Starting phenix.real_space_refine on Thu Mar 14 18:27:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/03_2024/7qey_13944_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/03_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_13944/03_2024/7qey_13944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/03_2024/7qey_13944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/03_2024/7qey_13944_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qey_13944/03_2024/7qey_13944_updated.pdb" } 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 Residue "G TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.73, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 3.88 Conformation dependent library (CDL) restraints added in 1.6 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... running ksdssp... Secondary structure from input PDB file: 42 helices and 6 sheets defined 66.5% alpha, 3.3% 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 10 through 13 No H-bonds generated for 'chain 'G' and resid 10 through 13' Processing helix chain 'G' and resid 24 through 38 Processing helix chain 'G' and resid 40 through 43 No H-bonds generated for 'chain 'G' and resid 40 through 43' Processing helix chain 'G' and resid 60 through 68 Processing helix chain 'G' and resid 73 through 100 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 130 through 158 removed outlier: 3.554A pdb=" N THR G 135 " --> pdb=" O SER G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 216 Processing helix chain 'H' and resid 10 through 13 No H-bonds generated for 'chain 'H' and resid 10 through 13' Processing helix chain 'H' and resid 24 through 38 Processing helix chain 'H' and resid 40 through 43 No H-bonds generated for 'chain 'H' and resid 40 through 43' Processing helix chain 'H' and resid 60 through 68 Processing helix chain 'H' and resid 73 through 100 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 130 through 158 removed outlier: 3.555A pdb=" N THR H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 216 Processing helix chain 'I' and resid 10 through 13 No H-bonds generated for 'chain 'I' and resid 10 through 13' Processing helix chain 'I' and resid 24 through 38 Processing helix chain 'I' and resid 40 through 43 No H-bonds generated for 'chain 'I' and resid 40 through 43' Processing helix chain 'I' and resid 60 through 68 Processing helix chain 'I' and resid 73 through 100 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 130 through 158 removed outlier: 3.555A pdb=" N THR I 135 " --> pdb=" O SER I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 216 Processing helix chain 'J' and resid 10 through 13 No H-bonds generated for 'chain 'J' and resid 10 through 13' Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 40 through 43 No H-bonds generated for 'chain 'J' and resid 40 through 43' Processing helix chain 'J' and resid 60 through 68 Processing helix chain 'J' and resid 73 through 100 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 130 through 158 removed outlier: 3.555A pdb=" N THR J 135 " --> pdb=" O SER J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 216 Processing helix chain 'K' and resid 10 through 13 No H-bonds generated for 'chain 'K' and resid 10 through 13' Processing helix chain 'K' and resid 24 through 38 Processing helix chain 'K' and resid 40 through 43 No H-bonds generated for 'chain 'K' and resid 40 through 43' Processing helix chain 'K' and resid 60 through 68 Processing helix chain 'K' and resid 73 through 100 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 130 through 158 removed outlier: 3.555A pdb=" N THR K 135 " --> pdb=" O SER K 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 216 Processing helix chain 'L' and resid 10 through 13 No H-bonds generated for 'chain 'L' and resid 10 through 13' Processing helix chain 'L' and resid 24 through 38 Processing helix chain 'L' and resid 40 through 43 No H-bonds generated for 'chain 'L' and resid 40 through 43' Processing helix chain 'L' and resid 60 through 68 Processing helix chain 'L' and resid 73 through 100 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 130 through 158 removed outlier: 3.556A pdb=" N THR L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 216 Processing sheet with id= A, first strand: chain 'G' and resid 166 through 169 Processing sheet with id= B, first strand: chain 'H' and resid 166 through 169 Processing sheet with id= C, first strand: chain 'I' and resid 166 through 169 Processing sheet with id= D, first strand: chain 'J' and resid 166 through 169 Processing sheet with id= E, first strand: chain 'K' and resid 166 through 169 Processing sheet with id= F, first strand: chain 'L' and resid 166 through 169 558 hydrogen bonds defined for protein. 1656 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: 2.50 Time building geometry restraints manager: 4.17 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: 100.74 - 107.39: 312 107.39 - 114.04: 5455 114.04 - 120.68: 4009 120.68 - 127.33: 2776 127.33 - 133.98: 138 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: 691 2.74 - 3.28: 9524 3.28 - 3.82: 15617 3.82 - 4.36: 18620 4.36 - 4.90: 31833 Nonbonded interactions: 76285 Sorted by model distance: nonbonded pdb=" O ILE J 71 " pdb=" OH TYR J 158 " model vdw 2.199 2.440 nonbonded pdb=" O ILE H 71 " pdb=" OH TYR H 158 " model vdw 2.199 2.440 nonbonded pdb=" O ILE G 71 " pdb=" OH TYR G 158 " model vdw 2.199 2.440 nonbonded pdb=" O ILE L 71 " pdb=" OH TYR L 158 " model vdw 2.200 2.440 nonbonded pdb=" O ILE I 71 " pdb=" OH TYR I 158 " model vdw 2.200 2.440 ... (remaining 76280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 16.430 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.330 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 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:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.810 ------------------------------------------------------------------------------- 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= 0.309 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 : 1.164 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: 0.8816 time to fit residues: 230.9435 Evaluate side-chains 173 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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: 0.0270 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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: 0.8781 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9414 Z= 0.214 Angle : 0.621 10.003 12690 Z= 0.323 Chirality : 0.043 0.145 1422 Planarity : 0.003 0.019 1500 Dihedral : 9.239 56.954 1372 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.07 % Allowed : 12.27 % Favored : 84.66 % 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: 3.00 (0.25), residues: 1068 helix: 2.86 (0.18), residues: 738 sheet: 3.28 (0.62), residues: 66 loop : -1.11 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 133 HIS 0.007 0.001 HIS J 16 PHE 0.014 0.002 PHE G 51 TYR 0.016 0.002 TYR L 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 226 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 1.066 Fit side-chains REVERT: H 216 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7215 (tpm170) REVERT: J 138 SER cc_start: 0.8706 (m) cc_final: 0.8435 (p) outliers start: 30 outliers final: 13 residues processed: 207 average time/residue: 0.9022 time to fit residues: 203.6559 Evaluate side-chains 189 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 176 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 140 ILE 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 199 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 98 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8797 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9414 Z= 0.220 Angle : 0.594 7.727 12690 Z= 0.305 Chirality : 0.042 0.146 1422 Planarity : 0.003 0.021 1500 Dihedral : 8.821 59.578 1368 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.37 % Allowed : 12.99 % Favored : 83.64 % 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: 3.27 (0.25), residues: 1068 helix: 3.23 (0.18), residues: 732 sheet: 2.78 (0.57), residues: 66 loop : -1.29 (0.34), residues: 270 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 G 51 TYR 0.015 0.002 TYR L 65 ARG 0.008 0.001 ARG J 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 213 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 1.030 Fit side-chains REVERT: G 151 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8307 (ttt) REVERT: H 93 MET cc_start: 0.7967 (mmp) cc_final: 0.7669 (mmp) REVERT: I 216 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7217 (tmm-80) REVERT: J 138 SER cc_start: 0.8731 (m) cc_final: 0.8494 (p) outliers start: 33 outliers final: 19 residues processed: 190 average time/residue: 0.9056 time to fit residues: 187.5783 Evaluate side-chains 190 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 170 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 151 MET Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 41 LYS 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 151 MET Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 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: 0.6980 chunk 73 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 93 optimal weight: 0.1980 chunk 28 optimal weight: 3.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- 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: 0.8770 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9414 Z= 0.158 Angle : 0.565 9.680 12690 Z= 0.281 Chirality : 0.040 0.147 1422 Planarity : 0.003 0.022 1500 Dihedral : 8.219 59.622 1366 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.17 % Allowed : 13.19 % Favored : 83.64 % 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: 3.39 (0.26), residues: 1068 helix: 3.27 (0.18), residues: 738 sheet: 2.88 (0.57), residues: 66 loop : -1.20 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 133 HIS 0.011 0.001 HIS J 94 PHE 0.010 0.002 PHE G 51 TYR 0.011 0.001 TYR I 158 ARG 0.006 0.001 ARG L 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 218 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 187 time to evaluate : 1.137 Fit side-chains REVERT: J 138 SER cc_start: 0.8706 (m) cc_final: 0.8481 (p) REVERT: K 212 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.6821 (t80) REVERT: L 212 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.6776 (t80) outliers start: 31 outliers final: 19 residues processed: 196 average time/residue: 0.8634 time to fit residues: 185.7908 Evaluate side-chains 194 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 173 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 212 TYR Chi-restraints excluded: chain H residue 41 LYS 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 210 LEU Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8803 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9414 Z= 0.224 Angle : 0.596 8.818 12690 Z= 0.306 Chirality : 0.042 0.137 1422 Planarity : 0.003 0.015 1500 Dihedral : 8.212 59.662 1366 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.37 % Allowed : 13.09 % 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: 3.26 (0.25), residues: 1068 helix: 3.19 (0.18), residues: 738 sheet: 2.48 (0.55), residues: 66 loop : -1.19 (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 0.014 0.002 PHE L 51 TYR 0.015 0.002 TYR L 65 ARG 0.005 0.001 ARG L 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 207 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 1.077 Fit side-chains REVERT: G 151 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8321 (ttt) REVERT: J 138 SER cc_start: 0.8784 (m) cc_final: 0.8561 (p) REVERT: K 212 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.6927 (t80) REVERT: L 212 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.6852 (t80) outliers start: 33 outliers final: 21 residues processed: 183 average time/residue: 0.9141 time to fit residues: 182.1215 Evaluate side-chains 193 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 MET Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 41 LYS 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 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 212 TYR Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 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: 2.9990 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 48 optimal weight: 0.0000 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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: 0.8795 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9414 Z= 0.198 Angle : 0.583 8.898 12690 Z= 0.296 Chirality : 0.042 0.141 1422 Planarity : 0.003 0.021 1500 Dihedral : 7.953 59.490 1366 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.78 % Allowed : 12.68 % 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: 3.25 (0.25), residues: 1068 helix: 3.20 (0.18), residues: 738 sheet: 2.48 (0.54), residues: 66 loop : -1.25 (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 0.031 0.002 PHE K 31 TYR 0.012 0.001 TYR I 65 ARG 0.008 0.001 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 214 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 177 time to evaluate : 1.079 Fit side-chains REVERT: G 151 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8330 (ttt) REVERT: I 209 GLU cc_start: 0.8239 (tp30) cc_final: 0.8033 (tp30) REVERT: K 212 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.7094 (t80) REVERT: L 209 GLU cc_start: 0.8273 (tp30) cc_final: 0.8065 (tp30) REVERT: L 212 TYR cc_start: 0.7477 (OUTLIER) cc_final: 0.6953 (t80) outliers start: 37 outliers final: 22 residues processed: 191 average time/residue: 0.8579 time to fit residues: 179.4671 Evaluate side-chains 189 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 MET Chi-restraints excluded: chain G residue 212 TYR Chi-restraints excluded: chain H residue 41 LYS 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 212 TYR 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 41 LYS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER 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 100 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 chunk 48 optimal weight: 0.0040 chunk 64 optimal weight: 0.6980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9414 Z= 0.168 Angle : 0.582 8.964 12690 Z= 0.293 Chirality : 0.041 0.141 1422 Planarity : 0.002 0.016 1500 Dihedral : 7.593 59.197 1366 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.86 % Allowed : 14.83 % Favored : 82.31 % 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: 3.27 (0.26), residues: 1068 helix: 3.20 (0.18), residues: 738 sheet: 2.64 (0.55), residues: 66 loop : -1.26 (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 0.031 0.002 PHE K 31 TYR 0.009 0.001 TYR J 65 ARG 0.006 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 193 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 0.968 Fit side-chains REVERT: G 151 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8347 (ttp) REVERT: K 212 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.7215 (t80) REVERT: L 212 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.7066 (t80) outliers start: 28 outliers final: 18 residues processed: 170 average time/residue: 0.8456 time to fit residues: 157.5382 Evaluate side-chains 186 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 151 MET 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 85 SER Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 212 TYR 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 41 LYS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 41 LYS 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: 1.9990 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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: 0.8810 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9414 Z= 0.256 Angle : 0.640 9.019 12690 Z= 0.322 Chirality : 0.044 0.166 1422 Planarity : 0.003 0.014 1500 Dihedral : 7.492 58.241 1366 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.76 % Allowed : 15.03 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.11 (0.25), residues: 1068 helix: 3.08 (0.18), residues: 738 sheet: 2.29 (0.53), residues: 66 loop : -1.22 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 172 HIS 0.011 0.001 HIS J 94 PHE 0.026 0.002 PHE K 31 TYR 0.017 0.002 TYR L 65 ARG 0.005 0.001 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 195 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 1.069 Fit side-chains REVERT: G 151 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8323 (ttt) REVERT: K 212 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.7208 (t80) REVERT: L 212 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.7070 (t80) outliers start: 27 outliers final: 19 residues processed: 173 average time/residue: 0.9033 time to fit residues: 170.6516 Evaluate side-chains 184 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 151 MET 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 140 ILE Chi-restraints excluded: chain H residue 212 TYR Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 140 ILE Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 212 TYR Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 63 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9414 Z= 0.211 Angle : 0.633 9.415 12690 Z= 0.314 Chirality : 0.043 0.196 1422 Planarity : 0.002 0.015 1500 Dihedral : 7.174 57.240 1366 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.66 % Allowed : 15.95 % 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: 3.11 (0.25), residues: 1068 helix: 3.09 (0.18), residues: 738 sheet: 2.39 (0.54), residues: 66 loop : -1.29 (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 0.025 0.002 PHE K 31 TYR 0.013 0.001 TYR L 65 ARG 0.005 0.000 ARG G 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 191 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 1.178 Fit side-chains REVERT: K 212 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.7172 (t80) REVERT: L 212 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.7170 (t80) outliers start: 26 outliers final: 16 residues processed: 172 average time/residue: 0.8845 time to fit residues: 166.3462 Evaluate side-chains 178 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 SER 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 I residue 85 SER Chi-restraints excluded: chain I residue 212 TYR 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 41 LYS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 0.0870 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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: 0.8797 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9414 Z= 0.212 Angle : 0.647 9.701 12690 Z= 0.320 Chirality : 0.043 0.231 1422 Planarity : 0.003 0.015 1500 Dihedral : 6.897 57.875 1366 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.45 % Allowed : 15.85 % 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: 3.02 (0.25), residues: 1068 helix: 3.01 (0.18), residues: 738 sheet: 2.38 (0.54), residues: 66 loop : -1.29 (0.35), 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 0.023 0.002 PHE K 31 TYR 0.013 0.002 TYR I 65 ARG 0.005 0.001 ARG G 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 189 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.077 Fit side-chains REVERT: G 18 THR cc_start: 0.6434 (t) cc_final: 0.5994 (p) REVERT: K 212 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.7182 (t80) REVERT: L 212 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.7234 (t80) outliers start: 24 outliers final: 18 residues processed: 170 average time/residue: 0.8619 time to fit residues: 160.5545 Evaluate side-chains 183 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 210 LEU 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 I residue 85 SER Chi-restraints excluded: chain I residue 212 TYR Chi-restraints excluded: chain J residue 10 LEU 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 K residue 41 LYS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 212 TYR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain L residue 212 TYR Rotamers are restrained with sigma=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: 0.6980 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.126374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080873 restraints weight = 12482.001| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.58 r_work: 0.2824 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9414 Z= 0.215 Angle : 0.654 9.730 12690 Z= 0.323 Chirality : 0.044 0.264 1422 Planarity : 0.003 0.015 1500 Dihedral : 6.647 58.817 1366 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.45 % Allowed : 16.16 % 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: 3.00 (0.25), residues: 1068 helix: 3.00 (0.18), residues: 738 sheet: 2.37 (0.54), residues: 66 loop : -1.31 (0.35), 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 0.021 0.002 PHE K 31 TYR 0.013 0.001 TYR I 65 ARG 0.005 0.001 ARG G 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4069.74 seconds wall clock time: 72 minutes 5.90 seconds (4325.90 seconds total)