time/residue: 0.8651 time to fit residues: 164.9550 Evaluate side-chains 183 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 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 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 102 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 85 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9414 Z= 0.195 Angle : 0.650 9.647 12690 Z= 0.322 Chirality : 0.042 0.219 1422 Planarity : 0.003 0.029 1500 Dihedral : 6.281 56.243 1366 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.45 % Allowed : 15.75 % Favored : 81.80 % 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: 3.41 (0.17), residues: 738 sheet: 2.75 (0.59), residues: 66 loop : -1.36 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 133 HIS 0.012 0.001 HIS J 94 PHE 0.020 0.002 PHE L 29 TYR 0.010 0.001 TYR J 68 ARG 0.011 0.001 ARG I 216 ********************** 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 197 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.071 Fit side-chains REVERT: G 18 THR cc_start: 0.6353 (t) cc_final: 0.5818 (p) outliers start: 24 outliers final: 19 residues processed: 182 average time/residue: 0.8555 time to fit residues: 171.3260 Evaluate side-chains 184 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 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 132 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 L residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 85 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.126744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.082751 restraints weight = 12473.952| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.55 r_work: 0.2859 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9414 Z= 0.209 Angle : 0.650 9.954 12690 Z= 0.328 Chirality : 0.043 0.227 1422 Planarity : 0.003 0.026 1500 Dihedral : 6.106 54.590 1366 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.15 % Allowed : 16.16 % 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 (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: 3.40 (0.25), residues: 1068 helix: 3.34 (0.17), residues: 738 sheet: 2.74 (0.59), residues: 66 loop : -1.35 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 133 HIS 0.012 0.001 HIS J 94 PHE 0.021 0.002 PHE K 29 TYR 0.012 0.002 TYR J 68 ARG 0.011 0.001 ARG I 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3997.31 seconds wall clock time: 70 minutes 22.91 seconds (4222.91 seconds total)